ChenYuans-MacBook-Pro:~ noelkuo$ fmriprep-docker /Users/noelkuo/Desktop/Data/Nifti /Users/noelkuo/Desktop/Data/derivatives participant --participant-label NC080001 --fs-license-file /Users/noelkuo/freesurfer.txt --ignore slicetiming RUNNING: docker run --rm -it -e DOCKER_VERSION_8395080871=18.09.2 -v /Users/noelkuo/freesurfer.txt:/opt/freesurfer/license.txt:ro -v /Users/noelkuo/Desktop/Data/Nifti:/data:ro -v /Users/noelkuo/Desktop/Data/derivatives:/out poldracklab/fmriprep:1.3.2 /data /out participant --participant-label NC080001 --ignore slicetiming Making sure the input data is BIDS compliant (warnings can be ignored in most cases). 1: [WARN] You should define 'SliceTiming' for this file. If you don't provide this information slice time correction will not be possible. (code: 13 - SLICE_TIMING_NOT_DEFINED) ./sub-NC080001/func/sub-NC080001_task-rest_bold.nii.gz Summary: Available Tasks: Available Modalities: 6 Files, 32.14MB RS T1w 1 - Subject bold 1 - Session If you have any questions please post on https://neurostars.org/tags/bids /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working from collections import Container /usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'> imp.find_module('pytest') 190414-19:12:22,839 nipype.workflow IMPORTANT: Running fMRIPREP version 1.3.2: * BIDS dataset path: /data. * Participant list: ['NC080001']. * Run identifier: 20190414-191222_1c3dc63c-5224-47c2-a1eb-2e70a2a5f8f7. /usr/local/miniconda/lib/python3.7/site-packages/networkx/classes/reportviews.py:95: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working from collections import Mapping, Set, Iterable 190414-19:12:24,417 nipype.workflow IMPORTANT: Creating bold processing workflow for "/data/sub-NC080001/func/sub-NC080001_task-rest_bold.nii.gz" (0.02 GB / 240 TRs). Memory resampled/largemem=0.10/0.16 GB. 190414-19:12:24,418 nipype.workflow IMPORTANT: No single-band-reference found for sub-NC080001_task-rest_bold.nii.gz 190414-19:12:24,694 nipype.workflow WARNING: SDC: no fieldmaps found or they were ignored (/data/sub-NC080001/func/sub-NC080001_task-rest_bold.nii.gz). 190414-19:12:25,233 nipype.workflow IMPORTANT: Creating BOLD surface-sampling workflow. /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working from collections import Container /usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'> imp.find_module('pytest') 190414-19:12:28,318 nipype.workflow IMPORTANT: Works derived from this fMRIPrep execution should include the following boilerplate: Results included in this manuscript come from preprocessing performed using *fMRIPrep* 1.3.2 (@fmriprep1; @fmriprep2; RRID:SCR_016216), which is based on *Nipype* 1.1.9 (@nipype1; @nipype2; RRID:SCR_002502). Anatomical data preprocessing : The T1-weighted (T1w) image was corrected for intensity non-uniformity (INU) with `N4BiasFieldCorrection` [@n4], distributed with ANTs 2.2.0 [@ants, RRID:SCR_004757], and used as T1w-reference throughout the workflow. The T1w-reference was then skull-stripped with a *Nipype* implementation of the `antsBrainExtraction.sh` workflow (from ANTs), using OASIS30ANTs as target template. Brain surfaces were reconstructed using `recon-all` [FreeSurfer 6.0.1, RRID:SCR_001847, @fs_reconall], and the brain mask estimated previously was refined with a custom variation of the method to reconcile ANTs-derived and FreeSurfer-derived segmentations of the cortical gray-matter of Mindboggle [RRID:SCR_002438, @mindboggle]. Spatial normalization to the *ICBM 152 Nonlinear Asymmetrical template version 2009c* [@mni152nlin2009casym, RRID:SCR_008796] was performed through nonlinear registration with `antsRegistration` (ANTs 2.2.0), using brain-extracted versions of both T1w volume and template. Brain tissue segmentation of cerebrospinal fluid (CSF), white-matter (WM) and gray-matter (GM) was performed on the brain-extracted T1w using `fast` [FSL 5.0.9, RRID:SCR_002823, @fsl_fast]. Functional data preprocessing : For each of the 1 BOLD runs found per subject (across all tasks and sessions), the following preprocessing was performed. First, a reference volume and its skull-stripped version were generated using a custom methodology of *fMRIPrep*. The BOLD reference was then co-registered to the T1w reference using `bbregister` (FreeSurfer) which implements boundary-based registration [@bbr]. Co-registration was configured with nine degrees of freedom to account for distortions remaining in the BOLD reference. Head-motion parameters with respect to the BOLD reference (transformation matrices, and six corresponding rotation and translation parameters) are estimated before any spatiotemporal filtering using `mcflirt` [FSL 5.0.9, @mcflirt]. The BOLD time-series, were resampled to surfaces on the following spaces: *fsaverage5*. The BOLD time-series (including slice-timing correction when applied) were resampled onto their original, native space by applying a single, composite transform to correct for head-motion and susceptibility distortions. These resampled BOLD time-series will be referred to as *preprocessed BOLD in original space*, or just *preprocessed BOLD*. The BOLD time-series were resampled to MNI152NLin2009cAsym standard space, generating a *preprocessed BOLD run in MNI152NLin2009cAsym space*. First, a reference volume and its skull-stripped version were generated using a custom methodology of *fMRIPrep*. Several confounding time-series were calculated based on the *preprocessed BOLD*: framewise displacement (FD), DVARS and three region-wise global signals. FD and DVARS are calculated for each functional run, both using their implementations in *Nipype* [following the definitions by @power_fd_dvars]. The three global signals are extracted within the CSF, the WM, and the whole-brain masks. Additionally, a set of physiological regressors were extracted to allow for component-based noise correction [*CompCor*, @compcor]. Principal components are estimated after high-pass filtering the *preprocessed BOLD* time-series (using a discrete cosine filter with 128s cut-off) for the two *CompCor* variants: temporal (tCompCor) and anatomical (aCompCor). Six tCompCor components are then calculated from the top 5% variable voxels within a mask covering the subcortical regions. This subcortical mask is obtained by heavily eroding the brain mask, which ensures it does not include cortical GM regions. For aCompCor, six components are calculated within the intersection of the aforementioned mask and the union of CSF and WM masks calculated in T1w space, after their projection to the native space of each functional run (using the inverse BOLD-to-T1w transformation). The head-motion estimates calculated in the correction step were also placed within the corresponding confounds file. All resamplings can be performed with *a single interpolation step* by composing all the pertinent transformations (i.e. head-motion transform matrices, susceptibility distortion correction when available, and co-registrations to anatomical and template spaces). Gridded (volumetric) resamplings were performed using `antsApplyTransforms` (ANTs), configured with Lanczos interpolation to minimize the smoothing effects of other kernels [@lanczos]. Non-gridded (surface) resamplings were performed using `mri_vol2surf` (FreeSurfer). Many internal operations of *fMRIPrep* use *Nilearn* 0.5.0 [@nilearn, RRID:SCR_001362], mostly within the functional processing workflow. For more details of the pipeline, see [the section corresponding to workflows in *fMRIPrep*'s documentation](https://fmriprep.readthedocs.io/en/latest/workflows.html "FMRIPrep's documentation"). ### References Captured warning (): can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ Captured warning (): can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ Captured warning (): can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ Captured warning (): Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working Captured warning (): unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'> 190414-19:12:38,938 nipype.workflow WARNING: Some nodes exceed the total amount of memory available (8.77GB). Captured warning (): the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 190414-19:12:39,632 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.func_derivatives_wf.raw_sources" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/func_derivatives_wf/raw_sources". 190414-19:12:39,635 nipype.workflow INFO: [Node] Running "raw_sources" ("nipype.interfaces.utility.wrappers.Function") 190414-19:12:39,644 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.func_derivatives_wf.raw_sources". /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working from collections import Container /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working from collections import Container /usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working from collections import Container /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working from collections import Container 190414-19:12:41,184 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.lap_tmpl" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/lap_tmpl". 190414-19:12:41,188 nipype.workflow INFO: [Node] Running "lap_tmpl" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 tpl-OASIS30ANTs_res-01_T1w_maths.nii.gz Laplacian /opt/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz 1.5 1 190414-19:12:41,265 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.bidssrc" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/bidssrc". 190414-19:12:41,267 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.validate" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/validate". 190414-19:12:41,268 nipype.workflow INFO: [Node] Running "bidssrc" ("niworkflows.interfaces.bids.BIDSDataGrabber") 190414-19:12:41,269 nipype.interface WARNING: No "t2w" images found for sub- 190414-19:12:41,270 nipype.interface WARNING: No "flair" images found for sub- 190414-19:12:41,270 nipype.interface WARNING: No "fmap" images found for sub- 190414-19:12:41,270 nipype.interface WARNING: No "sbref" images found for sub- 190414-19:12:41,270 nipype.interface WARNING: No "roi" images found for sub- 190414-19:12:41,271 nipype.workflow INFO: [Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage") 190414-19:12:41,284 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.bidssrc". 190414-19:12:41,365 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.res_tmpl" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/res_tmpl". 190414-19:12:41,368 nipype.workflow INFO: [Node] Running "res_tmpl" ("niworkflows.interfaces.ants.ResampleImageBySpacing"), a CommandLine Interface with command: ResampleImageBySpacing 3 /opt/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz tpl-OASIS30ANTs_res-01_T1w_resampled.nii.gz 4 4 4 1 190414-19:12:44,10 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.res_tmpl". 190414-19:12:44,475 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.validate". 190414-19:12:49,953 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.lap_tmpl". Captured warning (): the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 190414-19:12:58,868 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.mrg_tmpl" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/mrg_tmpl". 190414-19:12:58,871 nipype.workflow INFO: [Node] Running "mrg_tmpl" ("nipype.interfaces.utility.base.Merge") 190414-19:12:58,876 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.mrg_tmpl". 190414-19:12:58,882 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_template_wf.t1_template_dimensions" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_template_wf/t1_template_dimensions". 190414-19:12:58,885 nipype.workflow INFO: [Node] Running "t1_template_dimensions" ("niworkflows.interfaces.images.TemplateDimensions") 190414-19:12:58,973 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.bids_info" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/bids_info". 190414-19:12:58,975 nipype.workflow INFO: [Node] Running "bids_info" ("niworkflows.interfaces.bids.BIDSInfo") 190414-19:12:59,12 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.bids_info". /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) 190414-19:12:59,375 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_split" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_split". 190414-19:12:59,378 nipype.workflow INFO: [Node] Running "bold_split" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/validate/sub-NC080001_task-rest_bold_valid.nii.gz -t 190414-19:12:59,513 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_template_wf.t1_template_dimensions". /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working from collections import Container 190414-19:12:59,927 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.gen_ref" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/gen_ref". 190414-19:12:59,929 nipype.workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") 190414-19:13:00,756 nipype.interface INFO: stderr 2019-04-14T19:13:00.756262:++ 3dvolreg: AFNI version=Debian-16.2.07~dfsg.1-5~nd16.04+1 (Jun 12 2017) [64-bit] 190414-19:13:00,756 nipype.interface INFO: stderr 2019-04-14T19:13:00.756262:++ Authored by: RW Cox 190414-19:13:00,760 nipype.interface INFO: stderr 2019-04-14T19:13:00.760498:** AFNI converts NIFTI_datatype=4 (INT16) in file /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/gen_ref/slice.nii.gz to FLOAT32 190414-19:13:00,760 nipype.interface INFO: stderr 2019-04-14T19:13:00.760498: Warnings of this type will be muted for this session. 190414-19:13:00,760 nipype.interface INFO: stderr 2019-04-14T19:13:00.760498: Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none. 190414-19:13:00,766 nipype.interface INFO: stderr 2019-04-14T19:13:00.766170:*+ WARNING: If you are performing spatial transformations on an oblique dset, 190414-19:13:00,766 nipype.interface INFO: stderr 2019-04-14T19:13:00.766170: such as /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/gen_ref/slice.nii.gz, 190414-19:13:00,766 nipype.interface INFO: stderr 2019-04-14T19:13:00.766170: or viewing/combining it with volumes of differing obliquity, 190414-19:13:00,766 nipype.interface INFO: stderr 2019-04-14T19:13:00.766170: you should consider running: 190414-19:13:00,766 nipype.interface INFO: stderr 2019-04-14T19:13:00.766170: 3dWarp -deoblique 190414-19:13:00,766 nipype.interface INFO: stderr 2019-04-14T19:13:00.766170: on this and other oblique datasets in the same session. 190414-19:13:00,766 nipype.interface INFO: stderr 2019-04-14T19:13:00.766170: See 3dWarp -help for details. 190414-19:13:00,767 nipype.interface INFO: stderr 2019-04-14T19:13:00.766170:++ Oblique dataset:/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/gen_ref/slice.nii.gz is 8.719383 degrees from plumb. 190414-19:13:00,767 nipype.interface INFO: stderr 2019-04-14T19:13:00.767739:++ Coarse del was 10, replaced with 3 190414-19:13:00,974 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.raw_sources" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/raw_sources". 190414-19:13:00,976 nipype.workflow INFO: [Node] Running "raw_sources" ("nipype.interfaces.utility.wrappers.Function") 190414-19:13:00,982 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.raw_sources". 190414-19:13:00,984 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.t1_name" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/t1_name". 190414-19:13:00,986 nipype.workflow INFO: [Node] Running "t1_name" ("nipype.interfaces.utility.wrappers.Function") 190414-19:13:00,993 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.t1_name". 190414-19:13:00,996 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_template_wf.t1_conform" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_template_wf/t1_conform". 190414-19:13:00,999 nipype.workflow INFO: [Node] Setting-up "_t1_conform0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0". 190414-19:13:01,4 nipype.workflow INFO: [Node] Running "_t1_conform0" ("niworkflows.interfaces.images.Conform") 190414-19:13:01,766 nipype.workflow INFO: [Node] Finished "_t1_conform0". 190414-19:13:01,768 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_template_wf.t1_conform". 190414-19:13:02,785 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_template_wf.get1st" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_template_wf/get1st". 190414-19:13:02,787 nipype.workflow INFO: [Node] Running "get1st" ("nipype.interfaces.utility.base.Select") 190414-19:13:02,791 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_template_wf.get1st". 190414-19:13:04,785 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.fov_check" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/fov_check". 190414-19:13:04,787 nipype.workflow INFO: [Node] Running "fov_check" ("nipype.interfaces.utility.wrappers.Function") /usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'> imp.find_module('pytest') 190414-19:13:04,803 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.truncate_images" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/truncate_images". 190414-19:13:04,806 nipype.workflow INFO: [Node] Setting-up "_truncate_images0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/truncate_images/mapflow/_truncate_images0". 190414-19:13:04,808 nipype.workflow INFO: [Node] Running "_truncate_images0" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 sub-NC080001_T1w_ras_maths.nii.gz TruncateImageIntensity /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0/sub-NC080001_T1w_ras.nii.gz 0.01 0.999 256 190414-19:13:05,81 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.recon_config" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/recon_config". 190414-19:13:05,83 nipype.workflow INFO: [Node] Running "recon_config" ("niworkflows.interfaces.freesurfer.FSDetectInputs") 190414-19:13:05,97 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.recon_config". 190414-19:13:05,152 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_split". 190414-19:13:05,416 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.fov_check". 190414-19:13:06,793 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.gen_ref" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/gen_ref". 190414-19:13:06,795 nipype.workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.utils.GenerateSamplingReference") 190414-19:13:06,994 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.gen_ref". 190414-19:13:07,438 nipype.workflow INFO: [Node] Finished "_truncate_images0". 190414-19:13:07,440 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.truncate_images". 190414-19:13:08,800 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.inu_n4" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/inu_n4". 190414-19:13:08,803 nipype.workflow INFO: [Node] Setting-up "_inu_n40" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40". 190414-19:13:08,806 nipype.workflow INFO: [Node] Running "_inu_n40" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/truncate_images/mapflow/_truncate_images0/sub-NC080001_T1w_ras_maths.nii.gz --convergence [ 50x50x50x50, 1e-07 ] --output [ sub-NC080001_T1w_ras_maths_corrected.nii.gz, sub-NC080001_T1w_ras_maths_bias.nii.gz ] --shrink-factor 4 190414-19:13:16,766 nipype.interface INFO: stderr 2019-04-14T19:13:16.766698:++ Max displacement in automask = 0.13 (mm) at sub-brick 19 190414-19:13:16,766 nipype.interface INFO: stderr 2019-04-14T19:13:16.766698:++ Max delta displ in automask = 0.07 (mm) at sub-brick 11 190414-19:13:17,563 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.gen_ref". /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working from collections import Container 190414-19:13:19,607 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.validate_ref" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/validate_ref". 190414-19:13:19,612 nipype.workflow INFO: [Node] Running "validate_ref" ("niworkflows.interfaces.images.ValidateImage") 190414-19:13:19,750 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.validate_ref". 190414-19:13:20,787 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_hmc_wf.mcflirt" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_hmc_wf/mcflirt". 190414-19:13:20,790 nipype.workflow INFO: [Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command: mcflirt -in /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/validate/sub-NC080001_task-rest_bold_valid.nii.gz -out /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_hmc_wf/mcflirt/sub-NC080001_task-rest_bold_valid_mcf.nii.gz -reffile /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz -mats -plots 190414-19:14:06,29 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_hmc_wf.mcflirt". 190414-19:14:06,814 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_hmc_wf.normalize_motion" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_hmc_wf/normalize_motion". 190414-19:14:06,816 nipype.workflow INFO: [Node] Running "normalize_motion" ("niworkflows.interfaces.utils.NormalizeMotionParams") 190414-19:14:06,825 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_hmc_wf.normalize_motion". 190414-19:14:08,871 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.fdisp" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/fdisp". 190414-19:14:08,873 nipype.workflow INFO: [Node] Running "fdisp" ("nipype.algorithms.confounds.FramewiseDisplacement") 190414-19:14:08,880 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.fdisp". 190414-19:14:30,776 nipype.workflow INFO: [Node] Finished "_inu_n40". 190414-19:14:30,779 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.inu_n4". 190414-19:14:32,827 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_hmc_wf.fsl2itk" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_hmc_wf/fsl2itk". 190414-19:14:32,836 nipype.workflow INFO: [Node] Running "fsl2itk" ("niworkflows.interfaces.itk.MCFLIRT2ITK") 190414-19:14:42,480 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.lap_target" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/lap_target". 190414-19:14:42,482 nipype.workflow INFO: [Node] Running "lap_target" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 sub-NC080001_T1w_ras_maths_corrected_maths.nii.gz Laplacian /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-NC080001_T1w_ras_maths_corrected.nii.gz 1.5 1 190414-19:14:47,356 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_hmc_wf.fsl2itk". 190414-19:14:48,561 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff". 190414-19:14:48,564 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190414-19:14:48,887 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.lap_target". 190414-19:14:50,507 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.mrg_target" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/mrg_target". 190414-19:14:50,509 nipype.workflow INFO: [Node] Running "mrg_target" ("nipype.interfaces.utility.base.Merge") 190414-19:14:50,513 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.mrg_target". 190414-19:14:51,846 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff". 190414-19:14:52,533 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_transform" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_transform". 190414-19:14:52,535 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.res_target" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/res_target". 190414-19:14:52,538 nipype.workflow INFO: [Node] Running "res_target" ("niworkflows.interfaces.ants.ResampleImageBySpacing"), a CommandLine Interface with command: ResampleImageBySpacing 3 /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-NC080001_T1w_ras_maths_corrected.nii.gz sub-NC080001_T1w_ras_maths_corrected_resampled.nii.gz 4 4 4 1 190414-19:14:52,543 nipype.workflow INFO: [Node] Running "bold_transform" ("niworkflows.interfaces.itk.MultiApplyTransforms") 190414-19:14:54,29 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.res_target". 190414-19:15:44,105 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_transform". 190414-19:15:44,570 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm". 190414-19:15:44,580 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190414-19:15:44,714 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.merge" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/merge". 190414-19:15:44,723 nipype.workflow INFO: [Node] Running "merge" ("fmriprep.interfaces.nilearn.Merge") 190414-19:15:51,846 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm". 190414-19:15:52,521 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask". 190414-19:15:52,528 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz --transform [ /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] 190414-19:15:53,507 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190414-19:15:54,520 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 190414-19:15:54,522 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190414-19:15:54,642 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190414-19:15:56,155 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.merge". 190414-19:15:56,531 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.validate" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/validate". 190414-19:15:56,532 nipype.workflow INFO: [Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage") 190414-19:15:56,610 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.init_aff" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/init_aff". 190414-19:15:56,612 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /opt/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz -m Mattes[/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/res_tmpl/tpl-OASIS30ANTs_res-01_T1w_resampled.nii.gz,/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/res_target/sub-NC080001_T1w_ras_maths_corrected_resampled.nii.gz,32,Regular,0.250000] -o initialization.mat -p 0 -s [15.000000,0.100000] -t Affine[0.100000] -v 1 190414-19:15:58,834 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.init_aff". 190414-19:16:00,527 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190414-19:16:00,533 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection -d 3 --input-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz --mask-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output ref_image_valid_corrected.nii.gz 190414-19:16:01,310 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190414-19:16:01,316 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.validate". 190414-19:16:02,533 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/gen_ref". 190414-19:16:02,535 nipype.workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") 190414-19:16:02,553 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190414-19:16:02,556 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_image_valid_corrected.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain.nii.gz -f 0.20 -m 190414-19:16:03,231 nipype.interface INFO: stderr 2019-04-14T19:16:03.231523:++ 3dvolreg: AFNI version=Debian-16.2.07~dfsg.1-5~nd16.04+1 (Jun 12 2017) [64-bit] 190414-19:16:03,231 nipype.interface INFO: stderr 2019-04-14T19:16:03.231897:++ Authored by: RW Cox 190414-19:16:03,233 nipype.interface INFO: stderr 2019-04-14T19:16:03.232989:*+ WARNING: If you are performing spatial transformations on an oblique dset, 190414-19:16:03,233 nipype.interface INFO: stderr 2019-04-14T19:16:03.232989: such as /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/gen_ref/slice.nii.gz, 190414-19:16:03,233 nipype.interface INFO: stderr 2019-04-14T19:16:03.232989: or viewing/combining it with volumes of differing obliquity, 190414-19:16:03,233 nipype.interface INFO: stderr 2019-04-14T19:16:03.232989: you should consider running: 190414-19:16:03,233 nipype.interface INFO: stderr 2019-04-14T19:16:03.232989: 3dWarp -deoblique 190414-19:16:03,233 nipype.interface INFO: stderr 2019-04-14T19:16:03.232989: on this and other oblique datasets in the same session. 190414-19:16:03,233 nipype.interface INFO: stderr 2019-04-14T19:16:03.232989: See 3dWarp -help for details. 190414-19:16:03,233 nipype.interface INFO: stderr 2019-04-14T19:16:03.233599:++ Oblique dataset:/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/gen_ref/slice.nii.gz is 8.719383 degrees from plumb. 190414-19:16:03,233 nipype.interface INFO: stderr 2019-04-14T19:16:03.233889:++ Coarse del was 10, replaced with 3 190414-19:16:03,625 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190414-19:16:04,533 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190414-19:16:04,535 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_image_valid_corrected_brain_mask_dil.nii.gz 190414-19:16:04,793 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190414-19:16:06,534 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 190414-19:16:06,536 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain.nii.gz -mas /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_image_valid_corrected_brain_mask_dil.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_image_valid_corrected_brain_masked.nii.gz 190414-19:16:06,609 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190414-19:16:08,534 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize". 190414-19:16:08,541 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize/ref_image_valid_corrected_brain_masked.nii.gz 190414-19:16:09,192 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize". 190414-19:16:10,535 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 190414-19:16:10,537 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190414-19:16:10,559 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190414-19:16:12,540 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 190414-19:16:12,542 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 190414-19:16:12,642 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190414-19:16:14,543 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 190414-19:16:14,545 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190414-19:16:14,562 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190414-19:16:16,546 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks". 190414-19:16:16,549 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain_mask.nii.gz -mul /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_valid_corrected_brain_mask_maths.nii.gz 190414-19:16:16,614 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190414-19:16:17,205 nipype.interface INFO: stderr 2019-04-14T19:16:17.205153:++ Max displacement in automask = 0.06 (mm) at sub-brick 17 190414-19:16:17,205 nipype.interface INFO: stderr 2019-04-14T19:16:17.205153:++ Max delta displ in automask = 0.06 (mm) at sub-brick 2 190414-19:16:17,820 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref". 190414-19:16:18,524 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.validate_ref" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/validate_ref". 190414-19:16:18,525 nipype.workflow INFO: [Node] Running "validate_ref" ("niworkflows.interfaces.images.ValidateImage") 190414-19:16:18,525 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask". 190414-19:16:18,528 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_valid_corrected_brain_mask_maths.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 190414-19:16:18,572 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.validate_ref". 190414-19:16:18,599 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190414-19:16:20,529 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff". 190414-19:16:20,532 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190414-19:16:23,770 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff". 190414-19:16:24,539 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm". 190414-19:16:24,542 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190414-19:16:31,4 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm". 190414-19:16:32,542 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask". 190414-19:16:32,544 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz --transform [ /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] 190414-19:16:32,553 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.norm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/norm". 190414-19:16:32,558 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation LanczosWindowedSinc --output [ anat_to_template, anat_to_template_Warped.nii.gz ] --transform Rigid[ 0.1 ] --metric MI[ /opt/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz, /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-NC080001_T1w_ras_maths_corrected.nii.gz, 1, 32, Regular, 0.25 ] --convergence [ 1000x500x250x100, 1e-08, 10 ] --smoothing-sigmas 4.0x2.0x1.0x0.0vox --shrink-factors 8x4x2x1 --use-histogram-matching 1 --masks [ /opt/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz, NULL ] --transform Affine[ 0.1 ] --metric MI[ /opt/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz, /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-NC080001_T1w_ras_maths_corrected.nii.gz, 1, 32, Regular, 0.25 ] --convergence [ 1000x500x250x100, 1e-08, 10 ] --smoothing-sigmas 4.0x2.0x1.0x0.0vox --shrink-factors 8x4x2x1 --use-histogram-matching 1 --masks [ /opt/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz, NULL ] --transform SyN[ 0.1, 3.0, 0.0 ] --metric CC[ /opt/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz, /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-NC080001_T1w_ras_maths_corrected.nii.gz, 0.5, 4, None, 1 ] --metric CC[ /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/lap_tmpl/tpl-OASIS30ANTs_res-01_T1w_maths.nii.gz, /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/lap_target/sub-NC080001_T1w_ras_maths_corrected_maths.nii.gz, 0.5, 4, None, 1 ] --convergence [ 50x10x0, 1e-09, 15 ] --smoothing-sigmas 2.0x1.0x0.0vox --shrink-factors 4x2x1 --use-histogram-matching 1 --masks [ /opt/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz, NULL ] -v --winsorize-image-intensities [ 0.025, 0.975 ] --write-composite-transform 0 190414-19:16:33,491 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190414-19:16:34,540 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 190414-19:16:34,543 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190414-19:16:34,654 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190414-19:16:38,564 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190414-19:16:38,567 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection -d 3 --input-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz --mask-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output ref_image_valid_corrected.nii.gz 190414-19:16:39,467 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190414-19:16:40,556 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190414-19:16:40,558 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_image_valid_corrected.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain.nii.gz -f 0.20 -m 190414-19:16:42,1 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190414-19:16:42,557 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190414-19:16:42,560 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_image_valid_corrected_brain_mask_dil.nii.gz 190414-19:16:42,846 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190414-19:16:44,559 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 190414-19:16:44,562 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain.nii.gz -mas /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_image_valid_corrected_brain_mask_dil.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_image_valid_corrected_brain_masked.nii.gz 190414-19:16:44,655 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190414-19:16:46,562 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize". 190414-19:16:46,565 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize/ref_image_valid_corrected_brain_masked.nii.gz 190414-19:16:47,292 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize". 190414-19:16:48,527 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 190414-19:16:48,529 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190414-19:16:48,570 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190414-19:16:50,538 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 190414-19:16:50,541 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 190414-19:16:50,662 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190414-19:16:52,551 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 190414-19:16:52,553 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190414-19:16:52,582 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190414-19:16:54,545 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks". 190414-19:16:54,548 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain_mask.nii.gz -mul /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_valid_corrected_brain_mask_maths.nii.gz 190414-19:16:54,626 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190414-19:16:56,549 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.dvars" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/dvars". 190414-19:16:56,552 nipype.workflow INFO: [Node] Running "dvars" ("nipype.algorithms.confounds.ComputeDVARS") /usr/local/miniconda/lib/python3.7/site-packages/nitime/utils.py:980: FutureWarning: Conversion of the second argument of issubdtype from `complex` to `np.complexfloating` is deprecated. In future, it will be treated as `np.complex128 == np.dtype(complex).type`. complex_result = (np.issubdtype(in1.dtype, np.complex) or /usr/local/miniconda/lib/python3.7/site-packages/scipy/fftpack/basic.py:160: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. z[index] = x 190414-19:17:05,547 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.dvars". 190414-19:17:06,728 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask". 190414-19:17:06,736 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_valid_corrected_brain_mask_maths.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 190414-19:17:06,831 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190414-19:37:14,273 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.norm". 190414-19:37:15,55 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.map_brainmask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/map_brainmask". 190414-19:37:15,62 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /opt/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_label-brain_probseg.nii.gz --interpolation Gaussian --output tpl-OASIS30ANTs_res-01_label-brain_probseg_trans.nii.gz --reference-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0/sub-NC080001_T1w_ras.nii.gz --transform [ /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/norm/anat_to_template0GenericAffine.mat, 1 ] --transform [ /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/norm/anat_to_template1InverseWarp.nii.gz, 0 ] 190414-19:37:15,62 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/autorecon1". 190414-19:37:15,77 nipype.workflow INFO: [Node] Running "autorecon1" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command: recon-all -autorecon1 -i /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0/sub-NC080001_T1w_ras.nii.gz -noskullstrip -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer 190414-19:37:51,807 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.map_brainmask". 190414-19:37:52,995 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.thr_brainmask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/thr_brainmask". 190414-19:37:53,2 nipype.workflow INFO: [Node] Running "thr_brainmask" ("niworkflows.interfaces.ants.ThresholdImage"), a CommandLine Interface with command: ThresholdImage 3 /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/map_brainmask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans.nii.gz tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled.nii.gz 0.500000 1.000000 1.000000 0.000000 190414-19:37:53,689 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.thr_brainmask". 190414-19:37:55,0 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.03_pad_mask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/03_pad_mask". 190414-19:37:55,5 nipype.workflow INFO: [Node] Running "03_pad_mask" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths.nii.gz PadImage /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/thr_brainmask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled.nii.gz 10 190414-19:37:55,861 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.03_pad_mask". 190414-19:37:56,998 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.dil_brainmask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/dil_brainmask". 190414-19:37:57,2 nipype.workflow INFO: [Node] Running "dil_brainmask" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths.nii.gz MD /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/thr_brainmask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled.nii.gz 2 190414-19:37:58,165 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.dil_brainmask". 190414-19:37:59,2 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.get_brainmask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/get_brainmask". 190414-19:37:59,4 nipype.workflow INFO: [Node] Running "get_brainmask" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths_maths.nii.gz GetLargestComponent /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/dil_brainmask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths.nii.gz 190414-19:38:00,49 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.get_brainmask". 190414-19:45:07,29 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon1". 190414-19:45:07,169 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.01_atropos" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/01_atropos". 190414-19:45:07,173 nipype.workflow INFO: [Node] Running "01_atropos" ("nipype.interfaces.ants.segmentation.Atropos"), a CommandLine Interface with command: Atropos --image-dimensionality 3 --initialization KMeans[3] --intensity-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-NC080001_T1w_ras_maths_corrected.nii.gz --likelihood-model Gaussian --mask-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/get_brainmask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths_maths.nii.gz --mrf [0.1,1x1x1] --convergence [3,0] --output [sub-NC080001_T1w_ras_maths_corrected_labeled.nii.gz] --use-random-seed 1 /usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'> imp.find_module('pytest') 190414-19:45:07,354 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.fsnative_2_t1_xfm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/fsnative_2_t1_xfm". 190414-19:45:07,358 nipype.workflow INFO: [Node] Running "fsnative_2_t1_xfm" ("niworkflows.interfaces.freesurfer.PatchedRobustRegister"), a CommandLine Interface with command: mri_robust_register --satit --iscale --lta /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/fsnative_2_t1_xfm/T1_robustreg.lta --mov /out/freesurfer/sub-NC080001/mri/T1.mgz --dst /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0/sub-NC080001_T1w_ras.nii.gz 190414-19:45:56,463 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.fsnative_2_t1_xfm". /usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'> imp.find_module('pytest') 190414-19:45:57,382 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.t1_2_fsnative_xfm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/t1_2_fsnative_xfm". 190414-19:45:57,384 nipype.workflow INFO: [Node] Running "t1_2_fsnative_xfm" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command: lta_convert --inlta /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/fsnative_2_t1_xfm/T1_robustreg.lta --invert --outlta /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/t1_2_fsnative_xfm/out.lta 190414-19:45:57,475 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.t1_2_fsnative_xfm". 190414-19:45:57,701 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.01_atropos". 190414-19:45:59,220 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.02_pad_segm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/02_pad_segm". 190414-19:45:59,224 nipype.workflow INFO: [Node] Running "02_pad_segm" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 sub-NC080001_T1w_ras_maths_corrected_labeled_maths.nii.gz PadImage /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/01_atropos/sub-NC080001_T1w_ras_maths_corrected_labeled.nii.gz 10 /usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'> imp.find_module('pytest') 190414-19:45:59,361 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.lta_2_itk" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/lta_2_itk". 190414-19:45:59,363 nipype.workflow INFO: [Node] Running "lta_2_itk" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command: lta_convert --inlta /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/t1_2_fsnative_xfm/out.lta --outitk /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/lta_2_itk/out.txt 190414-19:45:59,464 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.lta_2_itk". 190414-19:45:59,995 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.02_pad_segm". 190414-19:46:01,222 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.04_sel_labels" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels". 190414-19:46:01,224 nipype.workflow INFO: [Node] Running "04_sel_labels" ("nipype.interfaces.utility.wrappers.Function") 190414-19:46:01,576 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.04_sel_labels". 190414-19:46:03,227 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.27_depad_csf" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/27_depad_csf". 190414-19:46:03,228 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.10_me_csf" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/10_me_csf". 190414-19:46:03,229 nipype.workflow INFO: [Node] Running "27_depad_csf" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 sub-NC080001_T1w_ras_maths_corrected_labeled_maths_class-01_maths.nii.gz PadImage /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels/sub-NC080001_T1w_ras_maths_corrected_labeled_maths_class-01.nii.gz -10 190414-19:46:03,231 nipype.workflow INFO: [Node] Running "10_me_csf" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 sub-NC080001_T1w_ras_maths_corrected_labeled_maths_class-01_maths.nii.gz ME /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels/sub-NC080001_T1w_ras_maths_corrected_labeled_maths_class-01.nii.gz 10 190414-19:46:03,232 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.06_get_gm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/06_get_gm". 190414-19:46:03,234 nipype.workflow INFO: [Node] Running "06_get_gm" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 sub-NC080001_T1w_ras_maths_corrected_labeled_maths_class-02_maths.nii.gz GetLargestComponent /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels/sub-NC080001_T1w_ras_maths_corrected_labeled_maths_class-02.nii.gz 190414-19:46:03,237 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.05_get_wm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/05_get_wm". 190414-19:46:03,240 nipype.workflow INFO: [Node] Running "05_get_wm" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 sub-NC080001_T1w_ras_maths_corrected_labeled_maths_class-03_maths.nii.gz GetLargestComponent /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels/sub-NC080001_T1w_ras_maths_corrected_labeled_maths_class-03.nii.gz 190414-19:46:03,820 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.27_depad_csf". 190414-19:46:04,369 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.05_get_wm". 190414-19:46:04,410 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.06_get_gm". 190414-19:46:05,222 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.07_fill_gm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/07_fill_gm". 190414-19:46:05,225 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.09_relabel_wm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/09_relabel_wm". 190414-19:46:05,227 nipype.workflow INFO: [Node] Running "09_relabel_wm" ("nipype.interfaces.ants.utils.MultiplyImages"), a CommandLine Interface with command: MultiplyImages 3 /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/05_get_wm/sub-NC080001_T1w_ras_maths_corrected_labeled_maths_class-03_maths.nii.gz 3.0 09_relabel_wm.nii.gz 190414-19:46:05,231 nipype.workflow INFO: [Node] Running "07_fill_gm" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 sub-NC080001_T1w_ras_maths_corrected_labeled_maths_class-02_maths_maths.nii.gz FillHoles /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/06_get_gm/sub-NC080001_T1w_ras_maths_corrected_labeled_maths_class-02_maths.nii.gz 2 190414-19:46:05,941 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.09_relabel_wm". 190414-19:46:06,537 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.10_me_csf". 190414-19:46:07,227 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.26_depad_wm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/26_depad_wm". 190414-19:46:07,229 nipype.workflow INFO: [Node] Running "26_depad_wm" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 09_relabel_wm_maths.nii.gz PadImage /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/09_relabel_wm/09_relabel_wm.nii.gz -10 190414-19:46:07,858 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.26_depad_wm". 190414-19:46:11,273 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.07_fill_gm". 190414-19:46:13,237 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.08_mult_gm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/08_mult_gm". 190414-19:46:13,239 nipype.workflow INFO: [Node] Running "08_mult_gm" ("nipype.interfaces.ants.utils.MultiplyImages"), a CommandLine Interface with command: MultiplyImages 3 /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/06_get_gm/sub-NC080001_T1w_ras_maths_corrected_labeled_maths_class-02_maths.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/07_fill_gm/sub-NC080001_T1w_ras_maths_corrected_labeled_maths_class-02_maths_maths.nii.gz 08_mult_gm.nii.gz 190414-19:46:14,109 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.08_mult_gm". 190414-19:46:15,242 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.11_add_gm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/11_add_gm". 190414-19:46:15,244 nipype.workflow INFO: [Node] Running "11_add_gm" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 08_mult_gm_maths.nii.gz addtozero /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/08_mult_gm/08_mult_gm.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/10_me_csf/sub-NC080001_T1w_ras_maths_corrected_labeled_maths_class-01_maths.nii.gz 190414-19:46:18,169 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.11_add_gm". 190414-19:46:19,193 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.12_relabel_gm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/12_relabel_gm". 190414-19:46:19,195 nipype.workflow INFO: [Node] Running "12_relabel_gm" ("nipype.interfaces.ants.utils.MultiplyImages"), a CommandLine Interface with command: MultiplyImages 3 /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/11_add_gm/08_mult_gm_maths.nii.gz 2.0 12_relabel_gm.nii.gz 190414-19:46:19,845 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.12_relabel_gm". 190414-19:46:21,206 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.25_depad_gm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/25_depad_gm". 190414-19:46:21,208 nipype.workflow INFO: [Node] Running "25_depad_gm" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 12_relabel_gm_maths.nii.gz PadImage /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/12_relabel_gm/12_relabel_gm.nii.gz -10 190414-19:46:21,209 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.13_add_gm_wm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/13_add_gm_wm". 190414-19:46:21,211 nipype.workflow INFO: [Node] Running "13_add_gm_wm" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 09_relabel_wm_maths.nii.gz addtozero /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/09_relabel_wm/09_relabel_wm.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/12_relabel_gm/12_relabel_gm.nii.gz 190414-19:46:21,874 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.25_depad_gm". 190414-19:46:23,203 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.merge_tpms" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/merge_tpms". 190414-19:46:23,208 nipype.workflow INFO: [Node] Running "merge_tpms" ("nipype.interfaces.utility.base.Merge") 190414-19:46:23,215 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.merge_tpms". 190414-19:46:24,291 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.13_add_gm_wm". 190414-19:46:25,215 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.24_depad_segm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/24_depad_segm". 190414-19:46:25,220 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.14_sel_labels2" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/14_sel_labels2". 190414-19:46:25,222 nipype.workflow INFO: [Node] Running "14_sel_labels2" ("nipype.interfaces.utility.wrappers.Function") 190414-19:46:25,222 nipype.workflow INFO: [Node] Running "24_depad_segm" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 09_relabel_wm_maths_maths.nii.gz PadImage /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/13_add_gm_wm/09_relabel_wm_maths.nii.gz -10 190414-19:46:25,472 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.14_sel_labels2". 190414-19:46:25,876 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.24_depad_segm". 190414-19:46:27,222 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.15_add_7" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/15_add_7". 190414-19:46:27,224 nipype.workflow INFO: [Node] Running "15_add_7" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 09_relabel_wm_maths_class-03_maths.nii.gz addtozero /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/14_sel_labels2/09_relabel_wm_maths_class-03.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/14_sel_labels2/09_relabel_wm_maths_class-02.nii.gz 190414-19:46:30,29 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.15_add_7". 190414-19:46:31,229 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.16_me_7" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/16_me_7". 190414-19:46:31,231 nipype.workflow INFO: [Node] Running "16_me_7" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 09_relabel_wm_maths_class-03_maths_maths.nii.gz ME /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/15_add_7/09_relabel_wm_maths_class-03_maths.nii.gz 2 190414-19:46:33,439 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.16_me_7". 190414-19:46:35,233 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.17_comp_7" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/17_comp_7". 190414-19:46:35,235 nipype.workflow INFO: [Node] Running "17_comp_7" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths.nii.gz GetLargestComponent /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/16_me_7/09_relabel_wm_maths_class-03_maths_maths.nii.gz 190414-19:46:36,323 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.17_comp_7". 190414-19:46:37,245 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.18_md_7" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/18_md_7". 190414-19:46:37,247 nipype.workflow INFO: [Node] Running "18_md_7" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths.nii.gz MD /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/17_comp_7/09_relabel_wm_maths_class-03_maths_maths_maths.nii.gz 4 190414-19:46:38,400 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.18_md_7". 190414-19:46:39,255 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.19_fill_7" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/19_fill_7". 190414-19:46:39,257 nipype.workflow INFO: [Node] Running "19_fill_7" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths.nii.gz FillHoles /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/18_md_7/09_relabel_wm_maths_class-03_maths_maths_maths_maths.nii.gz 2 190414-19:46:44,883 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.19_fill_7". 190414-19:46:45,269 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.20_add_7_2" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/20_add_7_2". 190414-19:46:45,272 nipype.workflow INFO: [Node] Running "20_add_7_2" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths.nii.gz addtozero /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/19_fill_7/09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/03_pad_mask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths.nii.gz 190414-19:46:48,153 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.20_add_7_2". 190414-19:46:49,236 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.21_md_7_2" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/21_md_7_2". 190414-19:46:49,238 nipype.workflow INFO: [Node] Running "21_md_7_2" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths.nii.gz MD /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/20_add_7_2/09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths.nii.gz 5 190414-19:46:50,385 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.21_md_7_2". 190414-19:46:51,241 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.22_me_7_2" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/22_me_7_2". 190414-19:46:51,243 nipype.workflow INFO: [Node] Running "22_me_7_2" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths_maths.nii.gz ME /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/21_md_7_2/09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths.nii.gz 5 190414-19:46:53,461 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.22_me_7_2". 190414-19:46:55,246 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.23_depad_mask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/23_depad_mask". 190414-19:46:55,248 nipype.workflow INFO: [Node] Running "23_depad_mask" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths_maths_maths.nii.gz PadImage /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/22_me_7_2/09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths_maths.nii.gz -10 190414-19:46:55,840 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.23_depad_mask". 190414-19:46:57,252 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.apply_mask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/apply_mask". 190414-19:46:57,261 nipype.workflow INFO: [Node] Setting-up "_apply_mask0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/apply_mask/mapflow/_apply_mask0". 190414-19:46:57,264 nipype.workflow INFO: [Node] Running "_apply_mask0" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-NC080001_T1w_ras_maths_corrected.nii.gz -mas /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/23_depad_mask/09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths_maths_maths.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/apply_mask/mapflow/_apply_mask0/sub-NC080001_T1w_ras_maths_corrected_masked.nii.gz 190414-19:46:58,511 nipype.workflow INFO: [Node] Finished "_apply_mask0". 190414-19:46:58,515 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.apply_mask". /usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'> imp.find_module('pytest') 190414-19:46:59,394 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.skull_strip_extern" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/skull_strip_extern". 190414-19:46:59,396 nipype.workflow INFO: [Node] Running "skull_strip_extern" ("niworkflows.interfaces.freesurfer.FSInjectBrainExtracted") 190414-19:47:00,846 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.skull_strip_extern". 190414-19:47:01,264 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon2_vol". 190414-19:47:01,272 nipype.interface INFO: resume recon-all : recon-all -autorecon2-volonly -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer 190414-19:47:01,273 nipype.workflow INFO: [Node] Running "autorecon2_vol" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command: recon-all -autorecon2-volonly -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer 190414-19:47:01,275 nipype.interface INFO: resume recon-all : recon-all -autorecon2-volonly -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer 190414-21:45:08,381 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol". 190414-21:45:11,814 nipype.workflow INFO: [Node] Setting-up "_autorecon_surfs0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs0". 190414-21:45:11,831 nipype.interface INFO: resume recon-all : recon-all -autorecon-hemi lh -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nohyporelabel -noaparc2aseg -noapas2aseg -nosegstats -nowmparc -nobalabels -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer 190414-21:45:11,832 nipype.workflow INFO: [Node] Running "_autorecon_surfs0" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command: recon-all -autorecon-hemi lh -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nohyporelabel -noaparc2aseg -noapas2aseg -nosegstats -nowmparc -nobalabels -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer 190414-21:45:11,838 nipype.interface INFO: resume recon-all : recon-all -autorecon-hemi lh -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nohyporelabel -noaparc2aseg -noapas2aseg -nosegstats -nowmparc -nobalabels -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer 190414-22:50:26,487 nipype.workflow INFO: [Node] Finished "_autorecon_surfs0". 190414-22:50:27,462 nipype.workflow INFO: [Node] Setting-up "_autorecon_surfs1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs1". 190414-22:50:27,476 nipype.interface INFO: resume recon-all : recon-all -autorecon-hemi rh -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nohyporelabel -noaparc2aseg -noapas2aseg -nosegstats -nowmparc -nobalabels -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer 190414-22:50:27,476 nipype.workflow INFO: [Node] Running "_autorecon_surfs1" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command: recon-all -autorecon-hemi rh -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nohyporelabel -noaparc2aseg -noapas2aseg -nosegstats -nowmparc -nobalabels -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer 190414-22:50:27,480 nipype.interface INFO: resume recon-all : recon-all -autorecon-hemi rh -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nohyporelabel -noaparc2aseg -noapas2aseg -nosegstats -nowmparc -nobalabels -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer 190415-00:08:03,813 nipype.workflow INFO: [Node] Finished "_autorecon_surfs1". 190415-00:08:05,568 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs". 190415-00:08:05,577 nipype.workflow INFO: [Node] Setting-up "_autorecon_surfs0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs0". 190415-00:08:05,617 nipype.interface INFO: recon-all complete : Not running 190415-00:08:05,617 nipype.workflow INFO: [Node] Running "_autorecon_surfs0" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command: echo recon-all: nothing to do 190415-00:08:05,648 nipype.interface INFO: recon-all complete : Not running 190415-00:08:05,841 nipype.workflow INFO: [Node] Finished "_autorecon_surfs0". 190415-00:08:05,846 nipype.workflow INFO: [Node] Setting-up "_autorecon_surfs1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs1". 190415-00:08:05,880 nipype.interface INFO: recon-all complete : Not running 190415-00:08:05,881 nipype.workflow INFO: [Node] Running "_autorecon_surfs1" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command: echo recon-all: nothing to do 190415-00:08:05,913 nipype.interface INFO: recon-all complete : Not running 190415-00:08:06,29 nipype.workflow INFO: [Node] Finished "_autorecon_surfs1". 190415-00:08:06,35 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs". 190415-00:08:09,575 nipype.workflow INFO: [Node] Setting-up "_autorecon30" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon3/mapflow/_autorecon30". 190415-00:08:09,614 nipype.interface INFO: resume recon-all : recon-all -autorecon3 -hemi lh -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial 190415-00:08:09,615 nipype.workflow INFO: [Node] Running "_autorecon30" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command: recon-all -autorecon3 -hemi lh -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial 190415-00:08:09,643 nipype.interface INFO: resume recon-all : recon-all -autorecon3 -hemi lh -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial 190415-00:30:52,606 nipype.workflow INFO: [Node] Finished "_autorecon30". 190415-00:30:54,534 nipype.workflow INFO: [Node] Setting-up "_autorecon31" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon3/mapflow/_autorecon31". 190415-00:30:54,581 nipype.interface INFO: resume recon-all : recon-all -autorecon3 -hemi rh -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortribbon -nohyporelabel -noapas2aseg -nosegstats -nowmparc 190415-00:30:54,582 nipype.workflow INFO: [Node] Running "_autorecon31" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command: recon-all -autorecon3 -hemi rh -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortribbon -nohyporelabel -noapas2aseg -nosegstats -nowmparc 190415-00:30:54,618 nipype.interface INFO: resume recon-all : recon-all -autorecon3 -hemi rh -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortribbon -nohyporelabel -noapas2aseg -nosegstats -nowmparc 190415-00:47:03,880 nipype.workflow INFO: [Node] Finished "_autorecon31". 190415-00:47:05,58 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon3" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon3". 190415-00:47:05,69 nipype.workflow INFO: [Node] Setting-up "_autorecon30" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon3/mapflow/_autorecon30". 190415-00:47:05,120 nipype.interface INFO: resume recon-all : recon-all -autorecon3 -hemi lh -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nocortribbon -nohyporelabel -noaparc2aseg -nosegstats -nowmparc -nobalabels 190415-00:47:05,120 nipype.workflow INFO: [Node] Running "_autorecon30" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command: recon-all -autorecon3 -hemi lh -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nocortribbon -nohyporelabel -noaparc2aseg -nosegstats -nowmparc -nobalabels 190415-00:47:05,168 nipype.interface INFO: resume recon-all : recon-all -autorecon3 -hemi lh -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nocortribbon -nohyporelabel -noaparc2aseg -nosegstats -nowmparc -nobalabels 190415-00:47:10,837 nipype.workflow INFO: [Node] Finished "_autorecon30". 190415-00:47:10,841 nipype.workflow INFO: [Node] Setting-up "_autorecon31" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon3/mapflow/_autorecon31". 190415-00:47:10,892 nipype.interface INFO: recon-all complete : Not running 190415-00:47:10,892 nipype.workflow INFO: [Node] Running "_autorecon31" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command: echo recon-all: nothing to do 190415-00:47:10,940 nipype.interface INFO: recon-all complete : Not running 190415-00:47:11,105 nipype.workflow INFO: [Node] Finished "_autorecon31". 190415-00:47:11,110 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon3". 190415-00:47:13,54 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.targets" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/targets". 190415-00:47:13,58 nipype.workflow INFO: [Node] Setting-up "_targets0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/targets/mapflow/_targets0". 190415-00:47:13,60 nipype.workflow INFO: [Node] Running "_targets0" ("nipype.interfaces.utility.wrappers.Function") 190415-00:47:13,63 nipype.workflow INFO: [Node] Finished "_targets0". 190415-00:47:13,65 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.targets". 190415-00:47:13,70 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.mri_coreg" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/mri_coreg". 190415-00:47:13,75 nipype.workflow INFO: [Node] Running "mri_coreg" ("niworkflows.interfaces.freesurfer.PatchedMRICoregRPT"), a CommandLine Interface with command: mri_coreg --s sub-NC080001 --dof 6 --ftol 1.000000e-04 --linmintol 1.000000e-02 --threads 5 --lta /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/mri_coreg/registration.lta --sep 4 --mov /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/mri_coreg/uni_xform_masked.nii.gz --sd /out/freesurfer 190415-00:47:15,61 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.fs_datasource" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/fs_datasource". 190415-00:47:15,65 nipype.workflow INFO: [Node] Running "fs_datasource" ("nipype.interfaces.io.FreeSurferSource") 190415-00:47:15,240 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.fs_datasource". 190415-00:47:17,84 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.tonative" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/tonative". 190415-00:47:17,91 nipype.workflow INFO: [Node] Running "tonative" ("nipype.interfaces.freesurfer.model.Label2Vol"), a CommandLine Interface with command: mri_label2vol --regheader /out/freesurfer/sub-NC080001/mri/aseg.mgz --seg /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/tonative/aparc+aseg.mgz --temp /out/freesurfer/sub-NC080001/mri/rawavg.mgz --o /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/tonative/aparc+aseg_vol.nii.gz 190415-00:47:23,537 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.tonative". 190415-00:47:25,85 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.tonii" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/tonii". 190415-00:47:25,89 nipype.workflow INFO: [Node] Running "tonii" ("nipype.interfaces.freesurfer.preprocess.MRIConvert"), a CommandLine Interface with command: mri_convert --out_type nii --resample_type nearest --reslice_like /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-NC080001_T1w_ras_maths_corrected.nii.gz --input_volume /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/tonative/aparc+aseg_vol.nii.gz --output_volume /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/tonii/aparc+aseg_vol_out.nii.gz 190415-00:47:28,61 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.tonii". 190415-00:47:30,838 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.fs_datasource" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/fs_datasource". 190415-00:47:30,841 nipype.workflow INFO: [Node] Running "fs_datasource" ("nipype.interfaces.io.FreeSurferSource") 190415-00:47:31,60 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.fs_datasource". 190415-00:47:33,85 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.tonative" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonative". 190415-00:47:33,95 nipype.workflow INFO: [Node] Running "tonative" ("nipype.interfaces.freesurfer.model.Label2Vol"), a CommandLine Interface with command: mri_label2vol --regheader /out/freesurfer/sub-NC080001/mri/aseg.mgz --seg /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonative/aseg.mgz --temp /out/freesurfer/sub-NC080001/mri/rawavg.mgz --o /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonative/aseg_vol.nii.gz 190415-00:47:42,907 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.tonative". 190415-00:47:43,91 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.tonii" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonii". 190415-00:47:43,97 nipype.workflow INFO: [Node] Running "tonii" ("nipype.interfaces.freesurfer.preprocess.MRIConvert"), a CommandLine Interface with command: mri_convert --out_type nii --resample_type nearest --reslice_like /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-NC080001_T1w_ras_maths_corrected.nii.gz --input_volume /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonative/aseg_vol.nii.gz --output_volume /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonii/aseg_vol_out.nii.gz 190415-00:47:47,65 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.tonii". 190415-00:47:49,172 nipype.interface INFO: stdout 2019-04-15T00:47:49.172028: 190415-00:47:49,172 nipype.interface INFO: stdout 2019-04-15T00:47:49.172028:Matrix from LTA: 190415-00:47:49,172 nipype.interface INFO: stdout 2019-04-15T00:47:49.172028: 0.99954 -0.03031 -0.00087 2.47096; 190415-00:47:49,172 nipype.interface INFO: stdout 2019-04-15T00:47:49.172028: 0.00630 0.17957 0.98373 -1.72582; 190415-00:47:49,172 nipype.interface INFO: stdout 2019-04-15T00:47:49.172028:-0.02966 -0.98328 0.17968 -0.60429; 190415-00:47:49,172 nipype.interface INFO: stdout 2019-04-15T00:47:49.172028: 0.00000 0.00000 0.00000 1.00000; 190415-00:47:49,295 nipype.interface INFO: stdout 2019-04-15T00:47:49.295140: 190415-00:47:49,295 nipype.interface INFO: stdout 2019-04-15T00:47:49.295140:/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/mri_coreg/uni_xform_masked.nii.gz /out/freesurfer/sub-NC080001/mri/brainmask.mgz 190415-00:47:49,295 nipype.interface INFO: stdout 2019-04-15T00:47:49.295140:movvol /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/mri_coreg/uni_xform_masked.nii.gz 190415-00:47:49,295 nipype.interface INFO: stdout 2019-04-15T00:47:49.295140:targvol /out/freesurfer/sub-NC080001/mri/brainmask.mgz 190415-00:47:49,295 nipype.interface INFO: stdout 2019-04-15T00:47:49.295140:outvol /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/mri_coreg/uni_xform_masked_warped.nii.gz 190415-00:47:49,295 nipype.interface INFO: stdout 2019-04-15T00:47:49.295140:regfile /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/mri_coreg/registration.lta 190415-00:47:49,295 nipype.interface INFO: stdout 2019-04-15T00:47:49.295140:invert 0 190415-00:47:49,296 nipype.interface INFO: stdout 2019-04-15T00:47:49.295140:tal 0 190415-00:47:49,296 nipype.interface INFO: stdout 2019-04-15T00:47:49.295140:talres 2 190415-00:47:49,296 nipype.interface INFO: stdout 2019-04-15T00:47:49.295140:regheader 0 190415-00:47:49,296 nipype.interface INFO: stdout 2019-04-15T00:47:49.295140:noresample 0 190415-00:47:49,296 nipype.interface INFO: stdout 2019-04-15T00:47:49.295140:interp nearest (0) 190415-00:47:49,296 nipype.interface INFO: stdout 2019-04-15T00:47:49.295140:precision float (3) 190415-00:47:49,296 nipype.interface INFO: stdout 2019-04-15T00:47:49.295140:Gdiag_no -1 190415-00:47:49,296 nipype.interface INFO: stdout 2019-04-15T00:47:49.295140:Synth 0 190415-00:47:49,296 nipype.interface INFO: stdout 2019-04-15T00:47:49.295140:SynthSeed 1555522725 190415-00:47:49,296 nipype.interface INFO: stdout 2019-04-15T00:47:49.295140: 190415-00:47:49,296 nipype.interface INFO: stdout 2019-04-15T00:47:49.295140:Final tkRAS-to-tkRAS Matrix is: 190415-00:47:49,297 nipype.interface INFO: stdout 2019-04-15T00:47:49.295140: 0.99954 -0.03031 -0.00087 2.47099; 190415-00:47:49,297 nipype.interface INFO: stdout 2019-04-15T00:47:49.295140: 0.00630 0.17957 0.98373 -1.72581; 190415-00:47:49,297 nipype.interface INFO: stdout 2019-04-15T00:47:49.295140:-0.02966 -0.98328 0.17968 -0.60428; 190415-00:47:49,297 nipype.interface INFO: stdout 2019-04-15T00:47:49.295140: 0.00000 0.00000 0.00000 1.00000; 190415-00:47:49,297 nipype.interface INFO: stdout 2019-04-15T00:47:49.295140: 190415-00:47:49,297 nipype.interface INFO: stdout 2019-04-15T00:47:49.295140: 190415-00:47:49,297 nipype.interface INFO: stdout 2019-04-15T00:47:49.295140:Vox2Vox Matrix is: 190415-00:47:49,297 nipype.interface INFO: stdout 2019-04-15T00:47:49.295140: 0.29078 -0.00025 0.00882 -7.03424; 190415-00:47:49,297 nipype.interface INFO: stdout 2019-04-15T00:47:49.295140:-0.00863 0.05227 0.28604 -10.02408; 190415-00:47:49,297 nipype.interface INFO: stdout 2019-04-15T00:47:49.295140:-0.00137 -0.21385 0.03904 38.67670; 190415-00:47:49,297 nipype.interface INFO: stdout 2019-04-15T00:47:49.295140: 0.00000 0.00000 0.00000 1.00000; 190415-00:47:49,845 nipype.interface INFO: stdout 2019-04-15T00:47:49.845874: 190415-00:47:49,846 nipype.interface INFO: stdout 2019-04-15T00:47:49.845874:Resampling 190415-00:47:49,846 nipype.interface INFO: stdout 2019-04-15T00:47:49.845874:Output registration matrix is identity 190415-00:47:49,846 nipype.interface INFO: stdout 2019-04-15T00:47:49.845874: 190415-00:47:49,846 nipype.interface INFO: stdout 2019-04-15T00:47:49.845874:mri_vol2vol done 190415-00:47:50,957 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.refine" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/refine". 190415-00:47:50,959 nipype.workflow INFO: [Node] Running "refine" ("niworkflows.interfaces.freesurfer.RefineBrainMask") /usr/local/miniconda/lib/python3.7/site-packages/matplotlib/cbook/__init__.py:2364: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working return list(data) if isinstance(data, collections.MappingView) else data /usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index return _nd_image.find_objects(input, max_label) 190415-00:48:02,630 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.mri_coreg". 190415-00:48:03,59 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.get_surfaces" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/get_surfaces". 190415-00:48:03,61 nipype.workflow INFO: [Node] Running "get_surfaces" ("nipype.interfaces.io.FreeSurferSource") 190415-00:48:03,65 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.recon_report" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/recon_report". 190415-00:48:03,117 nipype.interface INFO: recon-all complete : Not running 190415-00:48:03,118 nipype.workflow INFO: [Node] Running "recon_report" ("niworkflows.interfaces.segmentation.ReconAllRPT"), a CommandLine Interface with command: echo recon-all: nothing to do 190415-00:48:03,160 nipype.interface INFO: recon-all complete : Not running 190415-00:48:03,274 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.get_surfaces". /usr/local/miniconda/lib/python3.7/site-packages/matplotlib/cbook/__init__.py:2364: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working return list(data) if isinstance(data, collections.MappingView) else data /usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index return _nd_image.find_objects(input, max_label) 190415-00:48:07,62 nipype.workflow INFO: [Node] Setting-up "_midthickness0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0". 190415-00:48:07,70 nipype.workflow INFO: [Node] Setting-up "_midthickness1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness1". 190415-00:48:07,87 nipype.workflow INFO: [Node] Running "_midthickness0" ("niworkflows.interfaces.freesurfer.MakeMidthickness"), a CommandLine Interface with command: mris_expand -pial /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.pial -thickness -thickness_name /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.thickness /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.smoothwm 0.5 midthickness 190415-00:48:07,92 nipype.workflow INFO: [Node] Running "_midthickness1" ("niworkflows.interfaces.freesurfer.MakeMidthickness"), a CommandLine Interface with command: mris_expand -pial /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness1/lh.pial -thickness -thickness_name /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness1/lh.thickness /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness1/lh.smoothwm 0.5 midthickness 190415-00:48:10,895 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.recon_report". 190415-00:48:29,463 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.refine". 190415-00:48:31,515 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.applyrefined" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/applyrefined". 190415-00:48:31,517 nipype.workflow INFO: [Node] Running "applyrefined" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-NC080001_T1w_ras_maths_corrected.nii.gz -mas /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/refine/sub-NC080001_T1w_ras_maths_corrected_rbrainmask.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/applyrefined/sub-NC080001_T1w_ras_maths_corrected_masked.nii.gz 190415-00:48:32,792 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.applyrefined". 190415-00:48:33,63 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.gen_ref" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/gen_ref". 190415-00:48:33,68 nipype.workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.utils.GenerateSamplingReference") 190415-00:48:33,79 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_seg" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/t1_seg". 190415-00:48:33,82 nipype.workflow INFO: [Node] Running "t1_seg" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command: fast -N -p -g -S 1 /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/t1_seg/sub-NC080001_T1w_ras_maths_corrected_masked.nii.gz 190415-00:48:33,572 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.gen_ref". 190415-00:48:35,272 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.aparc_t1w_tfm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/aparc_t1w_tfm". 190415-00:48:35,319 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.aseg_t1w_tfm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/aseg_t1w_tfm". 190415-00:48:35,334 nipype.workflow INFO: [Node] Running "aparc_t1w_tfm" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/tonii/aparc+aseg_vol_out.nii.gz --interpolation MultiLabel --output aparc+aseg_vol_out_trans.nii.gz --reference-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/gen_ref/sub-NC080001_T1w_ras_maths_corrected_masked_reference.nii.gz -t identity 190415-00:48:35,348 nipype.workflow INFO: [Node] Running "aseg_t1w_tfm" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonii/aseg_vol_out.nii.gz --interpolation MultiLabel --output aseg_vol_out_trans.nii.gz --reference-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/gen_ref/sub-NC080001_T1w_ras_maths_corrected_masked_reference.nii.gz -t identity 190415-00:48:37,627 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.aparc_t1w_tfm". 190415-00:48:37,644 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.aseg_t1w_tfm". 190415-00:50:09,218 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_seg". 190415-00:50:15,718 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.lut_t1_seg" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/lut_t1_seg". 190415-00:50:15,722 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.wm_roi" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/wm_roi". 190415-00:50:15,724 nipype.workflow INFO: [Node] Running "wm_roi" ("niworkflows.interfaces.utils.TPM2ROI") 190415-00:50:15,728 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.csf_roi" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/csf_roi". 190415-00:50:15,729 nipype.workflow INFO: [Node] Running "lut_t1_seg" ("nipype.interfaces.utility.wrappers.Function") 190415-00:50:15,731 nipype.workflow INFO: [Node] Running "csf_roi" ("niworkflows.interfaces.utils.TPM2ROI") 190415-00:50:15,734 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.tpms_add_csf_wm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/tpms_add_csf_wm". 190415-00:50:15,737 nipype.workflow INFO: [Node] Running "tpms_add_csf_wm" ("niworkflows.interfaces.utils.AddTPMs") 190415-00:50:16,169 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.lut_t1_seg". 190415-00:50:16,725 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.csf_roi". 190415-00:50:17,33 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.tpms_add_csf_wm". 190415-00:50:19,393 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.wm_roi". 190415-00:50:19,521 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.acc_roi" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/acc_roi". 190415-00:50:19,525 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.seg_rpt" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/seg_rpt". 190415-00:50:19,527 nipype.workflow INFO: [Node] Running "seg_rpt" ("niworkflows.interfaces.masks.ROIsPlot") 190415-00:50:19,527 nipype.workflow INFO: [Node] Running "acc_roi" ("niworkflows.interfaces.utils.TPM2ROI") 190415-00:50:23,7 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.acc_roi". /usr/local/miniconda/lib/python3.7/site-packages/nilearn/image/resampling.py:510: UserWarning: Casting data from int32 to float32 warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux)) /usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index return _nd_image.find_objects(input, max_label) /usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index return _nd_image.find_objects(input, max_label) /usr/local/miniconda/lib/python3.7/site-packages/nilearn/image/resampling.py:510: UserWarning: Casting data from int32 to float32 warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux)) /usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index return _nd_image.find_objects(input, max_label) /usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index return _nd_image.find_objects(input, max_label) /usr/local/miniconda/lib/python3.7/site-packages/nilearn/image/resampling.py:510: UserWarning: Casting data from int32 to float32 warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux)) /usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index return _nd_image.find_objects(input, max_label) /usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index return _nd_image.find_objects(input, max_label) 190415-00:51:03,547 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.seg_rpt". 190415-00:59:05,143 nipype.workflow INFO: [Node] Finished "_midthickness0". 190415-00:59:06,86 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_2_mni" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/t1_2_mni". 190415-00:59:06,88 nipype.workflow INFO: [Node] Running "t1_2_mni" ("niworkflows.interfaces.registration.RobustMNINormalizationRPT") 190415-00:59:17,483 nipype.workflow INFO: [Node] Finished "_midthickness1". 190415-00:59:18,141 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.midthickness" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness". 190415-00:59:18,151 nipype.workflow INFO: [Node] Setting-up "_midthickness0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0". 190415-00:59:18,155 nipype.workflow INFO: [Node] Cached "_midthickness0" - collecting precomputed outputs 190415-00:59:18,155 nipype.workflow INFO: [Node] "_midthickness0" found cached. 190415-00:59:18,158 nipype.workflow INFO: [Node] Setting-up "_midthickness1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness1". 190415-00:59:18,170 nipype.workflow INFO: [Node] Cached "_midthickness1" - collecting precomputed outputs 190415-00:59:18,170 nipype.workflow INFO: [Node] "_midthickness1" found cached. 190415-00:59:18,174 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.midthickness". 190415-00:59:20,121 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.save_midthickness" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/save_midthickness". 190415-00:59:20,125 nipype.workflow INFO: [Node] Running "save_midthickness" ("nipype.interfaces.io.DataSink") 190415-00:59:20,504 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.save_midthickness". 190415-00:59:26,121 nipype.workflow INFO: [Node] Setting-up "_fs_2_gii0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii0". 190415-00:59:26,126 nipype.workflow INFO: [Node] Running "_fs_2_gii0" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command: mris_convert /out/freesurfer/sub-NC080001/surf/rh.smoothwm /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii0/rh.smoothwm_converted.gii 190415-00:59:27,547 nipype.workflow INFO: [Node] Finished "_fs_2_gii0". 190415-00:59:28,89 nipype.workflow INFO: [Node] Setting-up "_fs_2_gii1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii1". 190415-00:59:28,94 nipype.workflow INFO: [Node] Running "_fs_2_gii1" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command: mris_convert /out/freesurfer/sub-NC080001/surf/lh.smoothwm /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii1/lh.smoothwm_converted.gii 190415-00:59:29,533 nipype.workflow INFO: [Node] Finished "_fs_2_gii1". 190415-00:59:30,90 nipype.workflow INFO: [Node] Setting-up "_fs_2_gii2" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii2". 190415-00:59:30,94 nipype.workflow INFO: [Node] Running "_fs_2_gii2" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command: mris_convert /out/freesurfer/sub-NC080001/surf/lh.pial /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii2/lh.pial_converted.gii 190415-00:59:31,486 nipype.workflow INFO: [Node] Finished "_fs_2_gii2". 190415-00:59:32,100 nipype.workflow INFO: [Node] Setting-up "_fs_2_gii3" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii3". 190415-00:59:32,104 nipype.workflow INFO: [Node] Running "_fs_2_gii3" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command: mris_convert /out/freesurfer/sub-NC080001/surf/rh.pial /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii3/rh.pial_converted.gii 190415-00:59:33,518 nipype.workflow INFO: [Node] Finished "_fs_2_gii3". 190415-00:59:34,116 nipype.workflow INFO: [Node] Setting-up "_fs_2_gii4" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii4". 190415-00:59:34,119 nipype.workflow INFO: [Node] Running "_fs_2_gii4" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command: mris_convert /out/freesurfer/sub-NC080001/surf/lh.inflated /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii4/lh.inflated_converted.gii 190415-00:59:35,549 nipype.workflow INFO: [Node] Finished "_fs_2_gii4". 190415-00:59:36,104 nipype.workflow INFO: [Node] Setting-up "_fs_2_gii5" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii5". 190415-00:59:36,114 nipype.workflow INFO: [Node] Running "_fs_2_gii5" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command: mris_convert /out/freesurfer/sub-NC080001/surf/rh.inflated /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii5/rh.inflated_converted.gii 190415-00:59:37,567 nipype.workflow INFO: [Node] Finished "_fs_2_gii5". 190415-00:59:38,105 nipype.workflow INFO: [Node] Setting-up "_fs_2_gii6" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii6". 190415-00:59:38,109 nipype.workflow INFO: [Node] Running "_fs_2_gii6" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command: mris_convert /out/freesurfer/sub-NC080001/surf/rh.midthickness /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii6/rh.midthickness_converted.gii 190415-00:59:39,541 nipype.workflow INFO: [Node] Finished "_fs_2_gii6". 190415-00:59:40,110 nipype.workflow INFO: [Node] Setting-up "_fs_2_gii7" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii7". 190415-00:59:40,113 nipype.workflow INFO: [Node] Running "_fs_2_gii7" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command: mris_convert /out/freesurfer/sub-NC080001/surf/lh.midthickness /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii7/lh.midthickness_converted.gii 190415-00:59:41,555 nipype.workflow INFO: [Node] Finished "_fs_2_gii7". 190415-00:59:42,147 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.fs_2_gii" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii". 190415-00:59:42,154 nipype.workflow INFO: [Node] Setting-up "_fs_2_gii0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii0". 190415-00:59:42,157 nipype.workflow INFO: [Node] Cached "_fs_2_gii0" - collecting precomputed outputs 190415-00:59:42,157 nipype.workflow INFO: [Node] "_fs_2_gii0" found cached. 190415-00:59:42,159 nipype.workflow INFO: [Node] Setting-up "_fs_2_gii1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii1". 190415-00:59:42,163 nipype.workflow INFO: [Node] Cached "_fs_2_gii1" - collecting precomputed outputs 190415-00:59:42,163 nipype.workflow INFO: [Node] "_fs_2_gii1" found cached. 190415-00:59:42,165 nipype.workflow INFO: [Node] Setting-up "_fs_2_gii2" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii2". 190415-00:59:42,168 nipype.workflow INFO: [Node] Cached "_fs_2_gii2" - collecting precomputed outputs 190415-00:59:42,168 nipype.workflow INFO: [Node] "_fs_2_gii2" found cached. 190415-00:59:42,170 nipype.workflow INFO: [Node] Setting-up "_fs_2_gii3" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii3". 190415-00:59:42,177 nipype.workflow INFO: [Node] Cached "_fs_2_gii3" - collecting precomputed outputs 190415-00:59:42,177 nipype.workflow INFO: [Node] "_fs_2_gii3" found cached. 190415-00:59:42,180 nipype.workflow INFO: [Node] Setting-up "_fs_2_gii4" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii4". 190415-00:59:42,187 nipype.workflow INFO: [Node] Cached "_fs_2_gii4" - collecting precomputed outputs 190415-00:59:42,187 nipype.workflow INFO: [Node] "_fs_2_gii4" found cached. 190415-00:59:42,189 nipype.workflow INFO: [Node] Setting-up "_fs_2_gii5" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii5". 190415-00:59:42,192 nipype.workflow INFO: [Node] Cached "_fs_2_gii5" - collecting precomputed outputs 190415-00:59:42,192 nipype.workflow INFO: [Node] "_fs_2_gii5" found cached. 190415-00:59:42,194 nipype.workflow INFO: [Node] Setting-up "_fs_2_gii6" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii6". 190415-00:59:42,197 nipype.workflow INFO: [Node] Cached "_fs_2_gii6" - collecting precomputed outputs 190415-00:59:42,197 nipype.workflow INFO: [Node] "_fs_2_gii6" found cached. 190415-00:59:42,199 nipype.workflow INFO: [Node] Setting-up "_fs_2_gii7" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii7". 190415-00:59:42,203 nipype.workflow INFO: [Node] Cached "_fs_2_gii7" - collecting precomputed outputs 190415-00:59:42,203 nipype.workflow INFO: [Node] "_fs_2_gii7" found cached. 190415-00:59:42,206 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.fs_2_gii". 190415-00:59:46,109 nipype.workflow INFO: [Node] Setting-up "_fix_surfs0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs0". 190415-00:59:46,111 nipype.workflow INFO: [Node] Running "_fix_surfs0" ("niworkflows.interfaces.surf.NormalizeSurf") /usr/local/miniconda/lib/python3.7/site-packages/nibabel/gifti/gifti.py:760: ResourceWarning: unclosed file <_io.BufferedReader name='/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii0/rh.smoothwm_converted.gii'> parser.parse(fptr=file_map['image'].get_prepare_fileobj('rb')) /usr/local/miniconda/lib/python3.7/site-packages/nibabel/filebasedimages.py:334: ResourceWarning: unclosed file <_io.BufferedWriter name='/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs0/rh.smoothwm_converted.gii'> self.to_file_map() 190415-00:59:46,482 nipype.workflow INFO: [Node] Finished "_fix_surfs0". 190415-00:59:48,119 nipype.workflow INFO: [Node] Setting-up "_fix_surfs1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs1". 190415-00:59:48,123 nipype.workflow INFO: [Node] Running "_fix_surfs1" ("niworkflows.interfaces.surf.NormalizeSurf") /usr/local/miniconda/lib/python3.7/site-packages/nibabel/gifti/gifti.py:760: ResourceWarning: unclosed file <_io.BufferedReader name='/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii1/lh.smoothwm_converted.gii'> parser.parse(fptr=file_map['image'].get_prepare_fileobj('rb')) /usr/local/miniconda/lib/python3.7/site-packages/nibabel/filebasedimages.py:334: ResourceWarning: unclosed file <_io.BufferedWriter name='/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs1/lh.smoothwm_converted.gii'> self.to_file_map() 190415-00:59:48,489 nipype.workflow INFO: [Node] Finished "_fix_surfs1". 190415-00:59:50,114 nipype.workflow INFO: [Node] Setting-up "_fix_surfs2" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs2". 190415-00:59:50,116 nipype.workflow INFO: [Node] Running "_fix_surfs2" ("niworkflows.interfaces.surf.NormalizeSurf") 190415-00:59:50,463 nipype.workflow INFO: [Node] Finished "_fix_surfs2". 190415-00:59:52,118 nipype.workflow INFO: [Node] Setting-up "_fix_surfs3" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs3". 190415-00:59:52,120 nipype.workflow INFO: [Node] Running "_fix_surfs3" ("niworkflows.interfaces.surf.NormalizeSurf") /usr/local/miniconda/lib/python3.7/site-packages/nibabel/gifti/gifti.py:760: ResourceWarning: unclosed file <_io.BufferedReader name='/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii3/rh.pial_converted.gii'> parser.parse(fptr=file_map['image'].get_prepare_fileobj('rb')) /usr/local/miniconda/lib/python3.7/site-packages/nibabel/filebasedimages.py:334: ResourceWarning: unclosed file <_io.BufferedWriter name='/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs3/rh.pial_converted.gii'> self.to_file_map() 190415-00:59:52,498 nipype.workflow INFO: [Node] Finished "_fix_surfs3". 190415-00:59:54,128 nipype.workflow INFO: [Node] Setting-up "_fix_surfs4" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs4". 190415-00:59:54,130 nipype.workflow INFO: [Node] Running "_fix_surfs4" ("niworkflows.interfaces.surf.NormalizeSurf") /usr/local/miniconda/lib/python3.7/site-packages/nibabel/gifti/gifti.py:760: ResourceWarning: unclosed file <_io.BufferedReader name='/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii4/lh.inflated_converted.gii'> parser.parse(fptr=file_map['image'].get_prepare_fileobj('rb')) /usr/local/miniconda/lib/python3.7/site-packages/nibabel/filebasedimages.py:334: ResourceWarning: unclosed file <_io.BufferedWriter name='/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs4/lh.inflated_converted.gii'> self.to_file_map() 190415-00:59:54,484 nipype.workflow INFO: [Node] Finished "_fix_surfs4". 190415-00:59:56,135 nipype.workflow INFO: [Node] Setting-up "_fix_surfs5" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs5". 190415-00:59:56,138 nipype.workflow INFO: [Node] Running "_fix_surfs5" ("niworkflows.interfaces.surf.NormalizeSurf") /usr/local/miniconda/lib/python3.7/site-packages/nibabel/gifti/gifti.py:760: ResourceWarning: unclosed file <_io.BufferedReader name='/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii5/rh.inflated_converted.gii'> parser.parse(fptr=file_map['image'].get_prepare_fileobj('rb')) /usr/local/miniconda/lib/python3.7/site-packages/nibabel/filebasedimages.py:334: ResourceWarning: unclosed file <_io.BufferedWriter name='/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs5/rh.inflated_converted.gii'> self.to_file_map() 190415-00:59:56,455 nipype.workflow INFO: [Node] Finished "_fix_surfs5". 190415-00:59:58,92 nipype.workflow INFO: [Node] Setting-up "_fix_surfs6" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs6". 190415-00:59:58,96 nipype.workflow INFO: [Node] Running "_fix_surfs6" ("niworkflows.interfaces.surf.NormalizeSurf") /usr/local/miniconda/lib/python3.7/site-packages/nibabel/gifti/gifti.py:760: ResourceWarning: unclosed file <_io.BufferedReader name='/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii6/rh.midthickness_converted.gii'> parser.parse(fptr=file_map['image'].get_prepare_fileobj('rb')) /usr/local/miniconda/lib/python3.7/site-packages/nibabel/filebasedimages.py:334: ResourceWarning: unclosed file <_io.BufferedWriter name='/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs6/rh.midthickness_converted.gii'> self.to_file_map() 190415-00:59:58,442 nipype.workflow INFO: [Node] Finished "_fix_surfs6". 190415-01:00:00,90 nipype.workflow INFO: [Node] Setting-up "_fix_surfs7" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs7". 190415-01:00:00,92 nipype.workflow INFO: [Node] Running "_fix_surfs7" ("niworkflows.interfaces.surf.NormalizeSurf") 190415-01:00:00,442 nipype.workflow INFO: [Node] Finished "_fix_surfs7". 190415-01:00:02,100 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.fix_surfs" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs". 190415-01:00:02,103 nipype.workflow INFO: [Node] Setting-up "_fix_surfs0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs0". 190415-01:00:02,105 nipype.workflow INFO: [Node] Cached "_fix_surfs0" - collecting precomputed outputs 190415-01:00:02,105 nipype.workflow INFO: [Node] "_fix_surfs0" found cached. 190415-01:00:02,106 nipype.workflow INFO: [Node] Setting-up "_fix_surfs1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs1". 190415-01:00:02,108 nipype.workflow INFO: [Node] Cached "_fix_surfs1" - collecting precomputed outputs 190415-01:00:02,108 nipype.workflow INFO: [Node] "_fix_surfs1" found cached. 190415-01:00:02,109 nipype.workflow INFO: [Node] Setting-up "_fix_surfs2" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs2". 190415-01:00:02,111 nipype.workflow INFO: [Node] Cached "_fix_surfs2" - collecting precomputed outputs 190415-01:00:02,111 nipype.workflow INFO: [Node] "_fix_surfs2" found cached. 190415-01:00:02,112 nipype.workflow INFO: [Node] Setting-up "_fix_surfs3" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs3". 190415-01:00:02,113 nipype.workflow INFO: [Node] Cached "_fix_surfs3" - collecting precomputed outputs 190415-01:00:02,113 nipype.workflow INFO: [Node] "_fix_surfs3" found cached. 190415-01:00:02,114 nipype.workflow INFO: [Node] Setting-up "_fix_surfs4" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs4". 190415-01:00:02,115 nipype.workflow INFO: [Node] Cached "_fix_surfs4" - collecting precomputed outputs 190415-01:00:02,115 nipype.workflow INFO: [Node] "_fix_surfs4" found cached. 190415-01:00:02,117 nipype.workflow INFO: [Node] Setting-up "_fix_surfs5" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs5". 190415-01:00:02,118 nipype.workflow INFO: [Node] Cached "_fix_surfs5" - collecting precomputed outputs 190415-01:00:02,118 nipype.workflow INFO: [Node] "_fix_surfs5" found cached. 190415-01:00:02,119 nipype.workflow INFO: [Node] Setting-up "_fix_surfs6" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs6". 190415-01:00:02,120 nipype.workflow INFO: [Node] Cached "_fix_surfs6" - collecting precomputed outputs 190415-01:00:02,120 nipype.workflow INFO: [Node] "_fix_surfs6" found cached. 190415-01:00:02,122 nipype.workflow INFO: [Node] Setting-up "_fix_surfs7" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs7". 190415-01:00:02,122 nipype.workflow INFO: [Node] Cached "_fix_surfs7" - collecting precomputed outputs 190415-01:00:02,122 nipype.workflow INFO: [Node] "_fix_surfs7" found cached. 190415-01:00:02,126 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.fix_surfs". 190415-01:44:57,376 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_2_mni". 190415-01:44:59,178 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.bbregister" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/bbregister". 190415-01:44:59,184 nipype.workflow INFO: [Node] Running "bbregister" ("niworkflows.interfaces.freesurfer.PatchedBBRegisterRPT"), a CommandLine Interface with command: bbregister --t2 --6 --init-reg /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/mri_coreg/registration.lta --lta /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked_bbreg_sub-NC080001.lta --reg /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked_bbreg_sub-NC080001.dat --o /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked_bbreg.nii.gz --mov /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked.nii.gz --s sub-NC080001 190415-01:45:34,243 nipype.interface INFO: stdout 2019-04-15T01:45:34.243292: 190415-01:45:34,243 nipype.interface INFO: stdout 2019-04-15T01:45:34.243292:Matrix from LTA: 190415-01:45:34,243 nipype.interface INFO: stdout 2019-04-15T01:45:34.243292: 0.99972 -0.02371 0.00201 2.53764; 190415-01:45:34,243 nipype.interface INFO: stdout 2019-04-15T01:45:34.243292: 0.00179 0.15912 0.98726 -4.05743; 190415-01:45:34,243 nipype.interface INFO: stdout 2019-04-15T01:45:34.243292:-0.02373 -0.98697 0.15912 -0.62111; 190415-01:45:34,243 nipype.interface INFO: stdout 2019-04-15T01:45:34.243292: 0.00000 0.00000 0.00000 1.00000; 190415-01:45:34,362 nipype.interface INFO: stdout 2019-04-15T01:45:34.362317: 190415-01:45:34,362 nipype.interface INFO: stdout 2019-04-15T01:45:34.362317:/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked.nii.gz /out/freesurfer/sub-NC080001/mri/brainmask.mgz 190415-01:45:34,362 nipype.interface INFO: stdout 2019-04-15T01:45:34.362317:movvol /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked.nii.gz 190415-01:45:34,362 nipype.interface INFO: stdout 2019-04-15T01:45:34.362317:targvol /out/freesurfer/sub-NC080001/mri/brainmask.mgz 190415-01:45:34,362 nipype.interface INFO: stdout 2019-04-15T01:45:34.362317:outvol /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked_warped.nii.gz 190415-01:45:34,363 nipype.interface INFO: stdout 2019-04-15T01:45:34.362317:regfile /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked_bbreg_sub-NC080001.lta 190415-01:45:34,363 nipype.interface INFO: stdout 2019-04-15T01:45:34.362317:invert 0 190415-01:45:34,363 nipype.interface INFO: stdout 2019-04-15T01:45:34.362317:tal 0 190415-01:45:34,363 nipype.interface INFO: stdout 2019-04-15T01:45:34.362317:talres 2 190415-01:45:34,363 nipype.interface INFO: stdout 2019-04-15T01:45:34.362317:regheader 0 190415-01:45:34,363 nipype.interface INFO: stdout 2019-04-15T01:45:34.362317:noresample 0 190415-01:45:34,363 nipype.interface INFO: stdout 2019-04-15T01:45:34.362317:interp nearest (0) 190415-01:45:34,363 nipype.interface INFO: stdout 2019-04-15T01:45:34.362317:precision float (3) 190415-01:45:34,363 nipype.interface INFO: stdout 2019-04-15T01:45:34.362317:Gdiag_no -1 190415-01:45:34,363 nipype.interface INFO: stdout 2019-04-15T01:45:34.362317:Synth 0 190415-01:45:34,363 nipype.interface INFO: stdout 2019-04-15T01:45:34.362317:SynthSeed 1555593060 190415-01:45:34,363 nipype.interface INFO: stdout 2019-04-15T01:45:34.362317: 190415-01:45:34,363 nipype.interface INFO: stdout 2019-04-15T01:45:34.362317:Final tkRAS-to-tkRAS Matrix is: 190415-01:45:34,364 nipype.interface INFO: stdout 2019-04-15T01:45:34.362317: 0.99972 -0.02371 0.00201 2.53766; 190415-01:45:34,364 nipype.interface INFO: stdout 2019-04-15T01:45:34.362317: 0.00179 0.15912 0.98726 -4.05741; 190415-01:45:34,364 nipype.interface INFO: stdout 2019-04-15T01:45:34.362317:-0.02373 -0.98697 0.15912 -0.62111; 190415-01:45:34,364 nipype.interface INFO: stdout 2019-04-15T01:45:34.362317: 0.00000 0.00000 0.00000 1.00000; 190415-01:45:34,364 nipype.interface INFO: stdout 2019-04-15T01:45:34.362317: 190415-01:45:34,364 nipype.interface INFO: stdout 2019-04-15T01:45:34.362317: 190415-01:45:34,364 nipype.interface INFO: stdout 2019-04-15T01:45:34.362317:Vox2Vox Matrix is: 190415-01:45:34,364 nipype.interface INFO: stdout 2019-04-15T01:45:34.362317: 0.29083 0.00059 0.00690 -6.92185; 190415-01:45:34,364 nipype.interface INFO: stdout 2019-04-15T01:45:34.362317:-0.00690 0.04629 0.28712 -9.61213; 190415-01:45:34,364 nipype.interface INFO: stdout 2019-04-15T01:45:34.362317:-0.00039 -0.21462 0.03459 38.71147; 190415-01:45:34,364 nipype.interface INFO: stdout 2019-04-15T01:45:34.362317: 0.00000 0.00000 0.00000 1.00000; 190415-01:45:34,897 nipype.interface INFO: stdout 2019-04-15T01:45:34.897598: 190415-01:45:34,897 nipype.interface INFO: stdout 2019-04-15T01:45:34.897598:Resampling 190415-01:45:34,897 nipype.interface INFO: stdout 2019-04-15T01:45:34.897598:Output registration matrix is identity 190415-01:45:34,897 nipype.interface INFO: stdout 2019-04-15T01:45:34.897598: 190415-01:45:34,897 nipype.interface INFO: stdout 2019-04-15T01:45:34.897598:mri_vol2vol done /usr/local/miniconda/lib/python3.7/site-packages/matplotlib/cbook/__init__.py:2364: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working return list(data) if isinstance(data, collections.MappingView) else data /usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index return _nd_image.find_objects(input, max_label) 190415-01:45:47,591 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.bbregister". 190415-01:45:58,169 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.aparc_mni_tfm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/aparc_mni_tfm". 190415-01:45:58,174 nipype.workflow INFO: [Node] Running "aparc_mni_tfm" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/tonii/aparc+aseg_vol_out.nii.gz --interpolation MultiLabel --output aparc+aseg_vol_out_trans.nii.gz --reference-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/gen_ref/tpl-MNI152NLin2009cAsym_res-01_T1w_reference.nii.gz --transform /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/t1_2_mni/ants_t1_to_mniComposite.h5 190415-01:45:58,177 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.aseg_mni_tfm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/aseg_mni_tfm". 190415-01:45:58,178 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_mask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/mni_mask". 190415-01:45:58,178 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_seg" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/mni_seg". 190415-01:45:58,179 nipype.workflow INFO: [Node] Setting-up "_mni_tpms0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/mni_tpms/mapflow/_mni_tpms0". 190415-01:45:58,179 nipype.workflow INFO: [Node] Setting-up "_mni_tpms1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/mni_tpms/mapflow/_mni_tpms1". 190415-01:45:58,180 nipype.workflow INFO: [Node] Running "aseg_mni_tfm" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonii/aseg_vol_out.nii.gz --interpolation MultiLabel --output aseg_vol_out_trans.nii.gz --reference-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/gen_ref/tpl-MNI152NLin2009cAsym_res-01_T1w_reference.nii.gz --transform /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/t1_2_mni/ants_t1_to_mniComposite.h5 190415-01:45:58,181 nipype.workflow INFO: [Node] Running "mni_mask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/refine/sub-NC080001_T1w_ras_maths_corrected_rbrainmask.nii.gz --interpolation MultiLabel --output sub-NC080001_T1w_ras_maths_corrected_rbrainmask_trans.nii.gz --reference-image /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz --transform /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/t1_2_mni/ants_t1_to_mniComposite.h5 190415-01:45:58,181 nipype.workflow INFO: [Node] Running "mni_seg" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/t1_seg/sub-NC080001_T1w_ras_maths_corrected_masked_seg.nii.gz --interpolation MultiLabel --output sub-NC080001_T1w_ras_maths_corrected_masked_seg_trans.nii.gz --reference-image /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz --transform /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/t1_2_mni/ants_t1_to_mniComposite.h5 190415-01:45:58,182 nipype.workflow INFO: [Node] Running "_mni_tpms0" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/t1_seg/sub-NC080001_T1w_ras_maths_corrected_masked_prob_0.nii.gz --interpolation Linear --output sub-NC080001_T1w_ras_maths_corrected_masked_prob_0_trans.nii.gz --reference-image /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz --transform /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/t1_2_mni/ants_t1_to_mniComposite.h5 190415-01:45:58,182 nipype.workflow INFO: [Node] Running "_mni_tpms1" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/t1_seg/sub-NC080001_T1w_ras_maths_corrected_masked_prob_1.nii.gz --interpolation Linear --output sub-NC080001_T1w_ras_maths_corrected_masked_prob_1_trans.nii.gz --reference-image /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz --transform /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/t1_2_mni/ants_t1_to_mniComposite.h5 190415-01:46:00,877 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.aseg_mni_tfm". 190415-01:46:00,902 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.aparc_mni_tfm". 190415-01:46:01,509 nipype.workflow INFO: [Node] Finished "_mni_tpms1". 190415-01:46:01,608 nipype.workflow INFO: [Node] Finished "_mni_tpms0". 190415-01:46:02,551 nipype.workflow INFO: [Node] Setting-up "_mni_tpms2" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/mni_tpms/mapflow/_mni_tpms2". 190415-01:46:02,554 nipype.workflow INFO: [Node] Running "_mni_tpms2" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/t1_seg/sub-NC080001_T1w_ras_maths_corrected_masked_prob_2.nii.gz --interpolation Linear --output sub-NC080001_T1w_ras_maths_corrected_masked_prob_2_trans.nii.gz --reference-image /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz --transform /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/t1_2_mni/ants_t1_to_mniComposite.h5 190415-01:46:04,244 nipype.workflow INFO: [Node] Setting-up "_lta_ras2ras0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/lta_ras2ras/mapflow/_lta_ras2ras0". 190415-01:46:04,244 nipype.workflow INFO: [Node] Setting-up "_lta_ras2ras1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/lta_ras2ras/mapflow/_lta_ras2ras1". 190415-01:46:04,247 nipype.workflow INFO: [Node] Running "_lta_ras2ras0" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command: lta_convert --inlta /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked_bbreg_sub-NC080001.lta --outlta /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/lta_ras2ras/mapflow/_lta_ras2ras0/out.lta 190415-01:46:04,249 nipype.workflow INFO: [Node] Running "_lta_ras2ras1" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command: lta_convert --inlta /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/mri_coreg/registration.lta --outlta /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/lta_ras2ras/mapflow/_lta_ras2ras1/out.lta 190415-01:46:04,318 nipype.workflow INFO: [Node] Finished "_lta_ras2ras1". 190415-01:46:04,341 nipype.workflow INFO: [Node] Finished "_lta_ras2ras0". 190415-01:46:05,486 nipype.workflow INFO: [Node] Finished "_mni_tpms2". 190415-01:46:06,249 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.lta_ras2ras" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/lta_ras2ras". 190415-01:46:06,253 nipype.workflow INFO: [Node] Setting-up "_lta_ras2ras0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/lta_ras2ras/mapflow/_lta_ras2ras0". 190415-01:46:06,254 nipype.workflow INFO: [Node] Cached "_lta_ras2ras0" - collecting precomputed outputs 190415-01:46:06,254 nipype.workflow INFO: [Node] "_lta_ras2ras0" found cached. 190415-01:46:06,256 nipype.workflow INFO: [Node] Setting-up "_lta_ras2ras1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/lta_ras2ras/mapflow/_lta_ras2ras1". 190415-01:46:06,257 nipype.workflow INFO: [Node] Cached "_lta_ras2ras1" - collecting precomputed outputs 190415-01:46:06,257 nipype.workflow INFO: [Node] "_lta_ras2ras1" found cached. 190415-01:46:06,259 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.lta_ras2ras". 190415-01:46:06,263 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_tpms" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/mni_tpms". 190415-01:46:06,266 nipype.workflow INFO: [Node] Setting-up "_mni_tpms0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/mni_tpms/mapflow/_mni_tpms0". 190415-01:46:06,267 nipype.workflow INFO: [Node] Cached "_mni_tpms0" - collecting precomputed outputs 190415-01:46:06,267 nipype.workflow INFO: [Node] "_mni_tpms0" found cached. 190415-01:46:06,269 nipype.workflow INFO: [Node] Setting-up "_mni_tpms1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/mni_tpms/mapflow/_mni_tpms1". 190415-01:46:06,270 nipype.workflow INFO: [Node] Cached "_mni_tpms1" - collecting precomputed outputs 190415-01:46:06,270 nipype.workflow INFO: [Node] "_mni_tpms1" found cached. 190415-01:46:06,271 nipype.workflow INFO: [Node] Setting-up "_mni_tpms2" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/mni_tpms/mapflow/_mni_tpms2". 190415-01:46:06,272 nipype.workflow INFO: [Node] Cached "_mni_tpms2" - collecting precomputed outputs 190415-01:46:06,272 nipype.workflow INFO: [Node] "_mni_tpms2" found cached. 190415-01:46:06,274 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_tpms". 190415-01:46:08,245 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.compare_transforms" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/compare_transforms". 190415-01:46:08,248 nipype.workflow INFO: [Node] Running "compare_transforms" ("nipype.interfaces.utility.wrappers.Function") 190415-01:46:08,259 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.compare_transforms". Captured warning (): In future, it will be an error for 'np.bool_' scalars to be interpreted as an index 190415-01:46:13,483 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.lta_concat" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/lta_concat". 190415-01:46:13,489 nipype.workflow INFO: [Node] Running "lta_concat" ("niworkflows.interfaces.freesurfer.PatchedConcatenateLTA"), a CommandLine Interface with command: mri_concatenate_lta /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked_bbreg_sub-NC080001.lta /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/fsnative_2_t1_xfm/T1_robustreg.lta out.lta 190415-01:46:13,562 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.lta_concat". 190415-01:46:15,421 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.lta2fsl_inv" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/lta2fsl_inv". 190415-01:46:15,423 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.lta2fsl_fwd" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/lta2fsl_fwd". 190415-01:46:15,424 nipype.workflow INFO: [Node] Running "lta2fsl_inv" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command: lta_convert --inlta /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/lta_concat/out.lta --invert --outfsl /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/lta2fsl_inv/out.mat 190415-01:46:15,426 nipype.workflow INFO: [Node] Running "lta2fsl_fwd" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command: lta_convert --inlta /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/lta_concat/out.lta --outfsl /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/lta2fsl_fwd/out.mat 190415-01:46:15,500 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.lta2fsl_inv". 190415-01:46:15,503 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.lta2fsl_fwd". 190415-01:46:17,428 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.fsl2itk_inv" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/fsl2itk_inv". 190415-01:46:17,430 nipype.workflow INFO: [Node] Running "fsl2itk_inv" ("nipype.interfaces.c3.C3dAffineTool"), a CommandLine Interface with command: c3d_affine_tool -ref /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz -src /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/applyrefined/sub-NC080001_T1w_ras_maths_corrected_masked.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/lta2fsl_inv/out.mat -fsl2ras -oitk /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/fsl2itk_inv/affine.txt 190415-01:46:17,434 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.fsl2itk_fwd" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/fsl2itk_fwd". 190415-01:46:17,438 nipype.workflow INFO: [Node] Running "fsl2itk_fwd" ("nipype.interfaces.c3.C3dAffineTool"), a CommandLine Interface with command: c3d_affine_tool -ref /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/applyrefined/sub-NC080001_T1w_ras_maths_corrected_masked.nii.gz -src /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/lta2fsl_fwd/out.mat -fsl2ras -oitk /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/fsl2itk_fwd/affine.txt 190415-01:46:17,750 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.fsl2itk_inv". 190415-01:46:17,789 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.fsl2itk_fwd". 190415-01:46:19,429 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.carpetplot_wf.mrg_xfms" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/carpetplot_wf/mrg_xfms". 190415-01:46:19,432 nipype.workflow INFO: [Node] Running "mrg_xfms" ("nipype.interfaces.utility.base.Merge") 190415-01:46:19,436 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.carpetplot_wf.mrg_xfms". 190415-01:46:19,499 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.mask_t1w_tfm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/mask_t1w_tfm". 190415-01:46:19,501 nipype.workflow INFO: [Node] Running "mask_t1w_tfm" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_valid_corrected_brain_mask_maths.nii.gz --interpolation MultiLabel --output ref_image_valid_corrected_brain_mask_maths_trans.nii.gz --reference-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/gen_ref/sub-NC080001_T1w_ras_maths_corrected_masked_reference.nii.gz --transform /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/fsl2itk_fwd/affine.txt 190415-01:46:19,632 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.wm_tfm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/wm_tfm". 190415-01:46:19,635 nipype.workflow INFO: [Node] Running "wm_tfm" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/wm_roi/sub-NC080001_T1w_ras_maths_corrected_masked_prob_2_roi.nii.gz --interpolation NearestNeighbor --output sub-NC080001_T1w_ras_maths_corrected_masked_prob_2_roi_trans.nii.gz --reference-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_valid_corrected_brain_mask_maths.nii.gz --transform /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/fsl2itk_inv/affine.txt 190415-01:46:19,639 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.tcc_tfm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/tcc_tfm". 190415-01:46:19,641 nipype.workflow INFO: [Node] Running "tcc_tfm" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/csf_roi/sub-NC080001_T1w_ras_maths_corrected_rbrainmask_eroded.nii.gz --interpolation NearestNeighbor --output sub-NC080001_T1w_ras_maths_corrected_rbrainmask_eroded_trans.nii.gz --reference-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_valid_corrected_brain_mask_maths.nii.gz --transform /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/fsl2itk_inv/affine.txt 190415-01:46:19,801 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.wm_tfm". 190415-01:46:19,807 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.tcc_tfm". 190415-01:46:20,320 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.mask_t1w_tfm". 190415-01:46:21,438 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.carpetplot_wf.resample_parc" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/carpetplot_wf/resample_parc". 190415-01:46:21,441 nipype.workflow INFO: [Node] Running "resample_parc" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_desc-carpet_dseg.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-01_desc-carpet_dseg_trans.nii.gz --reference-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_valid_corrected_brain_mask_maths.nii.gz --transform /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/fsl2itk_inv/affine.txt --transform /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/t1_2_mni/ants_t1_to_mniInverseComposite.h5 190415-01:46:21,453 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate".190415-01:46:21,454 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.mask_mni_tfm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/mask_mni_tfm". 190415-01:46:21,457 nipype.workflow INFO: [Node] Running "mask_mni_tfm" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_valid_corrected_brain_mask_maths.nii.gz --interpolation MultiLabel --output ref_image_valid_corrected_brain_mask_maths_trans.nii.gz --reference-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/gen_ref/tpl-MNI152NLin2009cAsym_res-01_T1w_reference.nii.gz --transform /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/t1_2_mni/ants_t1_to_mniComposite.h5 --transform /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/fsl2itk_fwd/affine.txt 190415-01:46:21,459 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.wm_msk" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/wm_msk". 190415-01:46:21,461 nipype.workflow INFO: [Node] Running "wm_msk" ("nipype.interfaces.utility.wrappers.Function") 190415-01:46:21,462 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/mask_t1w_tfm/ref_image_valid_corrected_brain_mask_maths_trans.nii.gz -kernel sphere 3.0000 -dilF /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/ref_image_valid_corrected_brain_mask_maths_trans_dil.nii.gz 190415-01:46:21,479 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.wm_msk". 190415-01:46:21,573 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190415-01:46:22,808 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.carpetplot_wf.resample_parc". 190415-01:46:23,237 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.mask_mni_tfm". 190415-01:46:23,544 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 190415-01:46:23,546 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.tcc_msk" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/tcc_msk". 190415-01:46:23,546 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/mask_mni_tfm/ref_image_valid_corrected_brain_mask_maths_trans.nii.gz -kernel sphere 3.0000 -dilF /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/ref_image_valid_corrected_brain_mask_maths_trans_dil.nii.gz 190415-01:46:23,548 nipype.workflow INFO: [Node] Running "tcc_msk" ("nipype.interfaces.utility.wrappers.Function") 190415-01:46:23,559 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.csf_tfm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/csf_tfm". 190415-01:46:23,560 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.acc_tfm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/acc_tfm". 190415-01:46:23,563 nipype.workflow INFO: [Node] Running "acc_tfm" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/acc_roi/sub-NC080001_T1w_ras_maths_corrected_masked_prob_0_tpmsum_roi.nii.gz --interpolation NearestNeighbor --output sub-NC080001_T1w_ras_maths_corrected_masked_prob_0_tpmsum_roi_trans.nii.gz --reference-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_valid_corrected_brain_mask_maths.nii.gz --transform /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/fsl2itk_inv/affine.txt 190415-01:46:23,571 nipype.workflow INFO: [Node] Running "csf_tfm" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/csf_roi/sub-NC080001_T1w_ras_maths_corrected_masked_prob_0_roi.nii.gz --interpolation NearestNeighbor --output sub-NC080001_T1w_ras_maths_corrected_masked_prob_0_roi_trans.nii.gz --reference-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_valid_corrected_brain_mask_maths.nii.gz --transform /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/fsl2itk_inv/affine.txt 190415-01:46:23,592 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.tcc_msk". 190415-01:46:23,733 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190415-01:46:23,748 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.acc_tfm". 190415-01:46:23,772 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.csf_tfm". 190415-01:46:25,447 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.tcompcor" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/tcompcor". 190415-01:46:25,448 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.csf_msk" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/csf_msk". 190415-01:46:25,450 nipype.workflow INFO: [Node] Running "csf_msk" ("nipype.interfaces.utility.wrappers.Function") 190415-01:46:25,453 nipype.workflow INFO: [Node] Running "tcompcor" ("niworkflows.interfaces.patches.RobustTCompCor") 190415-01:46:25,463 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.acc_msk" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/acc_msk". 190415-01:46:25,465 nipype.workflow INFO: [Node] Running "acc_msk" ("nipype.interfaces.utility.wrappers.Function") 190415-01:46:25,475 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.csf_msk". 190415-01:46:25,484 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.acc_msk". /usr/local/miniconda/lib/python3.7/site-packages/nipype/algorithms/confounds.py:1037: FutureWarning: `rcond` parameter will change to the default of machine precision times ``max(M, N)`` where M and N are the input matrix dimensions. To use the future default and silence this warning we advise to pass `rcond=None`, to keep using the old, explicitly pass `rcond=-1`. betas = np.linalg.lstsq(X, data.T)[0] 190415-01:46:26,401 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.tcompcor". 190415-01:46:27,575 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.acompcor" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/acompcor". 190415-01:46:27,580 nipype.workflow INFO: [Node] Running "acompcor" ("niworkflows.interfaces.patches.RobustACompCor") /usr/local/miniconda/lib/python3.7/site-packages/nipype/algorithms/confounds.py:1037: FutureWarning: `rcond` parameter will change to the default of machine precision times ``max(M, N)`` where M and N are the input matrix dimensions. To use the future default and silence this warning we advise to pass `rcond=None`, to keep using the old, explicitly pass `rcond=-1`. betas = np.linalg.lstsq(X, data.T)[0] 190415-01:46:28,339 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.acompcor". 190415-01:46:29,448 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.signals" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/signals". 190415-01:46:29,450 nipype.workflow INFO: [Node] Running "signals" ("niworkflows.interfaces.images.SignalExtraction") 190415-01:46:29,471 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.rois_plot" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/rois_plot". 190415-01:46:29,474 nipype.workflow INFO: [Node] Running "rois_plot" ("niworkflows.interfaces.masks.ROIsPlot") 190415-01:46:30,310 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.signals". /usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index return _nd_image.find_objects(input, max_label) /usr/local/miniconda/lib/python3.7/site-packages/matplotlib/contour.py:1173: UserWarning: No contour levels were found within the data range. warnings.warn("No contour levels were found" /usr/local/miniconda/lib/python3.7/site-packages/matplotlib/contour.py:1173: UserWarning: No contour levels were found within the data range. warnings.warn("No contour levels were found" /usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index return _nd_image.find_objects(input, max_label) /usr/local/miniconda/lib/python3.7/site-packages/matplotlib/contour.py:1173: UserWarning: No contour levels were found within the data range. warnings.warn("No contour levels were found" /usr/local/miniconda/lib/python3.7/site-packages/matplotlib/contour.py:1173: UserWarning: No contour levels were found within the data range. warnings.warn("No contour levels were found" /usr/local/miniconda/lib/python3.7/site-packages/matplotlib/contour.py:1173: UserWarning: No contour levels were found within the data range. warnings.warn("No contour levels were found" /usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index return _nd_image.find_objects(input, max_label) /usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index return _nd_image.find_objects(input, max_label) /usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index return _nd_image.find_objects(input, max_label) /usr/local/miniconda/lib/python3.7/site-packages/matplotlib/contour.py:1173: UserWarning: No contour levels were found within the data range. warnings.warn("No contour levels were found" /usr/local/miniconda/lib/python3.7/site-packages/matplotlib/contour.py:1173: UserWarning: No contour levels were found within the data range. warnings.warn("No contour levels were found" /usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index return _nd_image.find_objects(input, max_label) /usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index return _nd_image.find_objects(input, max_label) /usr/local/miniconda/lib/python3.7/site-packages/matplotlib/contour.py:1173: UserWarning: No contour levels were found within the data range. warnings.warn("No contour levels were found" /usr/local/miniconda/lib/python3.7/site-packages/matplotlib/contour.py:1173: UserWarning: No contour levels were found within the data range. warnings.warn("No contour levels were found" /usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index return _nd_image.find_objects(input, max_label) /usr/local/miniconda/lib/python3.7/site-packages/matplotlib/contour.py:1173: UserWarning: No contour levels were found within the data range. warnings.warn("No contour levels were found" /usr/local/miniconda/lib/python3.7/site-packages/matplotlib/contour.py:1173: UserWarning: No contour levels were found within the data range. warnings.warn("No contour levels were found" /usr/local/miniconda/lib/python3.7/site-packages/matplotlib/contour.py:1173: UserWarning: No contour levels were found within the data range. warnings.warn("No contour levels were found" /usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index return _nd_image.find_objects(input, max_label) 190415-01:46:33,643 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.carpetplot_wf.conf_plot" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/carpetplot_wf/conf_plot". 190415-01:46:33,650 nipype.workflow INFO: [Node] Running "conf_plot" ("fmriprep.interfaces.confounds.FMRISummary") 190415-01:46:33,760 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.rois_plot". 190415-01:46:35,866 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.carpetplot_wf.conf_plot". 190415-01:47:27,669 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_mask". 190415-01:47:29,986 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_to_t1w_transform" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_to_t1w_transform". 190415-01:47:30,0 nipype.workflow INFO: [Node] Running "bold_to_t1w_transform" ("niworkflows.interfaces.itk.MultiApplyTransforms") 190415-01:47:33,889 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_seg". 190415-01:47:35,499 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.lut_mni_seg" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/lut_mni_seg". 190415-01:47:35,505 nipype.workflow INFO: [Node] Running "lut_mni_seg" ("nipype.interfaces.utility.wrappers.Function") 190415-01:47:35,753 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.lut_mni_seg". 190415-01:48:01,525 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_to_t1w_transform". 190415-01:48:03,531 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_to_mni_transform" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_to_mni_transform". 190415-01:48:03,537 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.merge" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/merge". 190415-01:48:03,542 nipype.workflow INFO: [Node] Running "bold_to_mni_transform" ("niworkflows.interfaces.itk.MultiApplyTransforms") 190415-01:48:03,546 nipype.workflow INFO: [Node] Running "merge" ("fmriprep.interfaces.nilearn.Merge") 190415-01:48:08,826 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.merge". 190415-01:48:09,526 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.resampling_xfm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/resampling_xfm". 190415-01:48:09,536 nipype.workflow INFO: [Node] Running "resampling_xfm" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command: lta_convert --inlta identity.nofile --outlta /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/resampling_xfm/out.lta --src /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/merge/vol0000_xform-00000_merged.nii --trg /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-NC080001_T1w_ras_maths_corrected.nii.gz 190415-01:48:09,674 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.resampling_xfm". 190415-01:48:11,536 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.set_xfm_source" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/set_xfm_source". 190415-01:48:11,538 nipype.workflow INFO: [Node] Running "set_xfm_source" ("niworkflows.interfaces.freesurfer.PatchedConcatenateLTA"), a CommandLine Interface with command: mri_concatenate_lta -out_type 1 /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/resampling_xfm/out.lta /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/t1_2_fsnative_xfm/out.lta out_concat.lta 190415-01:48:11,604 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.set_xfm_source". 190415-01:48:13,593 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.validate" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/validate". 190415-01:48:13,595 nipype.workflow INFO: [Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage") 190415-01:48:13,601 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.validate". 190415-01:48:15,515 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.sampler" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/_hemi_rh/sampler". 190415-01:48:15,520 nipype.workflow INFO: [Node] Setting-up "_sampler0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/_hemi_rh/sampler/mapflow/_sampler0". 190415-01:48:15,524 nipype.workflow INFO: [Node] Running "_sampler0" ("nipype.interfaces.freesurfer.utils.SampleToSurface"), a CommandLine Interface with command: mri_vol2surf --cortex --hemi rh --interp trilinear --o /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/_hemi_rh/sampler/mapflow/_sampler0/rh.fsaverage5.gii --srcsubject sub-NC080001 --reg /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/set_xfm_source/out_concat.lta --projfrac-avg 0.000 1.000 0.200 --mov /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/rename_src/mapflow/_rename_src0/fsaverage5.nii --trgsubject fsaverage5 190415-01:48:36,91 nipype.workflow INFO: [Node] Finished "_sampler0". 190415-01:48:36,93 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.sampler". 190415-01:48:37,551 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.sampler" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/_hemi_lh/sampler". 190415-01:48:37,566 nipype.workflow INFO: [Node] Setting-up "_sampler0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/_hemi_lh/sampler/mapflow/_sampler0". 190415-01:48:37,575 nipype.workflow INFO: [Node] Running "_sampler0" ("nipype.interfaces.freesurfer.utils.SampleToSurface"), a CommandLine Interface with command: mri_vol2surf --cortex --hemi lh --interp trilinear --o /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/_hemi_lh/sampler/mapflow/_sampler0/lh.fsaverage5.gii --srcsubject sub-NC080001 --reg /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/set_xfm_source/out_concat.lta --projfrac-avg 0.000 1.000 0.200 --mov /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/rename_src/mapflow/_rename_src0/fsaverage5.nii --trgsubject fsaverage5 190415-01:48:57,208 nipype.workflow INFO: [Node] Finished "_sampler0". 190415-01:48:57,212 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.sampler". 190415-01:48:57,598 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.gen_ref" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/gen_ref". 190415-01:48:57,601 nipype.workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") 190415-01:48:57,942 nipype.interface INFO: stderr 2019-04-15T01:48:57.942566:++ 3dvolreg: AFNI version=Debian-16.2.07~dfsg.1-5~nd16.04+1 (Jun 12 2017) [64-bit] 190415-01:48:57,943 nipype.interface INFO: stderr 2019-04-15T01:48:57.942566:++ Authored by: RW Cox 190415-01:48:57,947 nipype.interface INFO: stderr 2019-04-15T01:48:57.947464:++ Coarse del was 10, replaced with 3 190415-01:49:08,889 nipype.interface INFO: stderr 2019-04-15T01:49:08.889883:++ Max displacement in automask = 0.08 (mm) at sub-brick 17 190415-01:49:08,890 nipype.interface INFO: stderr 2019-04-15T01:49:08.889883:++ Max delta displ in automask = 0.07 (mm) at sub-brick 2 190415-01:49:09,337 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.gen_ref". 190415-01:49:09,593 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.validate_ref" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/validate_ref". 190415-01:49:09,597 nipype.workflow INFO: [Node] Running "validate_ref" ("niworkflows.interfaces.images.ValidateImage") 190415-01:49:09,612 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.validate_ref". 190415-01:49:11,602 nipype.workflow INFO: [Node] Setting-up "_update_metadata0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/update_metadata/mapflow/_update_metadata0". 190415-01:49:11,604 nipype.workflow INFO: [Node] Running "_update_metadata0" ("niworkflows.interfaces.surf.GiftiSetAnatomicalStructure") /usr/local/miniconda/lib/python3.7/site-packages/nibabel/gifti/gifti.py:760: ResourceWarning: unclosed file <_io.BufferedReader name='/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/_hemi_lh/sampler/mapflow/_sampler0/lh.fsaverage5.gii'> parser.parse(fptr=file_map['image'].get_prepare_fileobj('rb')) /usr/local/miniconda/lib/python3.7/site-packages/nibabel/filebasedimages.py:334: ResourceWarning: unclosed file <_io.BufferedWriter name='/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/update_metadata/mapflow/_update_metadata0/lh.fsaverage5.gii'> self.to_file_map() 190415-01:49:12,258 nipype.workflow INFO: [Node] Finished "_update_metadata0". 190415-01:49:13,435 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_to_mni_transform". 190415-01:49:13,535 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190415-01:49:13,537 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection -d 3 --input-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/gen_ref/ref_image.nii.gz --mask-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/check_hdr/ref_image_valid_corrected_brain_mask_maths_trans_dil_hdr.nii.gz --output ref_image_corrected.nii.gz 190415-01:49:13,559 nipype.workflow INFO: [Node] Setting-up "_update_metadata1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/update_metadata/mapflow/_update_metadata1". 190415-01:49:13,560 nipype.workflow INFO: [Node] Running "_update_metadata1" ("niworkflows.interfaces.surf.GiftiSetAnatomicalStructure") 190415-01:49:13,560 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.merge" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/merge". 190415-01:49:13,571 nipype.workflow INFO: [Node] Running "merge" ("fmriprep.interfaces.nilearn.Merge") 190415-01:49:14,31 nipype.workflow INFO: [Node] Finished "_update_metadata1". 190415-01:49:14,316 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190415-01:49:15,537 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.update_metadata" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/update_metadata". 190415-01:49:15,540 nipype.workflow INFO: [Node] Setting-up "_update_metadata0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/update_metadata/mapflow/_update_metadata0". 190415-01:49:15,541 nipype.workflow INFO: [Node] Cached "_update_metadata0" - collecting precomputed outputs 190415-01:49:15,541 nipype.workflow INFO: [Node] "_update_metadata0" found cached. 190415-01:49:15,542 nipype.workflow INFO: [Node] Setting-up "_update_metadata1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/update_metadata/mapflow/_update_metadata1". 190415-01:49:15,543 nipype.workflow INFO: [Node] Cached "_update_metadata1" - collecting precomputed outputs 190415-01:49:15,543 nipype.workflow INFO: [Node] "_update_metadata1" found cached. 190415-01:49:15,544 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.update_metadata". 190415-01:49:15,548 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190415-01:49:15,552 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_image_corrected.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_corrected_brain.nii.gz -f 0.20 -m 190415-01:49:16,707 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190415-01:49:17,548 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190415-01:49:17,551 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_image_corrected_brain_mask_dil.nii.gz 190415-01:49:17,727 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190415-01:49:19,546 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 190415-01:49:19,548 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_corrected_brain.nii.gz -mas /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_image_corrected_brain_mask_dil.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_image_corrected_brain_masked.nii.gz 190415-01:49:19,631 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190415-01:49:21,609 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize". 190415-01:49:21,612 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize/ref_image_corrected_brain_masked.nii.gz 190415-01:49:22,117 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize". 190415-01:49:23,492 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 190415-01:49:23,493 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190415-01:49:23,518 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190415-01:49:25,97 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.merge". 190415-01:49:25,494 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 190415-01:49:25,497 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 190415-01:49:25,605 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190415-01:49:42,266 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.validate" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/validate". 190415-01:49:42,268 nipype.workflow INFO: [Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage") 190415-01:49:42,289 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.validate". 190415-01:49:44,771 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 190415-01:49:44,773 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.gen_ref" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/gen_ref". 190415-01:49:44,773 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190415-01:49:44,775 nipype.workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") 190415-01:49:44,792 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190415-01:49:45,540 nipype.interface INFO: stderr 2019-04-15T01:49:45.540182:++ 3dvolreg: AFNI version=Debian-16.2.07~dfsg.1-5~nd16.04+1 (Jun 12 2017) [64-bit] 190415-01:49:45,540 nipype.interface INFO: stderr 2019-04-15T01:49:45.540182:++ Authored by: RW Cox 190415-01:49:45,541 nipype.interface INFO: stderr 2019-04-15T01:49:45.541539:++ Coarse del was 10, replaced with 4 190415-01:49:45,587 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks". 190415-01:49:45,591 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_corrected_brain_mask.nii.gz -mul /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_corrected_brain_mask_maths.nii.gz 190415-01:49:45,742 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190415-01:49:47,590 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask". 190415-01:49:47,593 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_corrected_brain_mask_maths.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 190415-01:49:47,671 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190415-01:50:00,371 nipype.interface INFO: stderr 2019-04-15T01:50:00.371890:++ Max displacement in automask = 0.08 (mm) at sub-brick 17 190415-01:50:00,372 nipype.interface INFO: stderr 2019-04-15T01:50:00.371890:++ Max delta displ in automask = 0.08 (mm) at sub-brick 2 190415-01:50:01,75 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.gen_ref". 190415-01:50:01,582 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.validate_ref" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/validate_ref". 190415-01:50:01,586 nipype.workflow INFO: [Node] Running "validate_ref" ("niworkflows.interfaces.images.ValidateImage") 190415-01:50:01,602 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.validate_ref". 190415-01:50:05,586 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190415-01:50:05,588 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection -d 3 --input-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/gen_ref/ref_image.nii.gz --mask-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/check_hdr/ref_image_valid_corrected_brain_mask_maths_trans_dil_hdr.nii.gz --output ref_image_corrected.nii.gz 190415-01:50:06,615 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190415-01:50:07,785 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190415-01:50:07,787 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_image_corrected.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_corrected_brain.nii.gz -f 0.20 -m 190415-01:50:08,830 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190415-01:50:09,592 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190415-01:50:09,595 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_image_corrected_brain_mask_dil.nii.gz 190415-01:50:09,878 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190415-01:50:11,596 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 190415-01:50:11,598 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_corrected_brain.nii.gz -mas /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_image_corrected_brain_mask_dil.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_image_corrected_brain_masked.nii.gz 190415-01:50:11,690 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190415-01:50:13,598 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize". 190415-01:50:13,601 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize/ref_image_corrected_brain_masked.nii.gz 190415-01:50:14,481 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize". 190415-01:50:15,603 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 190415-01:50:15,605 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190415-01:50:15,644 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190415-01:50:17,609 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 190415-01:50:17,612 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 190415-01:50:17,734 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190415-01:50:19,621 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 190415-01:50:19,623 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190415-01:50:19,647 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190415-01:50:21,631 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks". 190415-01:50:21,634 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_corrected_brain_mask.nii.gz -mul /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_corrected_brain_mask_maths.nii.gz 190415-01:50:21,706 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190415-01:50:23,597 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask". 190415-01:50:23,599 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_corrected_brain_mask_maths.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 190415-01:50:23,682 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask". Error in atexit._run_exitfuncs: Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/concurrent/futures/process.py", line 101, in _python_exit thread_wakeup.wakeup() File "/usr/local/miniconda/lib/python3.7/concurrent/futures/process.py", line 89, in wakeup self._writer.send_bytes(b"") File "/usr/local/miniconda/lib/python3.7/multiprocessing/connection.py", line 183, in send_bytes self._check_closed() File "/usr/local/miniconda/lib/python3.7/multiprocessing/connection.py", line 136, in _check_closed raise OSError("handle is closed") OSError: handle is closed Sentry is attempting to send 0 pending error messages Waiting up to 2.0 seconds Press Ctrl-C to quit ChenYuans-MacBook-Pro:~ noelkuo$ fmriprep-docker /Users/noelkuo/Desktop/Data/Nifti /Users/noelkuo/Desktop/Data/derivatives participant --participant-label NC080001 --fs-license-file /Users/noelkuo/freesurfer.txt --verbose --ignore slicetiming RUNNING: docker run --rm -it -e DOCKER_VERSION_8395080871=18.09.2 -v /Users/noelkuo/freesurfer.txt:/opt/freesurfer/license.txt:ro -v /Users/noelkuo/Desktop/Data/Nifti:/data:ro -v /Users/noelkuo/Desktop/Data/derivatives:/out poldracklab/fmriprep:1.3.2 /data /out participant --participant-label NC080001 --verbose --ignore slicetiming Making sure the input data is BIDS compliant (warnings can be ignored in most cases). 1: [WARN] You should define 'SliceTiming' for this file. If you don't provide this information slice time correction will not be possible. (code: 13 - SLICE_TIMING_NOT_DEFINED) ./sub-NC080001/func/sub-NC080001_task-rest_bold.nii.gz Summary: Available Tasks: Available Modalities: 6 Files, 32.14MB RS T1w 1 - Subject bold 1 - Session If you have any questions please post on https://neurostars.org/tags/bids /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working from collections import Container /usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'> imp.find_module('pytest') 190415-17:40:30,341 nipype.workflow IMPORTANT: Running fMRIPREP version 1.3.2: * BIDS dataset path: /data. * Participant list: ['NC080001']. * Run identifier: 20190415-174029_84e3fe5f-bcd7-4631-ac9d-e7ec21fff896. /usr/local/miniconda/lib/python3.7/site-packages/networkx/classes/reportviews.py:95: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working from collections import Mapping, Set, Iterable 190415-17:40:31,891 nipype.workflow IMPORTANT: Creating bold processing workflow for "/data/sub-NC080001/func/sub-NC080001_task-rest_bold.nii.gz" (0.02 GB / 240 TRs). Memory resampled/largemem=0.10/0.16 GB. 190415-17:40:31,892 nipype.workflow IMPORTANT: No single-band-reference found for sub-NC080001_task-rest_bold.nii.gz 190415-17:40:32,179 nipype.workflow WARNING: SDC: no fieldmaps found or they were ignored (/data/sub-NC080001/func/sub-NC080001_task-rest_bold.nii.gz). 190415-17:40:32,751 nipype.workflow IMPORTANT: Creating BOLD surface-sampling workflow. /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working from collections import Container /usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'> imp.find_module('pytest') 190415-17:40:35,562 nipype.workflow IMPORTANT: Works derived from this fMRIPrep execution should include the following boilerplate: Results included in this manuscript come from preprocessing performed using *fMRIPrep* 1.3.2 (@fmriprep1; @fmriprep2; RRID:SCR_016216), which is based on *Nipype* 1.1.9 (@nipype1; @nipype2; RRID:SCR_002502). Anatomical data preprocessing : The T1-weighted (T1w) image was corrected for intensity non-uniformity (INU) with `N4BiasFieldCorrection` [@n4], distributed with ANTs 2.2.0 [@ants, RRID:SCR_004757], and used as T1w-reference throughout the workflow. The T1w-reference was then skull-stripped with a *Nipype* implementation of the `antsBrainExtraction.sh` workflow (from ANTs), using OASIS30ANTs as target template. Brain surfaces were reconstructed using `recon-all` [FreeSurfer 6.0.1, RRID:SCR_001847, @fs_reconall], and the brain mask estimated previously was refined with a custom variation of the method to reconcile ANTs-derived and FreeSurfer-derived segmentations of the cortical gray-matter of Mindboggle [RRID:SCR_002438, @mindboggle]. Spatial normalization to the *ICBM 152 Nonlinear Asymmetrical template version 2009c* [@mni152nlin2009casym, RRID:SCR_008796] was performed through nonlinear registration with `antsRegistration` (ANTs 2.2.0), using brain-extracted versions of both T1w volume and template. Brain tissue segmentation of cerebrospinal fluid (CSF), white-matter (WM) and gray-matter (GM) was performed on the brain-extracted T1w using `fast` [FSL 5.0.9, RRID:SCR_002823, @fsl_fast]. Functional data preprocessing : For each of the 1 BOLD runs found per subject (across all tasks and sessions), the following preprocessing was performed. First, a reference volume and its skull-stripped version were generated using a custom methodology of *fMRIPrep*. The BOLD reference was then co-registered to the T1w reference using `bbregister` (FreeSurfer) which implements boundary-based registration [@bbr]. Co-registration was configured with nine degrees of freedom to account for distortions remaining in the BOLD reference. Head-motion parameters with respect to the BOLD reference (transformation matrices, and six corresponding rotation and translation parameters) are estimated before any spatiotemporal filtering using `mcflirt` [FSL 5.0.9, @mcflirt]. The BOLD time-series, were resampled to surfaces on the following spaces: *fsaverage5*. The BOLD time-series (including slice-timing correction when applied) were resampled onto their original, native space by applying a single, composite transform to correct for head-motion and susceptibility distortions. These resampled BOLD time-series will be referred to as *preprocessed BOLD in original space*, or just *preprocessed BOLD*. The BOLD time-series were resampled to MNI152NLin2009cAsym standard space, generating a *preprocessed BOLD run in MNI152NLin2009cAsym space*. First, a reference volume and its skull-stripped version were generated using a custom methodology of *fMRIPrep*. Several confounding time-series were calculated based on the *preprocessed BOLD*: framewise displacement (FD), DVARS and three region-wise global signals. FD and DVARS are calculated for each functional run, both using their implementations in *Nipype* [following the definitions by @power_fd_dvars]. The three global signals are extracted within the CSF, the WM, and the whole-brain masks. Additionally, a set of physiological regressors were extracted to allow for component-based noise correction [*CompCor*, @compcor]. Principal components are estimated after high-pass filtering the *preprocessed BOLD* time-series (using a discrete cosine filter with 128s cut-off) for the two *CompCor* variants: temporal (tCompCor) and anatomical (aCompCor). Six tCompCor components are then calculated from the top 5% variable voxels within a mask covering the subcortical regions. This subcortical mask is obtained by heavily eroding the brain mask, which ensures it does not include cortical GM regions. For aCompCor, six components are calculated within the intersection of the aforementioned mask and the union of CSF and WM masks calculated in T1w space, after their projection to the native space of each functional run (using the inverse BOLD-to-T1w transformation). The head-motion estimates calculated in the correction step were also placed within the corresponding confounds file. All resamplings can be performed with *a single interpolation step* by composing all the pertinent transformations (i.e. head-motion transform matrices, susceptibility distortion correction when available, and co-registrations to anatomical and template spaces). Gridded (volumetric) resamplings were performed using `antsApplyTransforms` (ANTs), configured with Lanczos interpolation to minimize the smoothing effects of other kernels [@lanczos]. Non-gridded (surface) resamplings were performed using `mri_vol2surf` (FreeSurfer). Many internal operations of *fMRIPrep* use *Nilearn* 0.5.0 [@nilearn, RRID:SCR_001362], mostly within the functional processing workflow. For more details of the pipeline, see [the section corresponding to workflows in *fMRIPrep*'s documentation](https://fmriprep.readthedocs.io/en/latest/workflows.html "FMRIPrep's documentation"). ### References Captured warning (): can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ Captured warning (): can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ Captured warning (): can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ Captured warning (): Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working Captured warning (): unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'> 190415-17:40:45,594 nipype.workflow INFO: Workflow fmriprep_wf settings: ['check', 'execution', 'logging', 'monitoring'] 190415-17:40:45,772 nipype.workflow INFO: Running in parallel. 190415-17:40:45,773 nipype.workflow WARNING: Some nodes exceed the total amount of memory available (8.77GB). Captured warning (): the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 190415-17:40:45,782 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 7 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-17:40:45,861 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.about" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/about". 190415-17:40:45,864 nipype.workflow INFO: [Node] Running "about" ("fmriprep.interfaces.reports.AboutSummary") 190415-17:40:45,871 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.about". 190415-17:40:45,872 nipype.workflow INFO: [Job 54] Completed (fmriprep_wf.single_subject_NC080001_wf.about). 190415-17:40:45,958 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.fsdir_run_20190415_174029_84e3fe5f_bcd7_4631_ac9d_e7ec21fff896" in "/tmp/work/fmriprep_wf/fsdir_run_20190415_174029_84e3fe5f_bcd7_4631_ac9d_e7ec21fff896". 190415-17:40:45,961 nipype.workflow INFO: [Node] Running "fsdir_run_20190415_174029_84e3fe5f_bcd7_4631_ac9d_e7ec21fff896" ("niworkflows.interfaces.bids.BIDSFreeSurferDir") 190415-17:40:46,461 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.func_derivatives_wf.raw_sources" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/func_derivatives_wf/raw_sources". 190415-17:40:46,464 nipype.workflow INFO: [Node] Running "raw_sources" ("nipype.interfaces.utility.wrappers.Function") 190415-17:40:46,470 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.func_derivatives_wf.raw_sources". /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working from collections import Container /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working from collections import Container /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working from collections import Container /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working from collections import Container 190415-17:40:47,516 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.validate" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/validate". 190415-17:40:47,519 nipype.workflow INFO: [Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage") 190415-17:40:47,590 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.lap_tmpl" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/lap_tmpl". 190415-17:40:47,599 nipype.workflow INFO: [Node] Running "lap_tmpl" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 tpl-OASIS30ANTs_res-01_T1w_maths.nii.gz Laplacian /opt/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz 1.5 1 190415-17:40:47,632 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.res_tmpl" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/res_tmpl". 190415-17:40:47,636 nipype.workflow INFO: [Node] Running "res_tmpl" ("niworkflows.interfaces.ants.ResampleImageBySpacing"), a CommandLine Interface with command: ResampleImageBySpacing 3 /opt/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz tpl-OASIS30ANTs_res-01_T1w_resampled.nii.gz 4 4 4 1 190415-17:40:47,657 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.bidssrc" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/bidssrc". 190415-17:40:47,660 nipype.workflow INFO: [Node] Running "bidssrc" ("niworkflows.interfaces.bids.BIDSDataGrabber") 190415-17:40:47,661 nipype.interface WARNING: No "t2w" images found for sub- 190415-17:40:47,661 nipype.interface WARNING: No "flair" images found for sub- 190415-17:40:47,662 nipype.interface WARNING: No "fmap" images found for sub- 190415-17:40:47,662 nipype.interface WARNING: No "sbref" images found for sub- 190415-17:40:47,663 nipype.interface WARNING: No "roi" images found for sub- 190415-17:40:47,679 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.bidssrc". 190415-17:40:49,968 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.res_tmpl". 190415-17:40:50,154 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.validate". 190415-17:40:55,807 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.lap_tmpl". 190415-17:41:05,448 nipype.workflow INFO: [Node] Finished "fmriprep_wf.fsdir_run_20190415_174029_84e3fe5f_bcd7_4631_ac9d_e7ec21fff896". 190415-17:41:05,449 nipype.workflow INFO: [Job 108] Completed (fmriprep_wf.fsdir_run_20190415_174029_84e3fe5f_bcd7_4631_ac9d_e7ec21fff896). Captured warning (): the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 190415-17:41:05,516 nipype.workflow INFO: [Job 0] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.func_derivatives_wf.raw_sources). 190415-17:41:05,518 nipype.workflow INFO: [Job 1] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.validate). 190415-17:41:05,519 nipype.workflow INFO: [Job 51] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.lap_tmpl). 190415-17:41:05,521 nipype.workflow INFO: [Job 53] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.res_tmpl). 190415-17:41:05,522 nipype.workflow INFO: [Job 55] Completed (fmriprep_wf.single_subject_NC080001_wf.bidssrc). 190415-17:41:05,525 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 7 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-17:41:05,600 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.ds_report_validation" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/ds_report_validation". 190415-17:41:05,602 nipype.workflow INFO: [Node] Running "ds_report_validation" ("fmriprep.interfaces.DerivativesDataSink") 190415-17:41:05,607 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.ds_report_validation". 190415-17:41:05,607 nipype.workflow INFO: [Job 4] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.ds_report_validation). 190415-17:41:05,678 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.mrg_tmpl" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/mrg_tmpl". 190415-17:41:05,680 nipype.workflow INFO: [Node] Running "mrg_tmpl" ("nipype.interfaces.utility.base.Merge") 190415-17:41:05,684 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.mrg_tmpl". 190415-17:41:05,689 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.ds_report_about" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/ds_report_about". 190415-17:41:05,689 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_template_wf.t1_template_dimensions" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_template_wf/t1_template_dimensions". 190415-17:41:05,691 nipype.workflow INFO: [Node] Running "ds_report_about" ("fmriprep.interfaces.DerivativesDataSink") 190415-17:41:05,692 nipype.workflow INFO: [Node] Running "t1_template_dimensions" ("niworkflows.interfaces.images.TemplateDimensions") 190415-17:41:05,696 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.ds_report_about". 190415-17:41:05,697 nipype.workflow INFO: [Job 106] Completed (fmriprep_wf.single_subject_NC080001_wf.ds_report_about). 190415-17:41:05,800 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.bids_info" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/bids_info". 190415-17:41:05,802 nipype.workflow INFO: [Node] Running "bids_info" ("niworkflows.interfaces.bids.BIDSInfo") 190415-17:41:05,827 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.bids_info". /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) 190415-17:41:06,26 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_template_wf.t1_template_dimensions". 190415-17:41:06,99 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_split" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_split". 190415-17:41:06,101 nipype.workflow INFO: [Node] Running "bold_split" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/validate/sub-NC080001_task-rest_bold_valid.nii.gz -t /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working from collections import Container 190415-17:41:06,592 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.gen_ref" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/gen_ref". 190415-17:41:06,594 nipype.workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") 190415-17:41:07,81 nipype.interface INFO: stderr 2019-04-15T17:41:07.081545:++ 3dvolreg: AFNI version=Debian-16.2.07~dfsg.1-5~nd16.04+1 (Jun 12 2017) [64-bit] 190415-17:41:07,81 nipype.interface INFO: stderr 2019-04-15T17:41:07.081545:++ Authored by: RW Cox 190415-17:41:07,82 nipype.interface INFO: stderr 2019-04-15T17:41:07.082028:** AFNI converts NIFTI_datatype=4 (INT16) in file /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/gen_ref/slice.nii.gz to FLOAT32 190415-17:41:07,82 nipype.interface INFO: stderr 2019-04-15T17:41:07.082028: Warnings of this type will be muted for this session. 190415-17:41:07,82 nipype.interface INFO: stderr 2019-04-15T17:41:07.082028: Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none. 190415-17:41:07,82 nipype.interface INFO: stderr 2019-04-15T17:41:07.082826:*+ WARNING: If you are performing spatial transformations on an oblique dset, 190415-17:41:07,83 nipype.interface INFO: stderr 2019-04-15T17:41:07.082826: such as /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/gen_ref/slice.nii.gz, 190415-17:41:07,83 nipype.interface INFO: stderr 2019-04-15T17:41:07.082826: or viewing/combining it with volumes of differing obliquity, 190415-17:41:07,83 nipype.interface INFO: stderr 2019-04-15T17:41:07.082826: you should consider running: 190415-17:41:07,83 nipype.interface INFO: stderr 2019-04-15T17:41:07.082826: 3dWarp -deoblique 190415-17:41:07,83 nipype.interface INFO: stderr 2019-04-15T17:41:07.082826: on this and other oblique datasets in the same session. 190415-17:41:07,83 nipype.interface INFO: stderr 2019-04-15T17:41:07.082826: See 3dWarp -help for details. 190415-17:41:07,83 nipype.interface INFO: stderr 2019-04-15T17:41:07.082826:++ Oblique dataset:/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/gen_ref/slice.nii.gz is 8.719383 degrees from plumb. 190415-17:41:07,83 nipype.interface INFO: stderr 2019-04-15T17:41:07.082826:++ Coarse del was 10, replaced with 3 190415-17:41:07,517 nipype.workflow INFO: [Job 52] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.mrg_tmpl). 190415-17:41:07,520 nipype.workflow INFO: [Job 56] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_template_wf.t1_template_dimensions). 190415-17:41:07,523 nipype.workflow INFO: [Job 107] Completed (fmriprep_wf.single_subject_NC080001_wf.bids_info). 190415-17:41:07,527 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 6 jobs ready. Free memory (GB): 7.69/8.77, Free processors: 4/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.gen_ref * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_split 190415-17:41:07,592 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_reports_wf.ds_t1_conform_report" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_reports_wf/ds_t1_conform_report". 190415-17:41:07,599 nipype.workflow INFO: [Node] Running "ds_t1_conform_report" ("smriprep.interfaces.DerivativesDataSink") 190415-17:41:07,606 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_reports_wf.ds_t1_conform_report". 190415-17:41:07,606 nipype.workflow INFO: [Job 57] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_reports_wf.ds_t1_conform_report). 190415-17:41:07,678 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_template_transforms" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/ds_t1_template_transforms". 190415-17:41:07,687 nipype.workflow INFO: [Node] Setting-up "_ds_t1_template_transforms0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/ds_t1_template_transforms/mapflow/_ds_t1_template_transforms0". 190415-17:41:07,695 nipype.workflow INFO: [Node] Running "_ds_t1_template_transforms0" ("smriprep.interfaces.DerivativesDataSink") 190415-17:41:07,712 nipype.workflow INFO: [Node] Finished "_ds_t1_template_transforms0". 190415-17:41:07,722 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_template_transforms". 190415-17:41:07,722 nipype.workflow INFO: [Job 58] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_template_transforms). 190415-17:41:07,790 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.raw_sources" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/raw_sources". 190415-17:41:07,797 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.t1_name" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/t1_name". 190415-17:41:07,797 nipype.workflow INFO: [Node] Running "raw_sources" ("nipype.interfaces.utility.wrappers.Function") 190415-17:41:07,799 nipype.workflow INFO: [Node] Running "t1_name" ("nipype.interfaces.utility.wrappers.Function") 190415-17:41:07,804 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.raw_sources". 190415-17:41:07,805 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_template_wf.t1_conform" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_template_wf/t1_conform". 190415-17:41:07,810 nipype.workflow INFO: [Node] Setting-up "_t1_conform0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0". 190415-17:41:07,811 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.t1_name". 190415-17:41:07,814 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.summary" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/summary". 190415-17:41:07,815 nipype.workflow INFO: [Node] Running "_t1_conform0" ("niworkflows.interfaces.images.Conform") 190415-17:41:07,818 nipype.workflow INFO: [Node] Running "summary" ("fmriprep.interfaces.reports.SubjectSummary") 190415-17:41:07,826 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.summary". 190415-17:41:07,826 nipype.workflow INFO: [Job 257] Completed (fmriprep_wf.single_subject_NC080001_wf.summary). 190415-17:41:08,496 nipype.workflow INFO: [Node] Finished "_t1_conform0". 190415-17:41:08,498 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_template_wf.t1_conform". 190415-17:41:09,519 nipype.workflow INFO: [Job 59] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.raw_sources). 190415-17:41:09,520 nipype.workflow INFO: [Job 60] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.t1_name). 190415-17:41:09,522 nipype.workflow INFO: [Job 61] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_template_wf.t1_conform). 190415-17:41:09,525 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 2 jobs ready. Free memory (GB): 7.69/8.77, Free processors: 4/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.gen_ref * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_split 190415-17:41:09,591 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_template_wf.get1st" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_template_wf/get1st". 190415-17:41:09,593 nipype.workflow INFO: [Node] Running "get1st" ("nipype.interfaces.utility.base.Select") 190415-17:41:09,594 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.ds_report_summary" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/ds_report_summary". 190415-17:41:09,597 nipype.workflow INFO: [Node] Running "ds_report_summary" ("fmriprep.interfaces.DerivativesDataSink") 190415-17:41:09,597 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_template_wf.get1st". 190415-17:41:09,603 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.ds_report_summary". 190415-17:41:09,603 nipype.workflow INFO: [Job 258] Completed (fmriprep_wf.single_subject_NC080001_wf.ds_report_summary). 190415-17:41:11,521 nipype.workflow INFO: [Job 62] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_template_wf.get1st). 190415-17:41:11,525 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 3 jobs ready. Free memory (GB): 7.69/8.77, Free processors: 4/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.gen_ref * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_split 190415-17:41:11,613 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.fov_check" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/fov_check". 190415-17:41:11,620 nipype.workflow INFO: [Node] Running "fov_check" ("nipype.interfaces.utility.wrappers.Function") /usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'> imp.find_module('pytest') 190415-17:41:11,627 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.truncate_images" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/truncate_images". 190415-17:41:11,630 nipype.workflow INFO: [Node] Setting-up "_truncate_images0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/truncate_images/mapflow/_truncate_images0". 190415-17:41:11,632 nipype.workflow INFO: [Node] Running "_truncate_images0" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 sub-NC080001_T1w_ras_maths.nii.gz TruncateImageIntensity /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0/sub-NC080001_T1w_ras.nii.gz 0.01 0.999 256 190415-17:41:11,689 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_split". 190415-17:41:11,908 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.recon_config" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/recon_config". 190415-17:41:11,910 nipype.workflow INFO: [Node] Running "recon_config" ("niworkflows.interfaces.freesurfer.FSDetectInputs") 190415-17:41:11,924 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.recon_config". 190415-17:41:12,160 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.fov_check". 190415-17:41:13,524 nipype.workflow INFO: [Job 2] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_split). 190415-17:41:13,528 nipype.workflow INFO: [Job 63] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.fov_check). 190415-17:41:13,533 nipype.workflow INFO: [Job 64] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.recon_config). 190415-17:41:13,537 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 2 jobs ready. Free memory (GB): 7.57/8.77, Free processors: 4/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.truncate_images * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.gen_ref 190415-17:41:13,605 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.gen_ref" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/gen_ref". 190415-17:41:13,607 nipype.workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.utils.GenerateSamplingReference") 190415-17:41:13,789 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.gen_ref". 190415-17:41:14,402 nipype.workflow INFO: [Node] Finished "_truncate_images0". 190415-17:41:14,405 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.truncate_images". 190415-17:41:15,527 nipype.workflow INFO: [Job 65] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.truncate_images). 190415-17:41:15,530 nipype.workflow INFO: [Job 3] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.gen_ref). 190415-17:41:15,537 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 7.77/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.gen_ref 190415-17:41:15,631 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.inu_n4" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/inu_n4". 190415-17:41:15,641 nipype.workflow INFO: [Node] Setting-up "_inu_n40" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40". 190415-17:41:15,644 nipype.workflow INFO: [Node] Running "_inu_n40" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/truncate_images/mapflow/_truncate_images0/sub-NC080001_T1w_ras_maths.nii.gz --convergence [ 50x50x50x50, 1e-07 ] --output [ sub-NC080001_T1w_ras_maths_corrected.nii.gz, sub-NC080001_T1w_ras_maths_bias.nii.gz ] --shrink-factor 4 190415-17:41:17,531 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 1 jobs ready. Free memory (GB): 7.57/8.77, Free processors: 0/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.inu_n4 * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.gen_ref 190415-17:41:23,102 nipype.interface INFO: stderr 2019-04-15T17:41:23.102125:++ Max displacement in automask = 0.13 (mm) at sub-brick 19 190415-17:41:23,102 nipype.interface INFO: stderr 2019-04-15T17:41:23.102125:++ Max delta displ in automask = 0.07 (mm) at sub-brick 11 190415-17:41:23,887 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.gen_ref". 190415-17:41:25,539 nipype.workflow INFO: [Job 5] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.gen_ref). 190415-17:41:25,547 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 8.57/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.inu_n4 190415-17:41:25,614 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.validate_ref" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/validate_ref". 190415-17:41:25,618 nipype.workflow INFO: [Node] Running "validate_ref" ("niworkflows.interfaces.images.ValidateImage") 190415-17:41:25,647 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.validate_ref". 190415-17:41:27,507 nipype.workflow INFO: [Job 6] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.validate_ref). 190415-17:41:27,516 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 8.57/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.inu_n4 190415-17:41:27,586 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_hmc_wf.mcflirt" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_hmc_wf/mcflirt". 190415-17:41:27,588 nipype.workflow INFO: [Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command: mcflirt -in /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/validate/sub-NC080001_task-rest_bold_valid.nii.gz -out /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_hmc_wf/mcflirt/sub-NC080001_task-rest_bold_valid_mcf.nii.gz -reffile /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz -mats -plots 190415-17:41:29,511 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 2 jobs ready. Free memory (GB): 8.49/8.77, Free processors: 0/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_hmc_wf.mcflirt * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.inu_n4 190415-17:42:13,553 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_hmc_wf.mcflirt". 190415-17:42:15,538 nipype.workflow INFO: [Job 7] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_hmc_wf.mcflirt). 190415-17:42:15,545 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 4 jobs ready. Free memory (GB): 8.57/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.inu_n4 190415-17:42:15,610 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_hmc_wf.normalize_motion" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_hmc_wf/normalize_motion". 190415-17:42:15,612 nipype.workflow INFO: [Node] Running "normalize_motion" ("niworkflows.interfaces.utils.NormalizeMotionParams") 190415-17:42:15,622 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_hmc_wf.normalize_motion". 190415-17:42:17,541 nipype.workflow INFO: [Job 8] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_hmc_wf.normalize_motion). 190415-17:42:17,547 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 5 jobs ready. Free memory (GB): 8.57/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.inu_n4 190415-17:42:17,628 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.add_motion_headers" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/add_motion_headers". 190415-17:42:17,632 nipype.workflow INFO: [Node] Running "add_motion_headers" ("niworkflows.interfaces.utils.AddTSVHeader") 190415-17:42:17,645 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.add_motion_headers". 190415-17:42:17,646 nipype.workflow INFO: [Job 9] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.add_motion_headers). 190415-17:42:17,712 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.fdisp" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/fdisp". 190415-17:42:17,714 nipype.workflow INFO: [Node] Running "fdisp" ("nipype.algorithms.confounds.FramewiseDisplacement") 190415-17:42:17,722 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.fdisp". 190415-17:42:19,543 nipype.workflow INFO: [Job 10] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.fdisp). 190415-17:42:19,550 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 8.57/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.inu_n4 190415-17:42:38,81 nipype.workflow INFO: [Node] Finished "_inu_n40". 190415-17:42:38,85 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.inu_n4". 190415-17:42:39,538 nipype.workflow INFO: [Job 66] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.inu_n4). 190415-17:42:39,542 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 6 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-17:42:39,623 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_hmc_wf.fsl2itk" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_hmc_wf/fsl2itk". 190415-17:42:39,627 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_preproc" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/ds_t1_preproc". 190415-17:42:39,629 nipype.workflow INFO: [Node] Running "ds_t1_preproc" ("smriprep.interfaces.DerivativesDataSink") 190415-17:42:39,636 nipype.workflow INFO: [Node] Running "fsl2itk" ("niworkflows.interfaces.itk.MCFLIRT2ITK") 190415-17:42:49,706 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_preproc". 190415-17:42:49,707 nipype.workflow INFO: [Job 67] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_preproc). 190415-17:42:49,799 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 3 jobs ready. Free memory (GB): 8.52/8.77, Free processors: 0/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.lap_target * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_hmc_wf.fsl2itk 190415-17:42:49,806 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.lap_target" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/lap_target". 190415-17:42:49,808 nipype.workflow INFO: [Node] Running "lap_target" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 sub-NC080001_T1w_ras_maths_corrected_maths.nii.gz Laplacian /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-NC080001_T1w_ras_maths_corrected.nii.gz 1.5 1 190415-17:42:55,350 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_hmc_wf.fsl2itk". 190415-17:42:55,804 nipype.workflow INFO: [Job 11] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_hmc_wf.fsl2itk). 190415-17:42:55,812 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 4 jobs ready. Free memory (GB): 8.57/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.lap_target 190415-17:42:55,877 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.merge_xforms" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/merge_xforms". 190415-17:42:55,883 nipype.workflow INFO: [Node] Running "merge_xforms" ("nipype.interfaces.utility.base.Merge") 190415-17:42:55,889 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.merge_xforms". 190415-17:42:55,889 nipype.workflow INFO: [Job 12] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.merge_xforms). 190415-17:42:55,923 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff". 190415-17:42:55,925 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190415-17:42:56,680 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.lap_target". 190415-17:42:57,807 nipype.workflow INFO: [Job 68] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.lap_target). 190415-17:42:57,811 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 4 jobs ready. Free memory (GB): 8.57/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff 190415-17:42:57,876 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.mrg_target" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/mrg_target". 190415-17:42:57,878 nipype.workflow INFO: [Node] Running "mrg_target" ("nipype.interfaces.utility.base.Merge") 190415-17:42:57,882 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.mrg_target". 190415-17:42:59,418 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff". 190415-17:42:59,813 nipype.workflow INFO: [Job 36] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff). 190415-17:42:59,815 nipype.workflow INFO: [Job 69] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.mrg_target). 190415-17:42:59,818 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 4 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-17:42:59,907 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_transform" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_transform". 190415-17:42:59,918 nipype.workflow INFO: [Node] Running "bold_transform" ("niworkflows.interfaces.itk.MultiApplyTransforms") /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/importlib/_bootstrap.py:219: ImportWarning: can't resolve package from __spec__ or __package__, falling back on __name__ and __path__ return f(*args, **kwds) /usr/local/miniconda/lib/python3.7/site-packages/nilearn/datasets/neurovault.py:16: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working from collections import Container 190415-17:43:00,988 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.res_target" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/res_target". 190415-17:43:00,994 nipype.workflow INFO: [Node] Running "res_target" ("niworkflows.interfaces.ants.ResampleImageBySpacing"), a CommandLine Interface with command: ResampleImageBySpacing 3 /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-NC080001_T1w_ras_maths_corrected.nii.gz sub-NC080001_T1w_ras_maths_corrected_resampled.nii.gz 4 4 4 1 190415-17:43:01,818 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 2 jobs ready. Free memory (GB): 7.08/8.77, Free processors: 0/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.res_target * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_transform 190415-17:43:02,510 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.res_target". 190415-17:43:03,819 nipype.workflow INFO: [Job 70] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.res_target). 190415-17:43:03,822 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 7.28/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_transform 190415-17:43:55,862 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_transform". 190415-17:43:55,842 nipype.workflow INFO: [Job 13] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_transform). 190415-17:43:55,844 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 4 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-17:43:55,931 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm". 190415-17:43:55,936 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190415-17:43:56,80 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.merge" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/merge". 190415-17:43:56,89 nipype.workflow INFO: [Node] Running "merge" ("fmriprep.interfaces.nilearn.Merge") 190415-17:43:57,881 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 2 jobs ready. Free memory (GB): 8.27/8.77, Free processors: 0/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.merge 190415-17:44:03,72 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm". 190415-17:44:03,883 nipype.workflow INFO: [Job 37] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm). 190415-17:44:03,886 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 8.47/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.merge 190415-17:44:03,947 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask". 190415-17:44:03,949 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz --transform [ /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] 190415-17:44:04,969 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190415-17:44:05,886 nipype.workflow INFO: [Job 38] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask). 190415-17:44:05,889 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 8.47/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.merge 190415-17:44:05,948 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 190415-17:44:05,951 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190415-17:44:06,68 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190415-17:44:07,696 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.merge". 190415-17:44:07,891 nipype.workflow INFO: [Job 14] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.merge). 190415-17:44:07,893 nipype.workflow INFO: [Job 39] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate). 190415-17:44:07,897 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 4 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-17:44:07,961 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.check_hdr" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/check_hdr". 190415-17:44:07,963 nipype.workflow INFO: [Node] Running "check_hdr" ("niworkflows.interfaces.images.MatchHeader") 190415-17:44:07,972 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.validate" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/validate". 190415-17:44:07,974 nipype.workflow INFO: [Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage") 190415-17:44:07,983 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.check_hdr". 190415-17:44:07,984 nipype.workflow INFO: [Job 40] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.check_hdr). 190415-17:44:08,49 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.init_aff" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/init_aff". 190415-17:44:08,52 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /opt/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz -m Mattes[/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/res_tmpl/tpl-OASIS30ANTs_res-01_T1w_resampled.nii.gz,/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/res_target/sub-NC080001_T1w_ras_maths_corrected_resampled.nii.gz,32,Regular,0.250000] -o initialization.mat -p 0 -s [15.000000,0.100000] -t Affine[0.100000] -v 1 190415-17:44:09,894 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 2 jobs ready. Free memory (GB): 8.56/8.77, Free processors: 0/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.init_aff * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.validate 190415-17:44:10,418 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.init_aff". 190415-17:44:11,896 nipype.workflow INFO: [Job 71] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.init_aff). 190415-17:44:11,899 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 8.76/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.validate 190415-17:44:11,962 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190415-17:44:11,964 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection -d 3 --input-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz --mask-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output ref_image_valid_corrected.nii.gz 190415-17:44:12,770 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190415-17:44:12,973 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.validate". 190415-17:44:13,900 nipype.workflow INFO: [Job 15] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.validate). 190415-17:44:13,902 nipype.workflow INFO: [Job 41] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct). 190415-17:44:13,905 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 4 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-17:44:13,973 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/gen_ref". 190415-17:44:13,975 nipype.workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") 190415-17:44:13,975 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190415-17:44:13,978 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_image_valid_corrected.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain.nii.gz -f 0.20 -m 190415-17:44:14,823 nipype.interface INFO: stderr 2019-04-15T17:44:14.823723:++ 3dvolreg: AFNI version=Debian-16.2.07~dfsg.1-5~nd16.04+1 (Jun 12 2017) [64-bit] 190415-17:44:14,824 nipype.interface INFO: stderr 2019-04-15T17:44:14.823723:++ Authored by: RW Cox 190415-17:44:14,825 nipype.interface INFO: stderr 2019-04-15T17:44:14.824775:*+ WARNING: If you are performing spatial transformations on an oblique dset, 190415-17:44:14,825 nipype.interface INFO: stderr 2019-04-15T17:44:14.824775: such as /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/gen_ref/slice.nii.gz, 190415-17:44:14,826 nipype.interface INFO: stderr 2019-04-15T17:44:14.824775: or viewing/combining it with volumes of differing obliquity, 190415-17:44:14,826 nipype.interface INFO: stderr 2019-04-15T17:44:14.824775: you should consider running: 190415-17:44:14,827 nipype.interface INFO: stderr 2019-04-15T17:44:14.824775: 3dWarp -deoblique 190415-17:44:14,827 nipype.interface INFO: stderr 2019-04-15T17:44:14.824775: on this and other oblique datasets in the same session. 190415-17:44:14,828 nipype.interface INFO: stderr 2019-04-15T17:44:14.824775: See 3dWarp -help for details. 190415-17:44:14,828 nipype.interface INFO: stderr 2019-04-15T17:44:14.824775:++ Oblique dataset:/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/gen_ref/slice.nii.gz is 8.719383 degrees from plumb. 190415-17:44:14,829 nipype.interface INFO: stderr 2019-04-15T17:44:14.824775:++ Coarse del was 10, replaced with 3 190415-17:44:15,303 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190415-17:44:15,901 nipype.workflow INFO: [Job 42] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass). 190415-17:44:15,905 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 7.77/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref 190415-17:44:15,973 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190415-17:44:15,980 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_image_valid_corrected_brain_mask_dil.nii.gz 190415-17:44:16,247 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190415-17:44:17,904 nipype.workflow INFO: [Job 43] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate). 190415-17:44:17,907 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 7.77/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref 190415-17:44:17,970 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 190415-17:44:17,972 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain.nii.gz -mas /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_image_valid_corrected_brain_mask_dil.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_image_valid_corrected_brain_masked.nii.gz 190415-17:44:18,54 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190415-17:44:19,906 nipype.workflow INFO: [Job 44] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask). 190415-17:44:19,909 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 7.77/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref 190415-17:44:19,980 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize". 190415-17:44:19,983 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize/ref_image_valid_corrected_brain_masked.nii.gz 190415-17:44:20,650 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize". 190415-17:44:21,910 nipype.workflow INFO: [Job 45] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize). 190415-17:44:21,913 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 7.77/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref 190415-17:44:21,978 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 190415-17:44:21,982 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190415-17:44:22,10 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190415-17:44:23,910 nipype.workflow INFO: [Job 46] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize). 190415-17:44:23,913 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 7.77/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref 190415-17:44:23,974 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 190415-17:44:23,976 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 190415-17:44:24,82 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190415-17:44:25,879 nipype.workflow INFO: [Job 47] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass). 190415-17:44:25,883 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 7.77/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref 190415-17:44:25,961 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 190415-17:44:25,963 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190415-17:44:25,988 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190415-17:44:27,881 nipype.workflow INFO: [Job 48] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2). 190415-17:44:27,884 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 7.77/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref 190415-17:44:27,946 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks". 190415-17:44:27,948 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain_mask.nii.gz -mul /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_valid_corrected_brain_mask_maths.nii.gz 190415-17:44:28,22 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190415-17:44:29,638 nipype.interface INFO: stderr 2019-04-15T17:44:29.638149:++ Max displacement in automask = 0.06 (mm) at sub-brick 17 190415-17:44:29,638 nipype.interface INFO: stderr 2019-04-15T17:44:29.638149:++ Max delta displ in automask = 0.06 (mm) at sub-brick 2 190415-17:44:29,884 nipype.workflow INFO: [Job 49] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks). 190415-17:44:29,888 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 7.77/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref 190415-17:44:29,960 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask". 190415-17:44:29,963 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_valid_corrected_brain_mask_maths.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 190415-17:44:30,45 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190415-17:44:30,317 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref". 190415-17:44:31,891 nipype.workflow INFO: [Job 16] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref). 190415-17:44:31,893 nipype.workflow INFO: [Job 50] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask). 190415-17:44:31,896 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 3 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-17:44:31,958 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.validate_ref" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/validate_ref". 190415-17:44:31,959 nipype.workflow INFO: [Node] Running "validate_ref" ("niworkflows.interfaces.images.ValidateImage") 190415-17:44:31,965 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.norm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/norm". 190415-17:44:31,970 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation LanczosWindowedSinc --output [ anat_to_template, anat_to_template_Warped.nii.gz ] --transform Rigid[ 0.1 ] --metric MI[ /opt/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz, /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-NC080001_T1w_ras_maths_corrected.nii.gz, 1, 32, Regular, 0.25 ] --convergence [ 1000x500x250x100, 1e-08, 10 ] --smoothing-sigmas 4.0x2.0x1.0x0.0vox --shrink-factors 8x4x2x1 --use-histogram-matching 1 --masks [ /opt/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz, NULL ] --transform Affine[ 0.1 ] --metric MI[ /opt/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz, /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-NC080001_T1w_ras_maths_corrected.nii.gz, 1, 32, Regular, 0.25 ] --convergence [ 1000x500x250x100, 1e-08, 10 ] --smoothing-sigmas 4.0x2.0x1.0x0.0vox --shrink-factors 8x4x2x1 --use-histogram-matching 1 --masks [ /opt/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz, NULL ] --transform SyN[ 0.1, 3.0, 0.0 ] --metric CC[ /opt/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz, /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-NC080001_T1w_ras_maths_corrected.nii.gz, 0.5, 4, None, 1 ] --metric CC[ /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/lap_tmpl/tpl-OASIS30ANTs_res-01_T1w_maths.nii.gz, /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/lap_target/sub-NC080001_T1w_ras_maths_corrected_maths.nii.gz, 0.5, 4, None, 1 ] --convergence [ 50x10x0, 1e-09, 15 ] --smoothing-sigmas 2.0x1.0x0.0vox --shrink-factors 4x2x1 --use-histogram-matching 1 --masks [ /opt/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz, NULL ] -v --winsorize-image-intensities [ 0.025, 0.975 ] --write-composite-transform 0 190415-17:44:32,5 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.validate_ref". 190415-17:44:33,893 nipype.workflow INFO: [Job 17] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.validate_ref). 190415-17:44:33,899 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 5.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.norm 190415-18:05:26,496 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.norm". 190415-18:05:28,71 nipype.workflow INFO: [Job 72] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.norm). 190415-18:05:28,76 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 3 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-18:05:28,151 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.map_brainmask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/map_brainmask". 190415-18:05:28,152 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff". 190415-18:05:28,155 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /opt/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_label-brain_probseg.nii.gz --interpolation Gaussian --output tpl-OASIS30ANTs_res-01_label-brain_probseg_trans.nii.gz --reference-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0/sub-NC080001_T1w_ras.nii.gz --transform [ /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/norm/anat_to_template0GenericAffine.mat, 1 ] --transform [ /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/norm/anat_to_template1InverseWarp.nii.gz, 0 ] 190415-18:05:28,156 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190415-18:05:30,74 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 1 jobs ready. Free memory (GB): 7.57/8.77, Free processors: 0/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.map_brainmask * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff 190415-18:05:32,88 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff". 190415-18:05:34,77 nipype.workflow INFO: [Job 18] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff). 190415-18:05:34,85 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 7.77/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.map_brainmask 190415-18:05:34,151 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm". 190415-18:05:34,163 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190415-18:05:36,81 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 1 jobs ready. Free memory (GB): 7.57/8.77, Free processors: 0/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.map_brainmask 190415-18:05:36,305 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm". 190415-18:05:38,82 nipype.workflow INFO: [Job 19] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm). 190415-18:05:38,90 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 7.77/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.map_brainmask 190415-18:05:38,153 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask". 190415-18:05:38,157 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz --transform [ /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] 190415-18:05:39,205 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190415-18:05:40,84 nipype.workflow INFO: [Job 20] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask). 190415-18:05:40,86 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 7.77/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.map_brainmask 190415-18:05:40,150 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 190415-18:05:40,154 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190415-18:05:40,303 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190415-18:05:42,87 nipype.workflow INFO: [Job 21] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate). 190415-18:05:42,89 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 7.77/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.map_brainmask 190415-18:05:42,154 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.check_hdr" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/check_hdr". 190415-18:05:42,159 nipype.workflow INFO: [Node] Running "check_hdr" ("niworkflows.interfaces.images.MatchHeader") 190415-18:05:42,188 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.check_hdr". 190415-18:05:42,189 nipype.workflow INFO: [Job 22] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.check_hdr). 190415-18:05:42,263 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/autorecon1". 190415-18:05:42,268 nipype.workflow INFO: [Node] Running "autorecon1" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command: recon-all -autorecon1 -i /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0/sub-NC080001_T1w_ras.nii.gz -noskullstrip -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer 190415-18:05:44,92 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 1 jobs ready. Free memory (GB): 2.77/8.77, Free processors: 0/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon1 * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.map_brainmask 190415-18:06:03,115 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.map_brainmask". 190415-18:06:04,77 nipype.workflow INFO: [Job 73] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.map_brainmask). 190415-18:06:04,80 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 3.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon1 190415-18:06:04,169 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190415-18:06:04,171 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection -d 3 --input-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz --mask-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output ref_image_valid_corrected.nii.gz 190415-18:06:05,146 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190415-18:06:06,80 nipype.workflow INFO: [Job 23] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct). 190415-18:06:06,83 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 3.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon1 190415-18:06:06,146 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190415-18:06:06,148 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_image_valid_corrected.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain.nii.gz -f 0.20 -m 190415-18:06:07,389 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190415-18:06:08,83 nipype.workflow INFO: [Job 24] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass). 190415-18:06:08,86 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 3.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon1 190415-18:06:08,151 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190415-18:06:08,153 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_image_valid_corrected_brain_mask_dil.nii.gz 190415-18:06:08,440 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190415-18:06:10,86 nipype.workflow INFO: [Job 25] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate). 190415-18:06:10,89 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 3.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon1 190415-18:06:10,152 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 190415-18:06:10,154 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain.nii.gz -mas /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_image_valid_corrected_brain_mask_dil.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_image_valid_corrected_brain_masked.nii.gz 190415-18:06:10,233 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190415-18:06:12,90 nipype.workflow INFO: [Job 26] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask). 190415-18:06:12,92 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 3.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon1 190415-18:06:12,154 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize". 190415-18:06:12,157 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize/ref_image_valid_corrected_brain_masked.nii.gz 190415-18:06:12,878 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize". 190415-18:06:14,92 nipype.workflow INFO: [Job 27] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize). 190415-18:06:14,95 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 3.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon1 190415-18:06:14,159 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 190415-18:06:14,161 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190415-18:06:14,198 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190415-18:06:16,95 nipype.workflow INFO: [Job 28] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize). 190415-18:06:16,98 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 3.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon1 190415-18:06:16,163 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 190415-18:06:16,166 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 190415-18:06:16,279 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190415-18:06:18,97 nipype.workflow INFO: [Job 29] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass). 190415-18:06:18,100 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 3.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon1 190415-18:06:18,166 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 190415-18:06:18,168 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190415-18:06:18,191 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190415-18:06:20,97 nipype.workflow INFO: [Job 30] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2). 190415-18:06:20,100 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 3.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon1 190415-18:06:20,167 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks". 190415-18:06:20,169 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain_mask.nii.gz -mul /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_valid_corrected_brain_mask_maths.nii.gz 190415-18:06:20,242 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190415-18:06:22,100 nipype.workflow INFO: [Job 31] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks). 190415-18:06:22,108 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 3.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon1 190415-18:06:22,172 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.dvars" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/dvars". 190415-18:06:22,175 nipype.workflow INFO: [Node] Running "dvars" ("nipype.algorithms.confounds.ComputeDVARS") /usr/local/miniconda/lib/python3.7/site-packages/nitime/utils.py:980: FutureWarning: Conversion of the second argument of issubdtype from `complex` to `np.complexfloating` is deprecated. In future, it will be treated as `np.complex128 == np.dtype(complex).type`. complex_result = (np.issubdtype(in1.dtype, np.complex) or /usr/local/miniconda/lib/python3.7/site-packages/scipy/fftpack/basic.py:160: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. z[index] = x 190415-18:06:24,104 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 2 jobs ready. Free memory (GB): 3.61/8.77, Free processors: 0/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.dvars * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon1 190415-18:06:29,229 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.dvars". 190415-18:06:30,75 nipype.workflow INFO: [Job 32] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.dvars). 190415-18:06:30,83 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 4 jobs ready. Free memory (GB): 3.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon1 190415-18:06:30,147 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.add_std_dvars_header" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/add_std_dvars_header". 190415-18:06:30,153 nipype.workflow INFO: [Node] Running "add_std_dvars_header" ("niworkflows.interfaces.utils.AddTSVHeader") 190415-18:06:30,162 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.add_std_dvars_header". 190415-18:06:30,162 nipype.workflow INFO: [Job 33] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.add_std_dvars_header). 190415-18:06:30,230 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.add_dvars_header" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/add_dvars_header". 190415-18:06:30,235 nipype.workflow INFO: [Node] Running "add_dvars_header" ("niworkflows.interfaces.utils.AddTSVHeader") 190415-18:06:30,244 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.add_dvars_header". 190415-18:06:30,244 nipype.workflow INFO: [Job 34] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.add_dvars_header). 190415-18:06:30,313 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask". 190415-18:06:30,320 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_valid_corrected_brain_mask_maths.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 190415-18:06:30,402 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190415-18:06:32,78 nipype.workflow INFO: [Job 35] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask). 190415-18:06:32,86 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 3.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon1 190415-18:06:32,152 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.thr_brainmask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/thr_brainmask". 190415-18:06:32,155 nipype.workflow INFO: [Node] Running "thr_brainmask" ("niworkflows.interfaces.ants.ThresholdImage"), a CommandLine Interface with command: ThresholdImage 3 /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/map_brainmask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans.nii.gz tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled.nii.gz 0.500000 1.000000 1.000000 0.000000 190415-18:06:32,774 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.thr_brainmask". 190415-18:06:34,81 nipype.workflow INFO: [Job 74] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.thr_brainmask). 190415-18:06:34,86 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 3.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon1 190415-18:06:34,150 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.03_pad_mask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/03_pad_mask". 190415-18:06:34,153 nipype.workflow INFO: [Node] Running "03_pad_mask" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths.nii.gz PadImage /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/thr_brainmask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled.nii.gz 10 190415-18:06:34,908 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.03_pad_mask". 190415-18:06:36,85 nipype.workflow INFO: [Job 75] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.03_pad_mask). 190415-18:06:36,87 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 3.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon1 190415-18:06:36,166 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.dil_brainmask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/dil_brainmask". 190415-18:06:36,172 nipype.workflow INFO: [Node] Running "dil_brainmask" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths.nii.gz MD /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/thr_brainmask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled.nii.gz 2 190415-18:06:37,219 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.dil_brainmask". 190415-18:06:38,87 nipype.workflow INFO: [Job 76] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.dil_brainmask). 190415-18:06:38,90 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 3.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon1 190415-18:06:38,154 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.get_brainmask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/get_brainmask". 190415-18:06:38,156 nipype.workflow INFO: [Node] Running "get_brainmask" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths_maths.nii.gz GetLargestComponent /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/dil_brainmask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths.nii.gz 190415-18:06:39,168 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.get_brainmask". 190415-18:06:40,90 nipype.workflow INFO: [Job 77] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.get_brainmask). 190415-18:06:40,98 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 3.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon1 190415-18:13:39,193 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon1". 190415-18:13:40,157 nipype.workflow INFO: [Job 109] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon1). 190415-18:13:40,162 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 2 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-18:13:40,227 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.01_atropos" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/01_atropos". 190415-18:13:40,237 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.fsnative_2_t1_xfm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/fsnative_2_t1_xfm". 190415-18:13:40,241 nipype.workflow INFO: [Node] Running "01_atropos" ("nipype.interfaces.ants.segmentation.Atropos"), a CommandLine Interface with command: Atropos --image-dimensionality 3 --initialization KMeans[3] --intensity-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-NC080001_T1w_ras_maths_corrected.nii.gz --likelihood-model Gaussian --mask-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/get_brainmask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths_maths.nii.gz --mrf [0.1,1x1x1] --convergence [3,0] --output [sub-NC080001_T1w_ras_maths_corrected_labeled.nii.gz] --use-random-seed 1 190415-18:13:40,245 nipype.workflow INFO: [Node] Running "fsnative_2_t1_xfm" ("niworkflows.interfaces.freesurfer.PatchedRobustRegister"), a CommandLine Interface with command: mri_robust_register --satit --iscale --lta /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/fsnative_2_t1_xfm/T1_robustreg.lta --mov /out/freesurfer/sub-NC080001/mri/T1.mgz --dst /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0/sub-NC080001_T1w_ras.nii.gz 190415-18:13:42,162 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 0 jobs ready. Free memory (GB): 5.57/8.77, Free processors: 0/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.fsnative_2_t1_xfm * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.01_atropos 190415-18:14:29,642 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.fsnative_2_t1_xfm". 190415-18:14:30,162 nipype.workflow INFO: [Job 110] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.fsnative_2_t1_xfm). 190415-18:14:30,165 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 5.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.01_atropos /usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'> imp.find_module('pytest') 190415-18:14:30,371 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.t1_2_fsnative_xfm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/t1_2_fsnative_xfm". 190415-18:14:30,373 nipype.workflow INFO: [Node] Running "t1_2_fsnative_xfm" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command: lta_convert --inlta /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/fsnative_2_t1_xfm/T1_robustreg.lta --invert --outlta /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/t1_2_fsnative_xfm/out.lta 190415-18:14:30,458 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.t1_2_fsnative_xfm". 190415-18:14:31,36 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.01_atropos". 190415-18:14:32,165 nipype.workflow INFO: [Job 78] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.01_atropos). 190415-18:14:32,167 nipype.workflow INFO: [Job 111] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.t1_2_fsnative_xfm). 190415-18:14:32,170 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 2 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-18:14:32,232 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.02_pad_segm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/02_pad_segm". 190415-18:14:32,236 nipype.workflow INFO: [Node] Running "02_pad_segm" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 sub-NC080001_T1w_ras_maths_corrected_labeled_maths.nii.gz PadImage /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/01_atropos/sub-NC080001_T1w_ras_maths_corrected_labeled.nii.gz 10 /usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'> imp.find_module('pytest') 190415-18:14:32,375 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.lta_2_itk" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/lta_2_itk". 190415-18:14:32,378 nipype.workflow INFO: [Node] Running "lta_2_itk" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command: lta_convert --inlta /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/t1_2_fsnative_xfm/out.lta --outitk /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/lta_2_itk/out.txt 190415-18:14:32,479 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.lta_2_itk". 190415-18:14:32,988 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.02_pad_segm". 190415-18:14:34,168 nipype.workflow INFO: [Job 79] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.02_pad_segm). 190415-18:14:34,170 nipype.workflow INFO: [Job 112] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.lta_2_itk). 190415-18:14:34,173 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 2 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-18:14:34,233 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.04_sel_labels" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels". 190415-18:14:34,236 nipype.workflow INFO: [Node] Running "04_sel_labels" ("nipype.interfaces.utility.wrappers.Function") 190415-18:14:34,239 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_fsnative" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/ds_t1_fsnative". 190415-18:14:34,241 nipype.workflow INFO: [Node] Running "ds_t1_fsnative" ("smriprep.interfaces.DerivativesDataSink") 190415-18:14:34,259 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_fsnative". 190415-18:14:34,259 nipype.workflow INFO: [Job 113] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_fsnative). 190415-18:14:34,544 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.04_sel_labels". 190415-18:14:36,172 nipype.workflow INFO: [Job 80] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.04_sel_labels). 190415-18:14:36,176 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 4 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-18:14:36,238 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.27_depad_csf" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/27_depad_csf". 190415-18:14:36,240 nipype.workflow INFO: [Node] Running "27_depad_csf" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 sub-NC080001_T1w_ras_maths_corrected_labeled_maths_class-01_maths.nii.gz PadImage /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels/sub-NC080001_T1w_ras_maths_corrected_labeled_maths_class-01.nii.gz -10 190415-18:14:36,241 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.10_me_csf" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/10_me_csf". 190415-18:14:36,241 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.06_get_gm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/06_get_gm". 190415-18:14:36,245 nipype.workflow INFO: [Node] Running "10_me_csf" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 sub-NC080001_T1w_ras_maths_corrected_labeled_maths_class-01_maths.nii.gz ME /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels/sub-NC080001_T1w_ras_maths_corrected_labeled_maths_class-01.nii.gz 10 190415-18:14:36,245 nipype.workflow INFO: [Node] Running "06_get_gm" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 sub-NC080001_T1w_ras_maths_corrected_labeled_maths_class-02_maths.nii.gz GetLargestComponent /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels/sub-NC080001_T1w_ras_maths_corrected_labeled_maths_class-02.nii.gz 190415-18:14:36,252 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.05_get_wm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/05_get_wm". 190415-18:14:36,255 nipype.workflow INFO: [Node] Running "05_get_wm" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 sub-NC080001_T1w_ras_maths_corrected_labeled_maths_class-03_maths.nii.gz GetLargestComponent /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels/sub-NC080001_T1w_ras_maths_corrected_labeled_maths_class-03.nii.gz 190415-18:14:36,811 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.27_depad_csf". 190415-18:14:37,376 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.05_get_wm". 190415-18:14:37,409 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.06_get_gm". 190415-18:14:38,176 nipype.workflow INFO: [Job 81] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.27_depad_csf). 190415-18:14:38,178 nipype.workflow INFO: [Job 83] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.06_get_gm). 190415-18:14:38,180 nipype.workflow INFO: [Job 89] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.05_get_wm). 190415-18:14:38,184 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 8.57/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.10_me_csf 190415-18:14:38,257 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.07_fill_gm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/07_fill_gm". 190415-18:14:38,258 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.09_relabel_wm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/09_relabel_wm". 190415-18:14:38,259 nipype.workflow INFO: [Node] Running "07_fill_gm" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 sub-NC080001_T1w_ras_maths_corrected_labeled_maths_class-02_maths_maths.nii.gz FillHoles /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/06_get_gm/sub-NC080001_T1w_ras_maths_corrected_labeled_maths_class-02_maths.nii.gz 2 190415-18:14:38,261 nipype.workflow INFO: [Node] Running "09_relabel_wm" ("nipype.interfaces.ants.utils.MultiplyImages"), a CommandLine Interface with command: MultiplyImages 3 /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/05_get_wm/sub-NC080001_T1w_ras_maths_corrected_labeled_maths_class-03_maths.nii.gz 3.0 09_relabel_wm.nii.gz 190415-18:14:39,134 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.09_relabel_wm". 190415-18:14:39,726 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.10_me_csf". 190415-18:14:40,181 nipype.workflow INFO: [Job 82] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.10_me_csf). 190415-18:14:40,183 nipype.workflow INFO: [Job 90] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.09_relabel_wm). 190415-18:14:40,185 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 8.57/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.07_fill_gm 190415-18:14:40,247 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.26_depad_wm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/26_depad_wm". 190415-18:14:40,249 nipype.workflow INFO: [Node] Running "26_depad_wm" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 09_relabel_wm_maths.nii.gz PadImage /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/09_relabel_wm/09_relabel_wm.nii.gz -10 190415-18:14:40,908 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.26_depad_wm". 190415-18:14:42,187 nipype.workflow INFO: [Job 91] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.26_depad_wm). 190415-18:14:42,189 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 8.57/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.07_fill_gm 190415-18:14:44,922 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.07_fill_gm". 190415-18:14:46,200 nipype.workflow INFO: [Job 84] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.07_fill_gm). 190415-18:14:46,210 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-18:14:46,271 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.08_mult_gm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/08_mult_gm". 190415-18:14:46,272 nipype.workflow INFO: [Node] Running "08_mult_gm" ("nipype.interfaces.ants.utils.MultiplyImages"), a CommandLine Interface with command: MultiplyImages 3 /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/06_get_gm/sub-NC080001_T1w_ras_maths_corrected_labeled_maths_class-02_maths.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/07_fill_gm/sub-NC080001_T1w_ras_maths_corrected_labeled_maths_class-02_maths_maths.nii.gz 08_mult_gm.nii.gz 190415-18:14:47,105 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.08_mult_gm". 190415-18:14:48,208 nipype.workflow INFO: [Job 85] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.08_mult_gm). 190415-18:14:48,212 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-18:14:48,272 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.11_add_gm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/11_add_gm". 190415-18:14:48,276 nipype.workflow INFO: [Node] Running "11_add_gm" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 08_mult_gm_maths.nii.gz addtozero /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/08_mult_gm/08_mult_gm.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/10_me_csf/sub-NC080001_T1w_ras_maths_corrected_labeled_maths_class-01_maths.nii.gz 190415-18:14:50,215 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 8.57/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.11_add_gm 190415-18:14:51,319 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.11_add_gm". 190415-18:14:52,223 nipype.workflow INFO: [Job 86] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.11_add_gm). 190415-18:14:52,227 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-18:14:52,286 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.12_relabel_gm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/12_relabel_gm". 190415-18:14:52,288 nipype.workflow INFO: [Node] Running "12_relabel_gm" ("nipype.interfaces.ants.utils.MultiplyImages"), a CommandLine Interface with command: MultiplyImages 3 /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/11_add_gm/08_mult_gm_maths.nii.gz 2.0 12_relabel_gm.nii.gz 190415-18:14:52,930 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.12_relabel_gm". 190415-18:14:54,191 nipype.workflow INFO: [Job 87] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.12_relabel_gm). 190415-18:14:54,195 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 2 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-18:14:54,255 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.25_depad_gm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/25_depad_gm". 190415-18:14:54,256 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.13_add_gm_wm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/13_add_gm_wm". 190415-18:14:54,257 nipype.workflow INFO: [Node] Running "25_depad_gm" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 12_relabel_gm_maths.nii.gz PadImage /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/12_relabel_gm/12_relabel_gm.nii.gz -10 190415-18:14:54,258 nipype.workflow INFO: [Node] Running "13_add_gm_wm" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 09_relabel_wm_maths.nii.gz addtozero /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/09_relabel_wm/09_relabel_wm.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/12_relabel_gm/12_relabel_gm.nii.gz 190415-18:14:54,918 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.25_depad_gm". 190415-18:14:56,192 nipype.workflow INFO: [Job 88] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.25_depad_gm). 190415-18:14:56,196 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 8.57/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.13_add_gm_wm 190415-18:14:56,256 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.merge_tpms" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/merge_tpms". 190415-18:14:56,260 nipype.workflow INFO: [Node] Running "merge_tpms" ("nipype.interfaces.utility.base.Merge") 190415-18:14:56,263 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.merge_tpms". 190415-18:14:57,292 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.13_add_gm_wm". 190415-18:14:58,198 nipype.workflow INFO: [Job 93] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.13_add_gm_wm). 190415-18:14:58,199 nipype.workflow INFO: [Job 92] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.merge_tpms). 190415-18:14:58,202 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 2 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-18:14:58,262 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.24_depad_segm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/24_depad_segm". 190415-18:14:58,263 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.14_sel_labels2" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/14_sel_labels2". 190415-18:14:58,264 nipype.workflow INFO: [Node] Running "24_depad_segm" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 09_relabel_wm_maths_maths.nii.gz PadImage /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/13_add_gm_wm/09_relabel_wm_maths.nii.gz -10 190415-18:14:58,266 nipype.workflow INFO: [Node] Running "14_sel_labels2" ("nipype.interfaces.utility.wrappers.Function") 190415-18:14:58,513 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.14_sel_labels2". 190415-18:14:58,927 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.24_depad_segm". 190415-18:15:00,203 nipype.workflow INFO: [Job 94] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.24_depad_segm). 190415-18:15:00,205 nipype.workflow INFO: [Job 95] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.14_sel_labels2). 190415-18:15:00,209 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-18:15:00,270 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.15_add_7" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/15_add_7". 190415-18:15:00,271 nipype.workflow INFO: [Node] Running "15_add_7" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 09_relabel_wm_maths_class-03_maths.nii.gz addtozero /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/14_sel_labels2/09_relabel_wm_maths_class-03.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/14_sel_labels2/09_relabel_wm_maths_class-02.nii.gz 190415-18:15:02,206 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 8.57/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.15_add_7 190415-18:15:03,33 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.15_add_7". 190415-18:15:04,210 nipype.workflow INFO: [Job 96] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.15_add_7). 190415-18:15:04,214 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-18:15:04,274 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.16_me_7" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/16_me_7". 190415-18:15:04,276 nipype.workflow INFO: [Node] Running "16_me_7" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 09_relabel_wm_maths_class-03_maths_maths.nii.gz ME /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/15_add_7/09_relabel_wm_maths_class-03_maths.nii.gz 2 190415-18:15:06,212 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 8.57/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.16_me_7 190415-18:15:06,460 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.16_me_7". 190415-18:15:08,220 nipype.workflow INFO: [Job 97] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.16_me_7). 190415-18:15:08,224 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-18:15:08,283 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.17_comp_7" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/17_comp_7". 190415-18:15:08,285 nipype.workflow INFO: [Node] Running "17_comp_7" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths.nii.gz GetLargestComponent /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/16_me_7/09_relabel_wm_maths_class-03_maths_maths.nii.gz 190415-18:15:09,379 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.17_comp_7". 190415-18:15:10,223 nipype.workflow INFO: [Job 98] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.17_comp_7). 190415-18:15:10,234 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-18:15:10,294 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.18_md_7" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/18_md_7". 190415-18:15:10,296 nipype.workflow INFO: [Node] Running "18_md_7" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths.nii.gz MD /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/17_comp_7/09_relabel_wm_maths_class-03_maths_maths_maths.nii.gz 4 190415-18:15:11,457 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.18_md_7". 190415-18:15:12,227 nipype.workflow INFO: [Job 99] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.18_md_7). 190415-18:15:12,231 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-18:15:12,293 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.19_fill_7" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/19_fill_7". 190415-18:15:12,300 nipype.workflow INFO: [Node] Running "19_fill_7" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths.nii.gz FillHoles /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/18_md_7/09_relabel_wm_maths_class-03_maths_maths_maths_maths.nii.gz 2 190415-18:15:14,233 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 8.57/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.19_fill_7 190415-18:15:18,34 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.19_fill_7". 190415-18:15:18,240 nipype.workflow INFO: [Job 100] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.19_fill_7). 190415-18:15:18,244 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-18:15:18,306 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.20_add_7_2" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/20_add_7_2". 190415-18:15:18,308 nipype.workflow INFO: [Node] Running "20_add_7_2" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths.nii.gz addtozero /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/19_fill_7/09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/03_pad_mask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths.nii.gz 190415-18:15:20,245 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 8.57/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.20_add_7_2 190415-18:15:21,264 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.20_add_7_2". 190415-18:15:22,255 nipype.workflow INFO: [Job 101] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.20_add_7_2). 190415-18:15:22,259 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-18:15:22,321 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.21_md_7_2" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/21_md_7_2". 190415-18:15:22,323 nipype.workflow INFO: [Node] Running "21_md_7_2" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths.nii.gz MD /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/20_add_7_2/09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths.nii.gz 5 190415-18:15:23,465 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.21_md_7_2". 190415-18:15:24,225 nipype.workflow INFO: [Job 102] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.21_md_7_2). 190415-18:15:24,229 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-18:15:24,291 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.22_me_7_2" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/22_me_7_2". 190415-18:15:24,293 nipype.workflow INFO: [Node] Running "22_me_7_2" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths_maths.nii.gz ME /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/21_md_7_2/09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths.nii.gz 5 190415-18:15:26,229 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 8.57/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.22_me_7_2 190415-18:15:26,544 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.22_me_7_2". 190415-18:15:28,233 nipype.workflow INFO: [Job 103] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.22_me_7_2). 190415-18:15:28,237 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-18:15:28,305 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.23_depad_mask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/23_depad_mask". 190415-18:15:28,308 nipype.workflow INFO: [Node] Running "23_depad_mask" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths_maths_maths.nii.gz PadImage /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/22_me_7_2/09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths_maths.nii.gz -10 190415-18:15:28,900 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.23_depad_mask". 190415-18:15:30,240 nipype.workflow INFO: [Job 104] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.23_depad_mask). 190415-18:15:30,244 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-18:15:30,314 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.apply_mask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/apply_mask". 190415-18:15:30,318 nipype.workflow INFO: [Node] Setting-up "_apply_mask0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/apply_mask/mapflow/_apply_mask0". 190415-18:15:30,320 nipype.workflow INFO: [Node] Running "_apply_mask0" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-NC080001_T1w_ras_maths_corrected.nii.gz -mas /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/23_depad_mask/09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths_maths_maths.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/apply_mask/mapflow/_apply_mask0/sub-NC080001_T1w_ras_maths_corrected_masked.nii.gz 190415-18:15:31,578 nipype.workflow INFO: [Node] Finished "_apply_mask0". 190415-18:15:31,580 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.apply_mask". 190415-18:15:32,245 nipype.workflow INFO: [Job 105] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.brain_extraction_wf.apply_mask). 190415-18:15:32,255 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-18:15:32,322 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.skull_strip_extern" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/skull_strip_extern". 190415-18:15:32,324 nipype.workflow INFO: [Node] Running "skull_strip_extern" ("niworkflows.interfaces.freesurfer.FSInjectBrainExtracted") 190415-18:15:33,675 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.skull_strip_extern". 190415-18:15:34,252 nipype.workflow INFO: [Job 114] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.skull_strip_extern). 190415-18:15:34,256 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-18:15:34,319 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon2_vol". 190415-18:15:34,327 nipype.interface INFO: resume recon-all : recon-all -autorecon2-volonly -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer 190415-18:15:34,327 nipype.workflow INFO: [Node] Running "autorecon2_vol" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command: recon-all -autorecon2-volonly -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer 190415-18:15:34,329 nipype.interface INFO: resume recon-all : recon-all -autorecon2-volonly -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer 190415-18:15:36,257 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 3.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol 190415-20:12:20,229 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol". 190415-20:12:20,365 nipype.workflow INFO: [Job 115] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol). 190415-20:12:20,374 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-20:12:22,376 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 2 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-20:12:22,443 nipype.workflow INFO: [Node] Setting-up "_autorecon_surfs0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs0". 190415-20:12:22,458 nipype.interface INFO: resume recon-all : recon-all -autorecon-hemi lh -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nohyporelabel -noaparc2aseg -noapas2aseg -nosegstats -nowmparc -nobalabels -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer 190415-20:12:22,458 nipype.workflow INFO: [Node] Running "_autorecon_surfs0" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command: recon-all -autorecon-hemi lh -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nohyporelabel -noaparc2aseg -noapas2aseg -nosegstats -nowmparc -nobalabels -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer 190415-20:12:22,461 nipype.interface INFO: resume recon-all : recon-all -autorecon-hemi lh -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nohyporelabel -noaparc2aseg -noapas2aseg -nosegstats -nowmparc -nobalabels -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer 190415-20:12:24,376 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 3.77/8.77, Free processors: 1/6. Currently running: * _autorecon_surfs0 190415-21:17:16,907 nipype.workflow INFO: [Node] Finished "_autorecon_surfs0". 190415-21:17:18,255 nipype.workflow INFO: [Job 259] Completed (_autorecon_surfs0). 190415-21:17:18,263 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-21:17:18,332 nipype.workflow INFO: [Node] Setting-up "_autorecon_surfs1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs1". 190415-21:17:18,346 nipype.interface INFO: resume recon-all : recon-all -autorecon-hemi rh -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nohyporelabel -noaparc2aseg -noapas2aseg -nosegstats -nowmparc -nobalabels -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer 190415-21:17:18,347 nipype.workflow INFO: [Node] Running "_autorecon_surfs1" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command: recon-all -autorecon-hemi rh -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nohyporelabel -noaparc2aseg -noapas2aseg -nosegstats -nowmparc -nobalabels -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer 190415-21:17:18,350 nipype.interface INFO: resume recon-all : recon-all -autorecon-hemi rh -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nohyporelabel -noaparc2aseg -noapas2aseg -nosegstats -nowmparc -nobalabels -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer 190415-21:17:20,258 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 3.77/8.77, Free processors: 1/6. Currently running: * _autorecon_surfs1 190415-22:16:30,781 nipype.workflow INFO: [Node] Finished "_autorecon_surfs1". 190415-22:16:31,963 nipype.workflow INFO: [Job 260] Completed (_autorecon_surfs1). 190415-22:16:31,967 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-22:16:32,50 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs". 190415-22:16:32,65 nipype.workflow INFO: [Node] Setting-up "_autorecon_surfs0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs0". 190415-22:16:32,92 nipype.interface INFO: recon-all complete : Not running 190415-22:16:32,92 nipype.workflow INFO: [Node] Running "_autorecon_surfs0" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command: echo recon-all: nothing to do 190415-22:16:32,113 nipype.interface INFO: recon-all complete : Not running 190415-22:16:32,378 nipype.workflow INFO: [Node] Finished "_autorecon_surfs0". 190415-22:16:32,382 nipype.workflow INFO: [Node] Setting-up "_autorecon_surfs1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs1". 190415-22:16:32,408 nipype.interface INFO: recon-all complete : Not running 190415-22:16:32,408 nipype.workflow INFO: [Node] Running "_autorecon_surfs1" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command: echo recon-all: nothing to do 190415-22:16:32,429 nipype.interface INFO: recon-all complete : Not running 190415-22:16:32,529 nipype.workflow INFO: [Node] Finished "_autorecon_surfs1". 190415-22:16:32,534 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs". 190415-22:16:33,969 nipype.workflow INFO: [Job 116] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs). 190415-22:16:33,973 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-22:16:35,972 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 2 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-22:16:36,48 nipype.workflow INFO: [Node] Setting-up "_autorecon30" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon3/mapflow/_autorecon30". 190415-22:16:36,81 nipype.interface INFO: resume recon-all : recon-all -autorecon3 -hemi lh -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial 190415-22:16:36,81 nipype.workflow INFO: [Node] Running "_autorecon30" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command: recon-all -autorecon3 -hemi lh -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial 190415-22:16:36,104 nipype.interface INFO: resume recon-all : recon-all -autorecon3 -hemi lh -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial 190415-22:16:37,973 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 3.77/8.77, Free processors: 1/6. Currently running: * _autorecon30 190415-22:38:33,116 nipype.workflow INFO: [Node] Finished "_autorecon30". 190415-22:38:34,725 nipype.workflow INFO: [Job 261] Completed (_autorecon30). 190415-22:38:34,728 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-22:38:34,796 nipype.workflow INFO: [Node] Setting-up "_autorecon31" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon3/mapflow/_autorecon31". 190415-22:38:34,844 nipype.interface INFO: resume recon-all : recon-all -autorecon3 -hemi rh -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortribbon -nohyporelabel -noapas2aseg -nosegstats -nowmparc 190415-22:38:34,845 nipype.workflow INFO: [Node] Running "_autorecon31" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command: recon-all -autorecon3 -hemi rh -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortribbon -nohyporelabel -noapas2aseg -nosegstats -nowmparc 190415-22:38:34,879 nipype.interface INFO: resume recon-all : recon-all -autorecon3 -hemi rh -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortribbon -nohyporelabel -noapas2aseg -nosegstats -nowmparc 190415-22:38:36,728 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 3.77/8.77, Free processors: 1/6. Currently running: * _autorecon31 190415-22:54:16,571 nipype.workflow INFO: [Node] Finished "_autorecon31". 190415-22:54:17,227 nipype.workflow INFO: [Job 262] Completed (_autorecon31). 190415-22:54:17,230 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-22:54:17,300 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon3" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon3". 190415-22:54:17,310 nipype.workflow INFO: [Node] Setting-up "_autorecon30" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon3/mapflow/_autorecon30". 190415-22:54:17,354 nipype.interface INFO: resume recon-all : recon-all -autorecon3 -hemi lh -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nocortribbon -nohyporelabel -noaparc2aseg -nosegstats -nowmparc -nobalabels 190415-22:54:17,354 nipype.workflow INFO: [Node] Running "_autorecon30" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command: recon-all -autorecon3 -hemi lh -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nocortribbon -nohyporelabel -noaparc2aseg -nosegstats -nowmparc -nobalabels 190415-22:54:17,390 nipype.interface INFO: resume recon-all : recon-all -autorecon3 -hemi lh -openmp 5 -subjid sub-NC080001 -sd /out/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nocortribbon -nohyporelabel -noaparc2aseg -nosegstats -nowmparc -nobalabels 190415-22:54:19,231 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 3.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon3 190415-22:54:23,139 nipype.workflow INFO: [Node] Finished "_autorecon30". 190415-22:54:23,143 nipype.workflow INFO: [Node] Setting-up "_autorecon31" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon3/mapflow/_autorecon31". 190415-22:54:23,182 nipype.interface INFO: recon-all complete : Not running 190415-22:54:23,183 nipype.workflow INFO: [Node] Running "_autorecon31" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command: echo recon-all: nothing to do 190415-22:54:23,220 nipype.interface INFO: recon-all complete : Not running 190415-22:54:23,366 nipype.workflow INFO: [Node] Finished "_autorecon31". 190415-22:54:23,376 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon3". 190415-22:54:25,240 nipype.workflow INFO: [Job 117] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon3). 190415-22:54:25,244 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 6 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-22:54:25,306 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.targets" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/targets". 190415-22:54:25,311 nipype.workflow INFO: [Node] Setting-up "_targets0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/targets/mapflow/_targets0". 190415-22:54:25,312 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.mri_coreg" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/mri_coreg". 190415-22:54:25,314 nipype.workflow INFO: [Node] Running "_targets0" ("nipype.interfaces.utility.wrappers.Function") 190415-22:54:25,318 nipype.workflow INFO: [Node] Running "mri_coreg" ("niworkflows.interfaces.freesurfer.PatchedMRICoregRPT"), a CommandLine Interface with command: mri_coreg --s sub-NC080001 --dof 6 --ftol 1.000000e-04 --linmintol 1.000000e-02 --threads 5 --lta /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/mri_coreg/registration.lta --sep 4 --mov /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/mri_coreg/uni_xform_masked.nii.gz --sd /out/freesurfer 190415-22:54:25,318 nipype.workflow INFO: [Node] Finished "_targets0". 190415-22:54:25,320 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.targets". 190415-22:54:27,241 nipype.workflow INFO: [Job 118] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.targets). 190415-22:54:27,244 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 4 jobs ready. Free memory (GB): 3.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.mri_coreg 190415-22:54:27,307 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.fs_datasource" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/fs_datasource". 190415-22:54:27,310 nipype.workflow INFO: [Node] Running "fs_datasource" ("nipype.interfaces.io.FreeSurferSource") 190415-22:54:27,511 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.fs_datasource". 190415-22:54:29,243 nipype.workflow INFO: [Job 131] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.fs_datasource). 190415-22:54:29,246 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 4 jobs ready. Free memory (GB): 3.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.mri_coreg 190415-22:54:29,330 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.tonative" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/tonative". 190415-22:54:29,336 nipype.workflow INFO: [Node] Running "tonative" ("nipype.interfaces.freesurfer.model.Label2Vol"), a CommandLine Interface with command: mri_label2vol --regheader /out/freesurfer/sub-NC080001/mri/aseg.mgz --seg /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/tonative/aparc+aseg.mgz --temp /out/freesurfer/sub-NC080001/mri/rawavg.mgz --o /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/tonative/aparc+aseg_vol.nii.gz 190415-22:54:31,247 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 3 jobs ready. Free memory (GB): 3.57/8.77, Free processors: 0/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.tonative * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.mri_coreg 190415-22:54:35,717 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.tonative". 190415-22:54:37,223 nipype.workflow INFO: [Job 132] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.tonative). 190415-22:54:37,226 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 4 jobs ready. Free memory (GB): 3.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.mri_coreg 190415-22:54:37,296 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.tonii" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/tonii". 190415-22:54:37,307 nipype.workflow INFO: [Node] Running "tonii" ("nipype.interfaces.freesurfer.preprocess.MRIConvert"), a CommandLine Interface with command: mri_convert --out_type nii --resample_type nearest --reslice_like /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-NC080001_T1w_ras_maths_corrected.nii.gz --input_volume /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/tonative/aparc+aseg_vol.nii.gz --output_volume /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/tonii/aparc+aseg_vol_out.nii.gz 190415-22:54:39,229 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 3 jobs ready. Free memory (GB): 3.57/8.77, Free processors: 0/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.tonii * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.mri_coreg 190415-22:54:40,421 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.tonii". 190415-22:54:41,231 nipype.workflow INFO: [Job 133] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.tonii). 190415-22:54:41,235 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 4 jobs ready. Free memory (GB): 3.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.mri_coreg 190415-22:54:41,311 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_fsparc" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/ds_t1_fsparc". 190415-22:54:41,314 nipype.workflow INFO: [Node] Running "ds_t1_fsparc" ("smriprep.interfaces.DerivativesDataSink") 190415-22:54:42,929 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_fsparc". 190415-22:54:42,929 nipype.workflow INFO: [Job 134] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_fsparc). 190415-22:54:42,996 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.fs_datasource" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/fs_datasource". 190415-22:54:42,998 nipype.workflow INFO: [Node] Running "fs_datasource" ("nipype.interfaces.io.FreeSurferSource") 190415-22:54:43,199 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.fs_datasource". 190415-22:54:43,233 nipype.workflow INFO: [Job 135] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.fs_datasource). 190415-22:54:43,235 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 3.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.mri_coreg 190415-22:54:43,313 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.tonative" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonative". 190415-22:54:43,323 nipype.workflow INFO: [Node] Running "tonative" ("nipype.interfaces.freesurfer.model.Label2Vol"), a CommandLine Interface with command: mri_label2vol --regheader /out/freesurfer/sub-NC080001/mri/aseg.mgz --seg /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonative/aseg.mgz --temp /out/freesurfer/sub-NC080001/mri/rawavg.mgz --o /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonative/aseg_vol.nii.gz 190415-22:54:45,238 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 2 jobs ready. Free memory (GB): 3.57/8.77, Free processors: 0/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.tonative * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.mri_coreg 190415-22:54:52,490 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.tonative". 190415-22:54:53,247 nipype.workflow INFO: [Job 136] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.tonative). 190415-22:54:53,260 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 3.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.mri_coreg 190415-22:54:53,347 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.tonii" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonii". 190415-22:54:53,352 nipype.workflow INFO: [Node] Running "tonii" ("nipype.interfaces.freesurfer.preprocess.MRIConvert"), a CommandLine Interface with command: mri_convert --out_type nii --resample_type nearest --reslice_like /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-NC080001_T1w_ras_maths_corrected.nii.gz --input_volume /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonative/aseg_vol.nii.gz --output_volume /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonii/aseg_vol_out.nii.gz 190415-22:54:55,249 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 2 jobs ready. Free memory (GB): 3.57/8.77, Free processors: 0/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.tonii * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.mri_coreg 190415-22:54:57,243 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.tonii". 190415-22:54:57,251 nipype.workflow INFO: [Job 137] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.tonii). 190415-22:54:57,257 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 4 jobs ready. Free memory (GB): 3.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.mri_coreg 190415-22:54:57,340 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_fsaseg" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/ds_t1_fsaseg". 190415-22:54:57,350 nipype.workflow INFO: [Node] Running "ds_t1_fsaseg" ("smriprep.interfaces.DerivativesDataSink") 190415-22:54:59,728 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_fsaseg". 190415-22:54:59,730 nipype.workflow INFO: [Job 138] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_fsaseg). 190415-22:54:59,819 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 2 jobs ready. Free memory (GB): 3.57/8.77, Free processors: 0/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.refine * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.mri_coreg 190415-22:54:59,821 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.refine" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/refine". 190415-22:54:59,824 nipype.workflow INFO: [Node] Running "refine" ("niworkflows.interfaces.freesurfer.RefineBrainMask") 190415-22:55:02,74 nipype.interface INFO: stdout 2019-04-15T22:55:02.074270: 190415-22:55:02,74 nipype.interface INFO: stdout 2019-04-15T22:55:02.074270:Matrix from LTA: 190415-22:55:02,74 nipype.interface INFO: stdout 2019-04-15T22:55:02.074270: 0.99954 -0.03025 -0.00059 2.46745; 190415-22:55:02,75 nipype.interface INFO: stdout 2019-04-15T22:55:02.074270: 0.00601 0.17943 0.98375 -1.68158; 190415-22:55:02,75 nipype.interface INFO: stdout 2019-04-15T22:55:02.074270:-0.02966 -0.98331 0.17953 -0.63049; 190415-22:55:02,75 nipype.interface INFO: stdout 2019-04-15T22:55:02.074270: 0.00000 0.00000 0.00000 1.00000; 190415-22:55:02,194 nipype.interface INFO: stdout 2019-04-15T22:55:02.194569: 190415-22:55:02,194 nipype.interface INFO: stdout 2019-04-15T22:55:02.194569:/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/mri_coreg/uni_xform_masked.nii.gz /out/freesurfer/sub-NC080001/mri/brainmask.mgz 190415-22:55:02,194 nipype.interface INFO: stdout 2019-04-15T22:55:02.194569:movvol /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/mri_coreg/uni_xform_masked.nii.gz 190415-22:55:02,195 nipype.interface INFO: stdout 2019-04-15T22:55:02.194569:targvol /out/freesurfer/sub-NC080001/mri/brainmask.mgz 190415-22:55:02,195 nipype.interface INFO: stdout 2019-04-15T22:55:02.194569:outvol /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/mri_coreg/uni_xform_masked_warped.nii.gz 190415-22:55:02,195 nipype.interface INFO: stdout 2019-04-15T22:55:02.194569:regfile /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/mri_coreg/registration.lta 190415-22:55:02,195 nipype.interface INFO: stdout 2019-04-15T22:55:02.194569:invert 0 190415-22:55:02,195 nipype.interface INFO: stdout 2019-04-15T22:55:02.194569:tal 0 190415-22:55:02,195 nipype.interface INFO: stdout 2019-04-15T22:55:02.194569:talres 2 190415-22:55:02,195 nipype.interface INFO: stdout 2019-04-15T22:55:02.194569:regheader 0 190415-22:55:02,195 nipype.interface INFO: stdout 2019-04-15T22:55:02.194569:noresample 0 190415-22:55:02,195 nipype.interface INFO: stdout 2019-04-15T22:55:02.194569:interp nearest (0) 190415-22:55:02,196 nipype.interface INFO: stdout 2019-04-15T22:55:02.194569:precision float (3) 190415-22:55:02,196 nipype.interface INFO: stdout 2019-04-15T22:55:02.194569:Gdiag_no -1 190415-22:55:02,197 nipype.interface INFO: stdout 2019-04-15T22:55:02.194569:Synth 0 190415-22:55:02,197 nipype.interface INFO: stdout 2019-04-15T22:55:02.194569:SynthSeed 1555501226 190415-22:55:02,198 nipype.interface INFO: stdout 2019-04-15T22:55:02.194569: 190415-22:55:02,198 nipype.interface INFO: stdout 2019-04-15T22:55:02.194569:Final tkRAS-to-tkRAS Matrix is: 190415-22:55:02,198 nipype.interface INFO: stdout 2019-04-15T22:55:02.194569: 0.99954 -0.03025 -0.00059 2.46750; 190415-22:55:02,199 nipype.interface INFO: stdout 2019-04-15T22:55:02.194569: 0.00601 0.17943 0.98375 -1.68156; 190415-22:55:02,199 nipype.interface INFO: stdout 2019-04-15T22:55:02.194569:-0.02966 -0.98331 0.17953 -0.63051; 190415-22:55:02,199 nipype.interface INFO: stdout 2019-04-15T22:55:02.194569: 0.00000 0.00000 0.00000 1.00000; 190415-22:55:02,200 nipype.interface INFO: stdout 2019-04-15T22:55:02.194569: 190415-22:55:02,201 nipype.interface INFO: stdout 2019-04-15T22:55:02.194569: 190415-22:55:02,201 nipype.interface INFO: stdout 2019-04-15T22:55:02.194569:Vox2Vox Matrix is: 190415-22:55:02,201 nipype.interface INFO: stdout 2019-04-15T22:55:02.194569: 0.29078 -0.00017 0.00880 -7.04169; 190415-22:55:02,202 nipype.interface INFO: stdout 2019-04-15T22:55:02.194569:-0.00863 0.05223 0.28605 -10.01204; 190415-22:55:02,202 nipype.interface INFO: stdout 2019-04-15T22:55:02.194569:-0.00131 -0.21386 0.03901 38.68290; 190415-22:55:02,203 nipype.interface INFO: stdout 2019-04-15T22:55:02.194569: 0.00000 0.00000 0.00000 1.00000; 190415-22:55:02,751 nipype.interface INFO: stdout 2019-04-15T22:55:02.750979: 190415-22:55:02,751 nipype.interface INFO: stdout 2019-04-15T22:55:02.750979:Resampling 190415-22:55:02,751 nipype.interface INFO: stdout 2019-04-15T22:55:02.750979:Output registration matrix is identity 190415-22:55:02,751 nipype.interface INFO: stdout 2019-04-15T22:55:02.750979: 190415-22:55:02,751 nipype.interface INFO: stdout 2019-04-15T22:55:02.750979:mri_vol2vol done /usr/local/miniconda/lib/python3.7/site-packages/matplotlib/cbook/__init__.py:2364: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working return list(data) if isinstance(data, collections.MappingView) else data /usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index return _nd_image.find_objects(input, max_label) 190415-22:55:15,327 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.mri_coreg". 190415-22:55:15,802 nipype.workflow INFO: [Job 119] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.mri_coreg). 190415-22:55:15,805 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 8.57/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.refine 190415-22:55:15,868 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.get_surfaces" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/get_surfaces". 190415-22:55:15,871 nipype.workflow INFO: [Node] Running "get_surfaces" ("nipype.interfaces.io.FreeSurferSource") 190415-22:55:15,873 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.recon_report" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/recon_report". 190415-22:55:15,943 nipype.interface INFO: recon-all complete : Not running 190415-22:55:15,943 nipype.workflow INFO: [Node] Running "recon_report" ("niworkflows.interfaces.segmentation.ReconAllRPT"), a CommandLine Interface with command: echo recon-all: nothing to do 190415-22:55:16,6 nipype.interface INFO: recon-all complete : Not running 190415-22:55:16,123 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.get_surfaces". /usr/local/miniconda/lib/python3.7/site-packages/matplotlib/cbook/__init__.py:2364: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working return list(data) if isinstance(data, collections.MappingView) else data 190415-22:55:17,804 nipype.workflow INFO: [Job 247] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.get_surfaces). 190415-22:55:17,806 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 2 jobs ready. Free memory (GB): 3.57/8.77, Free processors: 4/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.recon_report * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.refine /usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index return _nd_image.find_objects(input, max_label) 190415-22:55:19,808 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 3 jobs ready. Free memory (GB): 3.57/8.77, Free processors: 4/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.recon_report * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.refine /usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'> imp.find_module('pytest') /usr/local/miniconda/lib/python3.7/site-packages/skimage/__init__.py:80: ResourceWarning: unclosed file <_io.TextIOWrapper name='/usr/local/miniconda/lib/python3.7/site-packages/pytest.py' mode='r' encoding='utf-8'> imp.find_module('pytest') 190415-22:55:20,63 nipype.workflow INFO: [Node] Setting-up "_midthickness0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0". 190415-22:55:20,63 nipype.workflow INFO: [Node] Setting-up "_midthickness1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness1". 190415-22:55:20,84 nipype.workflow INFO: [Node] Running "_midthickness0" ("niworkflows.interfaces.freesurfer.MakeMidthickness"), a CommandLine Interface with command: mris_expand -pial /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.pial -thickness -thickness_name /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.thickness /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.smoothwm 0.5 midthickness 190415-22:55:20,84 nipype.workflow INFO: [Node] Running "_midthickness1" ("niworkflows.interfaces.freesurfer.MakeMidthickness"), a CommandLine Interface with command: mris_expand -pial /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness1/lh.pial -thickness -thickness_name /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness1/lh.thickness /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness1/lh.smoothwm 0.5 midthickness 190415-22:55:21,815 nipype.workflow INFO: [MultiProc] Running 4 tasks, and 1 jobs ready. Free memory (GB): 3.17/8.77, Free processors: 2/6. Currently running: * _midthickness1 * _midthickness0 * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.recon_report * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.refine 190415-22:55:23,885 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.recon_report". 190415-22:55:25,824 nipype.workflow INFO: [Job 255] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.recon_report). 190415-22:55:25,827 nipype.workflow INFO: [MultiProc] Running 3 tasks, and 2 jobs ready. Free memory (GB): 8.17/8.77, Free processors: 3/6. Currently running: * _midthickness1 * _midthickness0 * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.refine 190415-22:55:25,894 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_reports_wf.ds_recon_report" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_reports_wf/ds_recon_report". 190415-22:55:25,897 nipype.workflow INFO: [Node] Running "ds_recon_report" ("smriprep.interfaces.DerivativesDataSink") 190415-22:55:25,901 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_reports_wf.ds_recon_report". 190415-22:55:25,902 nipype.workflow INFO: [Job 256] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_reports_wf.ds_recon_report). 190415-22:55:27,831 nipype.workflow INFO: [MultiProc] Running 3 tasks, and 1 jobs ready. Free memory (GB): 8.17/8.77, Free processors: 3/6. Currently running: * _midthickness1 * _midthickness0 * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.refine 190415-22:55:38,750 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.refine". 190415-22:55:39,825 nipype.workflow INFO: [Job 139] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.refine). 190415-22:55:39,828 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 4 jobs ready. Free memory (GB): 8.37/8.77, Free processors: 4/6. Currently running: * _midthickness1 * _midthickness0 190415-22:55:39,893 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_mask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/ds_t1_mask". 190415-22:55:39,896 nipype.workflow INFO: [Node] Running "ds_t1_mask" ("smriprep.interfaces.DerivativesDataSink") 190415-22:55:40,291 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_mask". 190415-22:55:40,291 nipype.workflow INFO: [Job 140] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_mask). 190415-22:55:40,353 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.applyrefined" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/applyrefined". 190415-22:55:40,356 nipype.workflow INFO: [Node] Running "applyrefined" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-NC080001_T1w_ras_maths_corrected.nii.gz -mas /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/refine/sub-NC080001_T1w_ras_maths_corrected_rbrainmask.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/applyrefined/sub-NC080001_T1w_ras_maths_corrected_masked.nii.gz 190415-22:55:41,595 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.applyrefined". 190415-22:55:41,828 nipype.workflow INFO: [Job 152] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.applyrefined). 190415-22:55:41,830 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 4 jobs ready. Free memory (GB): 8.37/8.77, Free processors: 4/6. Currently running: * _midthickness1 * _midthickness0 190415-22:55:41,892 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.gen_ref" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/gen_ref". 190415-22:55:41,892 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_seg" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/t1_seg". 190415-22:55:41,894 nipype.workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.utils.GenerateSamplingReference") 190415-22:55:41,895 nipype.workflow INFO: [Node] Running "t1_seg" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command: fast -N -p -g -S 1 /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/t1_seg/sub-NC080001_T1w_ras_maths_corrected_masked.nii.gz 190415-22:55:42,406 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.gen_ref". 190415-22:55:43,830 nipype.workflow INFO: [Job 153] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.gen_ref). 190415-22:55:43,833 nipype.workflow INFO: [MultiProc] Running 3 tasks, and 4 jobs ready. Free memory (GB): 5.37/8.77, Free processors: 3/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_seg * _midthickness1 * _midthickness0 190415-22:55:43,899 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.aparc_t1w_tfm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/aparc_t1w_tfm". 190415-22:55:43,902 nipype.workflow INFO: [Node] Running "aparc_t1w_tfm" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/tonii/aparc+aseg_vol_out.nii.gz --interpolation MultiLabel --output aparc+aseg_vol_out_trans.nii.gz --reference-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/gen_ref/sub-NC080001_T1w_ras_maths_corrected_masked_reference.nii.gz -t identity 190415-22:55:43,903 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.aseg_t1w_tfm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/aseg_t1w_tfm". 190415-22:55:43,906 nipype.workflow INFO: [Node] Running "aseg_t1w_tfm" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonii/aseg_vol_out.nii.gz --interpolation MultiLabel --output aseg_vol_out_trans.nii.gz --reference-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/gen_ref/sub-NC080001_T1w_ras_maths_corrected_masked_reference.nii.gz -t identity 190415-22:55:45,59 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.aseg_t1w_tfm". 190415-22:55:45,76 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.aparc_t1w_tfm". 190415-22:55:45,833 nipype.workflow INFO: [Job 154] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.aparc_t1w_tfm). 190415-22:55:45,835 nipype.workflow INFO: [Job 155] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.aseg_t1w_tfm). 190415-22:55:45,838 nipype.workflow INFO: [MultiProc] Running 3 tasks, and 2 jobs ready. Free memory (GB): 5.37/8.77, Free processors: 3/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_seg * _midthickness1 * _midthickness0 190415-22:57:16,645 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_seg". 190415-22:57:17,907 nipype.workflow INFO: [Job 211] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_seg). 190415-22:57:17,910 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 8 jobs ready. Free memory (GB): 8.37/8.77, Free processors: 4/6. Currently running: * _midthickness1 * _midthickness0 190415-22:57:17,977 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_tpms" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/ds_t1_tpms". 190415-22:57:17,980 nipype.workflow INFO: [Node] Running "ds_t1_tpms" ("smriprep.interfaces.DerivativesDataSink") 190415-22:57:22,325 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_tpms". 190415-22:57:22,326 nipype.workflow INFO: [Job 212] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_tpms). 190415-22:57:22,392 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.lut_t1_seg" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/lut_t1_seg". 190415-22:57:22,392 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.wm_roi" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/wm_roi". 190415-22:57:22,394 nipype.workflow INFO: [Node] Running "lut_t1_seg" ("nipype.interfaces.utility.wrappers.Function") 190415-22:57:22,395 nipype.workflow INFO: [Node] Running "wm_roi" ("niworkflows.interfaces.utils.TPM2ROI") 190415-22:57:22,399 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.csf_roi" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/csf_roi". 190415-22:57:22,401 nipype.workflow INFO: [Node] Running "csf_roi" ("niworkflows.interfaces.utils.TPM2ROI") 190415-22:57:22,404 nipype.workflow INFO: [MultiProc] Running 6 tasks, and 3 jobs ready. Free memory (GB): 7.57/8.77, Free processors: 0/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.tpms_add_csf_wm * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.csf_roi * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.wm_roi * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.lut_t1_seg * _midthickness1 * _midthickness0190415-22:57:22,406 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.tpms_add_csf_wm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/tpms_add_csf_wm". 190415-22:57:22,408 nipype.workflow INFO: [Node] Running "tpms_add_csf_wm" ("niworkflows.interfaces.utils.AddTPMs") 190415-22:57:22,886 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.lut_t1_seg". 190415-22:57:23,372 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.csf_roi". 190415-22:57:23,683 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.tpms_add_csf_wm". 190415-22:57:24,406 nipype.workflow INFO: [Job 213] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.lut_t1_seg). 190415-22:57:24,408 nipype.workflow INFO: [Job 218] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.csf_roi). 190415-22:57:24,409 nipype.workflow INFO: [Job 226] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.tpms_add_csf_wm). 190415-22:57:24,411 nipype.workflow INFO: [MultiProc] Running 3 tasks, and 5 jobs ready. Free memory (GB): 8.17/8.77, Free processors: 3/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.wm_roi * _midthickness1 * _midthickness0 190415-22:57:24,475 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_seg" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/ds_t1_seg". 190415-22:57:24,477 nipype.workflow INFO: [Node] Running "ds_t1_seg" ("smriprep.interfaces.DerivativesDataSink") 190415-22:57:26,30 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.wm_roi". 190415-22:57:26,63 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_seg". 190415-22:57:26,63 nipype.workflow INFO: [Job 214] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_seg). 190415-22:57:26,125 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.acc_roi" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/acc_roi". 190415-22:57:26,127 nipype.workflow INFO: [Node] Running "acc_roi" ("niworkflows.interfaces.utils.TPM2ROI") 190415-22:57:26,139 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.seg_rpt" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/seg_rpt". 190415-22:57:26,146 nipype.workflow INFO: [Node] Running "seg_rpt" ("niworkflows.interfaces.masks.ROIsPlot") 190415-22:57:26,409 nipype.workflow INFO: [Job 215] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.wm_roi). 190415-22:57:26,413 nipype.workflow INFO: [MultiProc] Running 4 tasks, and 2 jobs ready. Free memory (GB): 7.97/8.77, Free processors: 2/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.seg_rpt * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.acc_roi * _midthickness1 * _midthickness0 /usr/local/miniconda/lib/python3.7/site-packages/matplotlib/cbook/__init__.py:2364: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working return list(data) if isinstance(data, collections.MappingView) else data 190415-22:57:29,565 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.acc_roi". 190415-22:57:30,417 nipype.workflow INFO: [Job 227] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.acc_roi). 190415-22:57:30,420 nipype.workflow INFO: [MultiProc] Running 3 tasks, and 2 jobs ready. Free memory (GB): 8.17/8.77, Free processors: 3/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.seg_rpt * _midthickness1 * _midthickness0 /usr/local/miniconda/lib/python3.7/site-packages/nilearn/image/resampling.py:510: UserWarning: Casting data from int32 to float32 warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux)) /usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index return _nd_image.find_objects(input, max_label) /usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index return _nd_image.find_objects(input, max_label) /usr/local/miniconda/lib/python3.7/site-packages/nilearn/image/resampling.py:510: UserWarning: Casting data from int32 to float32 warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux)) /usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index return _nd_image.find_objects(input, max_label) /usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index return _nd_image.find_objects(input, max_label) /usr/local/miniconda/lib/python3.7/site-packages/nilearn/image/resampling.py:510: UserWarning: Casting data from int32 to float32 warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux)) /usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index return _nd_image.find_objects(input, max_label) /usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index return _nd_image.find_objects(input, max_label) 190415-22:58:10,514 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.seg_rpt". 190415-22:58:12,420 nipype.workflow INFO: [Job 240] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.seg_rpt). 190415-22:58:12,427 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 3 jobs ready. Free memory (GB): 8.37/8.77, Free processors: 4/6. Currently running: * _midthickness1 * _midthickness0 190415-22:58:12,494 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_reports_wf.ds_t1_seg_mask_report" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_reports_wf/ds_t1_seg_mask_report". 190415-22:58:12,496 nipype.workflow INFO: [Node] Running "ds_t1_seg_mask_report" ("smriprep.interfaces.DerivativesDataSink") 190415-22:58:12,501 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_reports_wf.ds_t1_seg_mask_report". 190415-22:58:12,501 nipype.workflow INFO: [Job 241] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_reports_wf.ds_t1_seg_mask_report). 190415-22:58:14,426 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 2 jobs ready. Free memory (GB): 8.37/8.77, Free processors: 4/6. Currently running: * _midthickness1 * _midthickness0 190415-23:06:19,166 nipype.workflow INFO: [Node] Finished "_midthickness0". 190415-23:06:19,316 nipype.workflow INFO: [Job 263] Completed (_midthickness0). 190415-23:06:19,318 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 8.57/8.77, Free processors: 5/6. Currently running: * _midthickness1 190415-23:06:19,380 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_2_mni" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/t1_2_mni". 190415-23:06:19,383 nipype.workflow INFO: [Node] Running "t1_2_mni" ("niworkflows.interfaces.registration.RobustMNINormalizationRPT") 190415-23:06:21,321 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 1 jobs ready. Free memory (GB): 6.57/8.77, Free processors: 0/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_2_mni * _midthickness1 190415-23:06:26,888 nipype.workflow INFO: [Node] Finished "_midthickness1". 190415-23:06:27,330 nipype.workflow INFO: [Job 264] Completed (_midthickness1). 190415-23:06:27,333 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 6.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_2_mni 190415-23:06:27,417 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.midthickness" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness". 190415-23:06:27,425 nipype.workflow INFO: [Node] Setting-up "_midthickness0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0". 190415-23:06:27,429 nipype.workflow INFO: [Node] Cached "_midthickness0" - collecting precomputed outputs 190415-23:06:27,429 nipype.workflow INFO: [Node] "_midthickness0" found cached. 190415-23:06:27,432 nipype.workflow INFO: [Node] Setting-up "_midthickness1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness1". 190415-23:06:27,436 nipype.workflow INFO: [Node] Cached "_midthickness1" - collecting precomputed outputs 190415-23:06:27,436 nipype.workflow INFO: [Node] "_midthickness1" found cached. 190415-23:06:27,439 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.midthickness". 190415-23:06:29,332 nipype.workflow INFO: [Job 248] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.midthickness). 190415-23:06:29,336 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 6.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_2_mni 190415-23:06:29,415 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.save_midthickness" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/save_midthickness". 190415-23:06:29,418 nipype.workflow INFO: [Node] Running "save_midthickness" ("nipype.interfaces.io.DataSink") 190415-23:06:29,775 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.save_midthickness". 190415-23:06:31,335 nipype.workflow INFO: [Job 249] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.save_midthickness). 190415-23:06:31,339 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 6.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_2_mni 190415-23:06:31,444 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.surface_list" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/surface_list". 190415-23:06:31,448 nipype.workflow INFO: [Node] Running "surface_list" ("nipype.interfaces.utility.base.Merge") 190415-23:06:31,474 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.surface_list". 190415-23:06:31,474 nipype.workflow INFO: [Job 250] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.surface_list). 190415-23:06:33,338 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 6.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_2_mni 190415-23:06:35,343 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 9 jobs ready. Free memory (GB): 6.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_2_mni 190415-23:06:35,417 nipype.workflow INFO: [Node] Setting-up "_fs_2_gii0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii0". 190415-23:06:35,420 nipype.workflow INFO: [Node] Running "_fs_2_gii0" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command: mris_convert /out/freesurfer/sub-NC080001/surf/rh.smoothwm /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii0/rh.smoothwm_converted.gii 190415-23:06:36,892 nipype.workflow INFO: [Node] Finished "_fs_2_gii0". 190415-23:06:37,307 nipype.workflow INFO: [Job 265] Completed (_fs_2_gii0). 190415-23:06:37,310 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 8 jobs ready. Free memory (GB): 6.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_2_mni 190415-23:06:37,384 nipype.workflow INFO: [Node] Setting-up "_fs_2_gii1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii1". 190415-23:06:37,387 nipype.workflow INFO: [Node] Running "_fs_2_gii1" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command: mris_convert /out/freesurfer/sub-NC080001/surf/lh.smoothwm /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii1/lh.smoothwm_converted.gii 190415-23:06:38,810 nipype.workflow INFO: [Node] Finished "_fs_2_gii1". 190415-23:06:39,309 nipype.workflow INFO: [Job 266] Completed (_fs_2_gii1). 190415-23:06:39,312 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 7 jobs ready. Free memory (GB): 6.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_2_mni 190415-23:06:39,380 nipype.workflow INFO: [Node] Setting-up "_fs_2_gii2" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii2". 190415-23:06:39,386 nipype.workflow INFO: [Node] Running "_fs_2_gii2" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command: mris_convert /out/freesurfer/sub-NC080001/surf/lh.pial /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii2/lh.pial_converted.gii 190415-23:06:40,791 nipype.workflow INFO: [Node] Finished "_fs_2_gii2". 190415-23:06:41,311 nipype.workflow INFO: [Job 267] Completed (_fs_2_gii2). 190415-23:06:41,314 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 6 jobs ready. Free memory (GB): 6.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_2_mni 190415-23:06:41,383 nipype.workflow INFO: [Node] Setting-up "_fs_2_gii3" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii3". 190415-23:06:41,386 nipype.workflow INFO: [Node] Running "_fs_2_gii3" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command: mris_convert /out/freesurfer/sub-NC080001/surf/rh.pial /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii3/rh.pial_converted.gii 190415-23:06:42,830 nipype.workflow INFO: [Node] Finished "_fs_2_gii3". 190415-23:06:43,315 nipype.workflow INFO: [Job 268] Completed (_fs_2_gii3). 190415-23:06:43,317 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 5 jobs ready. Free memory (GB): 6.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_2_mni 190415-23:06:43,397 nipype.workflow INFO: [Node] Setting-up "_fs_2_gii4" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii4". 190415-23:06:43,400 nipype.workflow INFO: [Node] Running "_fs_2_gii4" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command: mris_convert /out/freesurfer/sub-NC080001/surf/lh.inflated /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii4/lh.inflated_converted.gii 190415-23:06:44,799 nipype.workflow INFO: [Node] Finished "_fs_2_gii4". 190415-23:06:45,315 nipype.workflow INFO: [Job 269] Completed (_fs_2_gii4). 190415-23:06:45,318 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 4 jobs ready. Free memory (GB): 6.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_2_mni 190415-23:06:45,391 nipype.workflow INFO: [Node] Setting-up "_fs_2_gii5" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii5". 190415-23:06:45,395 nipype.workflow INFO: [Node] Running "_fs_2_gii5" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command: mris_convert /out/freesurfer/sub-NC080001/surf/rh.inflated /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii5/rh.inflated_converted.gii 190415-23:06:46,809 nipype.workflow INFO: [Node] Finished "_fs_2_gii5". 190415-23:06:47,318 nipype.workflow INFO: [Job 270] Completed (_fs_2_gii5). 190415-23:06:47,321 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 6.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_2_mni 190415-23:06:47,416 nipype.workflow INFO: [Node] Setting-up "_fs_2_gii6" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii6". 190415-23:06:47,419 nipype.workflow INFO: [Node] Running "_fs_2_gii6" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command: mris_convert /out/freesurfer/sub-NC080001/surf/rh.midthickness /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii6/rh.midthickness_converted.gii 190415-23:06:48,860 nipype.workflow INFO: [Node] Finished "_fs_2_gii6". 190415-23:06:49,321 nipype.workflow INFO: [Job 271] Completed (_fs_2_gii6). 190415-23:06:49,325 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 6.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_2_mni 190415-23:06:49,398 nipype.workflow INFO: [Node] Setting-up "_fs_2_gii7" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii7". 190415-23:06:49,401 nipype.workflow INFO: [Node] Running "_fs_2_gii7" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command: mris_convert /out/freesurfer/sub-NC080001/surf/lh.midthickness /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii7/lh.midthickness_converted.gii 190415-23:06:50,856 nipype.workflow INFO: [Node] Finished "_fs_2_gii7". 190415-23:06:51,322 nipype.workflow INFO: [Job 272] Completed (_fs_2_gii7). 190415-23:06:51,325 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 6.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_2_mni 190415-23:06:51,471 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.fs_2_gii" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii". 190415-23:06:51,481 nipype.workflow INFO: [Node] Setting-up "_fs_2_gii0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii0". 190415-23:06:51,485 nipype.workflow INFO: [Node] Cached "_fs_2_gii0" - collecting precomputed outputs 190415-23:06:51,485 nipype.workflow INFO: [Node] "_fs_2_gii0" found cached. 190415-23:06:51,487 nipype.workflow INFO: [Node] Setting-up "_fs_2_gii1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii1". 190415-23:06:51,490 nipype.workflow INFO: [Node] Cached "_fs_2_gii1" - collecting precomputed outputs 190415-23:06:51,490 nipype.workflow INFO: [Node] "_fs_2_gii1" found cached. 190415-23:06:51,492 nipype.workflow INFO: [Node] Setting-up "_fs_2_gii2" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii2". 190415-23:06:51,496 nipype.workflow INFO: [Node] Cached "_fs_2_gii2" - collecting precomputed outputs 190415-23:06:51,496 nipype.workflow INFO: [Node] "_fs_2_gii2" found cached. 190415-23:06:51,498 nipype.workflow INFO: [Node] Setting-up "_fs_2_gii3" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii3". 190415-23:06:51,500 nipype.workflow INFO: [Node] Cached "_fs_2_gii3" - collecting precomputed outputs 190415-23:06:51,501 nipype.workflow INFO: [Node] "_fs_2_gii3" found cached. 190415-23:06:51,502 nipype.workflow INFO: [Node] Setting-up "_fs_2_gii4" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii4". 190415-23:06:51,507 nipype.workflow INFO: [Node] Cached "_fs_2_gii4" - collecting precomputed outputs 190415-23:06:51,507 nipype.workflow INFO: [Node] "_fs_2_gii4" found cached. 190415-23:06:51,509 nipype.workflow INFO: [Node] Setting-up "_fs_2_gii5" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii5". 190415-23:06:51,512 nipype.workflow INFO: [Node] Cached "_fs_2_gii5" - collecting precomputed outputs 190415-23:06:51,512 nipype.workflow INFO: [Node] "_fs_2_gii5" found cached. 190415-23:06:51,514 nipype.workflow INFO: [Node] Setting-up "_fs_2_gii6" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii6". 190415-23:06:51,519 nipype.workflow INFO: [Node] Cached "_fs_2_gii6" - collecting precomputed outputs 190415-23:06:51,519 nipype.workflow INFO: [Node] "_fs_2_gii6" found cached. 190415-23:06:51,521 nipype.workflow INFO: [Node] Setting-up "_fs_2_gii7" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii7". 190415-23:06:51,524 nipype.workflow INFO: [Node] Cached "_fs_2_gii7" - collecting precomputed outputs 190415-23:06:51,524 nipype.workflow INFO: [Node] "_fs_2_gii7" found cached. 190415-23:06:51,527 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.fs_2_gii". 190415-23:06:53,324 nipype.workflow INFO: [Job 251] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.fs_2_gii). 190415-23:06:53,328 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 6.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_2_mni 190415-23:06:55,328 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 9 jobs ready. Free memory (GB): 6.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_2_mni 190415-23:06:55,404 nipype.workflow INFO: [Node] Setting-up "_fix_surfs0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs0". 190415-23:06:55,409 nipype.workflow INFO: [Node] Running "_fix_surfs0" ("niworkflows.interfaces.surf.NormalizeSurf") 190415-23:06:55,779 nipype.workflow INFO: [Node] Finished "_fix_surfs0". 190415-23:06:57,327 nipype.workflow INFO: [Job 273] Completed (_fix_surfs0). 190415-23:06:57,330 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 8 jobs ready. Free memory (GB): 6.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_2_mni 190415-23:06:57,405 nipype.workflow INFO: [Node] Setting-up "_fix_surfs1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs1". 190415-23:06:57,408 nipype.workflow INFO: [Node] Running "_fix_surfs1" ("niworkflows.interfaces.surf.NormalizeSurf") /usr/local/miniconda/lib/python3.7/site-packages/nibabel/gifti/gifti.py:760: ResourceWarning: unclosed file <_io.BufferedReader name='/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii1/lh.smoothwm_converted.gii'> parser.parse(fptr=file_map['image'].get_prepare_fileobj('rb')) /usr/local/miniconda/lib/python3.7/site-packages/nibabel/filebasedimages.py:334: ResourceWarning: unclosed file <_io.BufferedWriter name='/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs1/lh.smoothwm_converted.gii'> self.to_file_map() 190415-23:06:57,776 nipype.workflow INFO: [Node] Finished "_fix_surfs1". 190415-23:06:59,330 nipype.workflow INFO: [Job 274] Completed (_fix_surfs1). 190415-23:06:59,333 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 7 jobs ready. Free memory (GB): 6.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_2_mni 190415-23:06:59,407 nipype.workflow INFO: [Node] Setting-up "_fix_surfs2" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs2". 190415-23:06:59,408 nipype.workflow INFO: [Node] Running "_fix_surfs2" ("niworkflows.interfaces.surf.NormalizeSurf") /usr/local/miniconda/lib/python3.7/site-packages/nibabel/gifti/gifti.py:760: ResourceWarning: unclosed file <_io.BufferedReader name='/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii2/lh.pial_converted.gii'> parser.parse(fptr=file_map['image'].get_prepare_fileobj('rb')) /usr/local/miniconda/lib/python3.7/site-packages/nibabel/filebasedimages.py:334: ResourceWarning: unclosed file <_io.BufferedWriter name='/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs2/lh.pial_converted.gii'> self.to_file_map() 190415-23:06:59,779 nipype.workflow INFO: [Node] Finished "_fix_surfs2". 190415-23:07:01,333 nipype.workflow INFO: [Job 275] Completed (_fix_surfs2). 190415-23:07:01,336 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 6 jobs ready. Free memory (GB): 6.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_2_mni 190415-23:07:01,407 nipype.workflow INFO: [Node] Setting-up "_fix_surfs3" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs3". 190415-23:07:01,409 nipype.workflow INFO: [Node] Running "_fix_surfs3" ("niworkflows.interfaces.surf.NormalizeSurf") /usr/local/miniconda/lib/python3.7/site-packages/nibabel/gifti/gifti.py:760: ResourceWarning: unclosed file <_io.BufferedReader name='/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii3/rh.pial_converted.gii'> parser.parse(fptr=file_map['image'].get_prepare_fileobj('rb')) /usr/local/miniconda/lib/python3.7/site-packages/nibabel/filebasedimages.py:334: ResourceWarning: unclosed file <_io.BufferedWriter name='/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs3/rh.pial_converted.gii'> self.to_file_map() 190415-23:07:01,760 nipype.workflow INFO: [Node] Finished "_fix_surfs3". 190415-23:07:03,337 nipype.workflow INFO: [Job 276] Completed (_fix_surfs3). 190415-23:07:03,340 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 5 jobs ready. Free memory (GB): 6.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_2_mni 190415-23:07:03,413 nipype.workflow INFO: [Node] Setting-up "_fix_surfs4" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs4". 190415-23:07:03,417 nipype.workflow INFO: [Node] Running "_fix_surfs4" ("niworkflows.interfaces.surf.NormalizeSurf") /usr/local/miniconda/lib/python3.7/site-packages/nibabel/gifti/gifti.py:760: ResourceWarning: unclosed file <_io.BufferedReader name='/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii4/lh.inflated_converted.gii'> parser.parse(fptr=file_map['image'].get_prepare_fileobj('rb')) /usr/local/miniconda/lib/python3.7/site-packages/nibabel/filebasedimages.py:334: ResourceWarning: unclosed file <_io.BufferedWriter name='/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs4/lh.inflated_converted.gii'> self.to_file_map() 190415-23:07:03,784 nipype.workflow INFO: [Node] Finished "_fix_surfs4". 190415-23:07:05,340 nipype.workflow INFO: [Job 277] Completed (_fix_surfs4). 190415-23:07:05,342 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 4 jobs ready. Free memory (GB): 6.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_2_mni 190415-23:07:05,417 nipype.workflow INFO: [Node] Setting-up "_fix_surfs5" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs5". 190415-23:07:05,421 nipype.workflow INFO: [Node] Running "_fix_surfs5" ("niworkflows.interfaces.surf.NormalizeSurf") 190415-23:07:05,770 nipype.workflow INFO: [Node] Finished "_fix_surfs5". 190415-23:07:07,308 nipype.workflow INFO: [Job 278] Completed (_fix_surfs5). 190415-23:07:07,310 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 6.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_2_mni 190415-23:07:07,388 nipype.workflow INFO: [Node] Setting-up "_fix_surfs6" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs6". 190415-23:07:07,390 nipype.workflow INFO: [Node] Running "_fix_surfs6" ("niworkflows.interfaces.surf.NormalizeSurf") /usr/local/miniconda/lib/python3.7/site-packages/nibabel/gifti/gifti.py:760: ResourceWarning: unclosed file <_io.BufferedReader name='/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii6/rh.midthickness_converted.gii'> parser.parse(fptr=file_map['image'].get_prepare_fileobj('rb')) /usr/local/miniconda/lib/python3.7/site-packages/nibabel/filebasedimages.py:334: ResourceWarning: unclosed file <_io.BufferedWriter name='/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs6/rh.midthickness_converted.gii'> self.to_file_map() 190415-23:07:07,734 nipype.workflow INFO: [Node] Finished "_fix_surfs6". 190415-23:07:09,310 nipype.workflow INFO: [Job 279] Completed (_fix_surfs6). 190415-23:07:09,312 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 6.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_2_mni 190415-23:07:09,378 nipype.workflow INFO: [Node] Setting-up "_fix_surfs7" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs7". 190415-23:07:09,380 nipype.workflow INFO: [Node] Running "_fix_surfs7" ("niworkflows.interfaces.surf.NormalizeSurf") /usr/local/miniconda/lib/python3.7/site-packages/nibabel/gifti/gifti.py:760: ResourceWarning: unclosed file <_io.BufferedReader name='/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs_2_gii/mapflow/_fs_2_gii7/lh.midthickness_converted.gii'> parser.parse(fptr=file_map['image'].get_prepare_fileobj('rb')) /usr/local/miniconda/lib/python3.7/site-packages/nibabel/filebasedimages.py:334: ResourceWarning: unclosed file <_io.BufferedWriter name='/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs7/lh.midthickness_converted.gii'> self.to_file_map() 190415-23:07:09,743 nipype.workflow INFO: [Node] Finished "_fix_surfs7". 190415-23:07:11,312 nipype.workflow INFO: [Job 280] Completed (_fix_surfs7). 190415-23:07:11,315 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 6.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_2_mni 190415-23:07:11,397 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.fix_surfs" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs". 190415-23:07:11,401 nipype.workflow INFO: [Node] Setting-up "_fix_surfs0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs0". 190415-23:07:11,402 nipype.workflow INFO: [Node] Cached "_fix_surfs0" - collecting precomputed outputs 190415-23:07:11,402 nipype.workflow INFO: [Node] "_fix_surfs0" found cached. 190415-23:07:11,404 nipype.workflow INFO: [Node] Setting-up "_fix_surfs1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs1". 190415-23:07:11,405 nipype.workflow INFO: [Node] Cached "_fix_surfs1" - collecting precomputed outputs 190415-23:07:11,405 nipype.workflow INFO: [Node] "_fix_surfs1" found cached. 190415-23:07:11,407 nipype.workflow INFO: [Node] Setting-up "_fix_surfs2" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs2". 190415-23:07:11,408 nipype.workflow INFO: [Node] Cached "_fix_surfs2" - collecting precomputed outputs 190415-23:07:11,408 nipype.workflow INFO: [Node] "_fix_surfs2" found cached. 190415-23:07:11,410 nipype.workflow INFO: [Node] Setting-up "_fix_surfs3" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs3". 190415-23:07:11,411 nipype.workflow INFO: [Node] Cached "_fix_surfs3" - collecting precomputed outputs 190415-23:07:11,412 nipype.workflow INFO: [Node] "_fix_surfs3" found cached. 190415-23:07:11,413 nipype.workflow INFO: [Node] Setting-up "_fix_surfs4" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs4". 190415-23:07:11,414 nipype.workflow INFO: [Node] Cached "_fix_surfs4" - collecting precomputed outputs 190415-23:07:11,415 nipype.workflow INFO: [Node] "_fix_surfs4" found cached. 190415-23:07:11,416 nipype.workflow INFO: [Node] Setting-up "_fix_surfs5" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs5". 190415-23:07:11,417 nipype.workflow INFO: [Node] Cached "_fix_surfs5" - collecting precomputed outputs 190415-23:07:11,418 nipype.workflow INFO: [Node] "_fix_surfs5" found cached. 190415-23:07:11,419 nipype.workflow INFO: [Node] Setting-up "_fix_surfs6" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs6". 190415-23:07:11,421 nipype.workflow INFO: [Node] Cached "_fix_surfs6" - collecting precomputed outputs 190415-23:07:11,421 nipype.workflow INFO: [Node] "_fix_surfs6" found cached. 190415-23:07:11,423 nipype.workflow INFO: [Node] Setting-up "_fix_surfs7" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs7". 190415-23:07:11,425 nipype.workflow INFO: [Node] Cached "_fix_surfs7" - collecting precomputed outputs 190415-23:07:11,425 nipype.workflow INFO: [Node] "_fix_surfs7" found cached. 190415-23:07:11,429 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.fix_surfs". 190415-23:07:13,315 nipype.workflow INFO: [Job 252] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.fix_surfs). 190415-23:07:13,318 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 6.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_2_mni 190415-23:07:15,321 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 9 jobs ready. Free memory (GB): 6.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_2_mni 190415-23:07:15,393 nipype.workflow INFO: [Node] Setting-up "_name_surfs0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/name_surfs/mapflow/_name_surfs0". 190415-23:07:15,395 nipype.workflow INFO: [Node] Running "_name_surfs0" ("niworkflows.interfaces.surf.GiftiNameSource") 190415-23:07:15,400 nipype.workflow INFO: [Node] Finished "_name_surfs0". 190415-23:07:15,400 nipype.workflow INFO: [Job 281] Completed (_name_surfs0). 190415-23:07:15,466 nipype.workflow INFO: [Node] Setting-up "_name_surfs1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/name_surfs/mapflow/_name_surfs1". 190415-23:07:15,470 nipype.workflow INFO: [Node] Running "_name_surfs1" ("niworkflows.interfaces.surf.GiftiNameSource") 190415-23:07:15,473 nipype.workflow INFO: [Node] Finished "_name_surfs1". 190415-23:07:15,473 nipype.workflow INFO: [Job 282] Completed (_name_surfs1). 190415-23:07:15,541 nipype.workflow INFO: [Node] Setting-up "_name_surfs2" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/name_surfs/mapflow/_name_surfs2". 190415-23:07:15,543 nipype.workflow INFO: [Node] Running "_name_surfs2" ("niworkflows.interfaces.surf.GiftiNameSource") 190415-23:07:15,546 nipype.workflow INFO: [Node] Finished "_name_surfs2". 190415-23:07:15,547 nipype.workflow INFO: [Job 283] Completed (_name_surfs2). 190415-23:07:15,612 nipype.workflow INFO: [Node] Setting-up "_name_surfs3" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/name_surfs/mapflow/_name_surfs3". 190415-23:07:15,614 nipype.workflow INFO: [Node] Running "_name_surfs3" ("niworkflows.interfaces.surf.GiftiNameSource") 190415-23:07:15,618 nipype.workflow INFO: [Node] Finished "_name_surfs3". 190415-23:07:15,618 nipype.workflow INFO: [Job 284] Completed (_name_surfs3). 190415-23:07:15,685 nipype.workflow INFO: [Node] Setting-up "_name_surfs4" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/name_surfs/mapflow/_name_surfs4". 190415-23:07:15,687 nipype.workflow INFO: [Node] Running "_name_surfs4" ("niworkflows.interfaces.surf.GiftiNameSource") 190415-23:07:15,690 nipype.workflow INFO: [Node] Finished "_name_surfs4". 190415-23:07:15,691 nipype.workflow INFO: [Job 285] Completed (_name_surfs4). 190415-23:07:15,760 nipype.workflow INFO: [Node] Setting-up "_name_surfs5" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/name_surfs/mapflow/_name_surfs5". 190415-23:07:15,762 nipype.workflow INFO: [Node] Running "_name_surfs5" ("niworkflows.interfaces.surf.GiftiNameSource") 190415-23:07:15,766 nipype.workflow INFO: [Node] Finished "_name_surfs5". 190415-23:07:15,767 nipype.workflow INFO: [Job 286] Completed (_name_surfs5). 190415-23:07:15,853 nipype.workflow INFO: [Node] Setting-up "_name_surfs6" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/name_surfs/mapflow/_name_surfs6". 190415-23:07:15,856 nipype.workflow INFO: [Node] Running "_name_surfs6" ("niworkflows.interfaces.surf.GiftiNameSource") 190415-23:07:15,859 nipype.workflow INFO: [Node] Finished "_name_surfs6". 190415-23:07:15,860 nipype.workflow INFO: [Job 287] Completed (_name_surfs6). 190415-23:07:15,935 nipype.workflow INFO: [Node] Setting-up "_name_surfs7" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/name_surfs/mapflow/_name_surfs7". 190415-23:07:15,937 nipype.workflow INFO: [Node] Running "_name_surfs7" ("niworkflows.interfaces.surf.GiftiNameSource") 190415-23:07:15,941 nipype.workflow INFO: [Node] Finished "_name_surfs7". 190415-23:07:15,941 nipype.workflow INFO: [Job 288] Completed (_name_surfs7). 190415-23:07:17,323 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 6.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_2_mni 190415-23:07:17,391 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.name_surfs" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/name_surfs". 190415-23:07:17,394 nipype.workflow INFO: [Node] Setting-up "_name_surfs0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/name_surfs/mapflow/_name_surfs0". 190415-23:07:17,395 nipype.workflow INFO: [Node] Cached "_name_surfs0" - collecting precomputed outputs 190415-23:07:17,395 nipype.workflow INFO: [Node] "_name_surfs0" found cached. 190415-23:07:17,396 nipype.workflow INFO: [Node] Setting-up "_name_surfs1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/name_surfs/mapflow/_name_surfs1". 190415-23:07:17,397 nipype.workflow INFO: [Node] Cached "_name_surfs1" - collecting precomputed outputs 190415-23:07:17,398 nipype.workflow INFO: [Node] "_name_surfs1" found cached. 190415-23:07:17,399 nipype.workflow INFO: [Node] Setting-up "_name_surfs2" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/name_surfs/mapflow/_name_surfs2". 190415-23:07:17,400 nipype.workflow INFO: [Node] Cached "_name_surfs2" - collecting precomputed outputs 190415-23:07:17,401 nipype.workflow INFO: [Node] "_name_surfs2" found cached. 190415-23:07:17,402 nipype.workflow INFO: [Node] Setting-up "_name_surfs3" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/name_surfs/mapflow/_name_surfs3". 190415-23:07:17,403 nipype.workflow INFO: [Node] Cached "_name_surfs3" - collecting precomputed outputs 190415-23:07:17,403 nipype.workflow INFO: [Node] "_name_surfs3" found cached. 190415-23:07:17,404 nipype.workflow INFO: [Node] Setting-up "_name_surfs4" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/name_surfs/mapflow/_name_surfs4". 190415-23:07:17,405 nipype.workflow INFO: [Node] Cached "_name_surfs4" - collecting precomputed outputs 190415-23:07:17,406 nipype.workflow INFO: [Node] "_name_surfs4" found cached. 190415-23:07:17,407 nipype.workflow INFO: [Node] Setting-up "_name_surfs5" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/name_surfs/mapflow/_name_surfs5". 190415-23:07:17,408 nipype.workflow INFO: [Node] Cached "_name_surfs5" - collecting precomputed outputs 190415-23:07:17,408 nipype.workflow INFO: [Node] "_name_surfs5" found cached. 190415-23:07:17,409 nipype.workflow INFO: [Node] Setting-up "_name_surfs6" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/name_surfs/mapflow/_name_surfs6". 190415-23:07:17,410 nipype.workflow INFO: [Node] Cached "_name_surfs6" - collecting precomputed outputs 190415-23:07:17,410 nipype.workflow INFO: [Node] "_name_surfs6" found cached. 190415-23:07:17,412 nipype.workflow INFO: [Node] Setting-up "_name_surfs7" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/name_surfs/mapflow/_name_surfs7". 190415-23:07:17,413 nipype.workflow INFO: [Node] Cached "_name_surfs7" - collecting precomputed outputs 190415-23:07:17,413 nipype.workflow INFO: [Node] "_name_surfs7" found cached. 190415-23:07:17,416 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.name_surfs". 190415-23:07:17,416 nipype.workflow INFO: [Job 253] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.name_surfs). 190415-23:07:19,325 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 6.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_2_mni 190415-23:07:21,327 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 9 jobs ready. Free memory (GB): 6.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_2_mni 190415-23:07:21,401 nipype.workflow INFO: [Node] Setting-up "_ds_surfs0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/ds_surfs/mapflow/_ds_surfs0". 190415-23:07:21,409 nipype.workflow INFO: [Node] Running "_ds_surfs0" ("smriprep.interfaces.DerivativesDataSink") 190415-23:07:21,629 nipype.workflow INFO: [Node] Finished "_ds_surfs0". 190415-23:07:21,629 nipype.workflow INFO: [Job 289] Completed (_ds_surfs0). 190415-23:07:21,707 nipype.workflow INFO: [Node] Setting-up "_ds_surfs1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/ds_surfs/mapflow/_ds_surfs1". 190415-23:07:21,713 nipype.workflow INFO: [Node] Running "_ds_surfs1" ("smriprep.interfaces.DerivativesDataSink") 190415-23:07:21,901 nipype.workflow INFO: [Node] Finished "_ds_surfs1". 190415-23:07:21,902 nipype.workflow INFO: [Job 290] Completed (_ds_surfs1). 190415-23:07:21,985 nipype.workflow INFO: [Node] Setting-up "_ds_surfs2" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/ds_surfs/mapflow/_ds_surfs2". 190415-23:07:21,990 nipype.workflow INFO: [Node] Running "_ds_surfs2" ("smriprep.interfaces.DerivativesDataSink") 190415-23:07:22,188 nipype.workflow INFO: [Node] Finished "_ds_surfs2". 190415-23:07:22,189 nipype.workflow INFO: [Job 291] Completed (_ds_surfs2). 190415-23:07:22,276 nipype.workflow INFO: [Node] Setting-up "_ds_surfs3" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/ds_surfs/mapflow/_ds_surfs3". 190415-23:07:22,282 nipype.workflow INFO: [Node] Running "_ds_surfs3" ("smriprep.interfaces.DerivativesDataSink") 190415-23:07:22,456 nipype.workflow INFO: [Node] Finished "_ds_surfs3". 190415-23:07:22,456 nipype.workflow INFO: [Job 292] Completed (_ds_surfs3). 190415-23:07:22,536 nipype.workflow INFO: [Node] Setting-up "_ds_surfs4" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/ds_surfs/mapflow/_ds_surfs4". 190415-23:07:22,543 nipype.workflow INFO: [Node] Running "_ds_surfs4" ("smriprep.interfaces.DerivativesDataSink") 190415-23:07:22,738 nipype.workflow INFO: [Node] Finished "_ds_surfs4". 190415-23:07:22,739 nipype.workflow INFO: [Job 293] Completed (_ds_surfs4). 190415-23:07:22,824 nipype.workflow INFO: [Node] Setting-up "_ds_surfs5" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/ds_surfs/mapflow/_ds_surfs5". 190415-23:07:22,830 nipype.workflow INFO: [Node] Running "_ds_surfs5" ("smriprep.interfaces.DerivativesDataSink") 190415-23:07:23,45 nipype.workflow INFO: [Node] Finished "_ds_surfs5". 190415-23:07:23,46 nipype.workflow INFO: [Job 294] Completed (_ds_surfs5). 190415-23:07:23,124 nipype.workflow INFO: [Node] Setting-up "_ds_surfs6" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/ds_surfs/mapflow/_ds_surfs6". 190415-23:07:23,131 nipype.workflow INFO: [Node] Running "_ds_surfs6" ("smriprep.interfaces.DerivativesDataSink") 190415-23:07:23,326 nipype.workflow INFO: [Node] Finished "_ds_surfs6". 190415-23:07:23,327 nipype.workflow INFO: [Job 295] Completed (_ds_surfs6). 190415-23:07:23,412 nipype.workflow INFO: [Node] Setting-up "_ds_surfs7" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/ds_surfs/mapflow/_ds_surfs7". 190415-23:07:23,414 nipype.workflow INFO: [Node] Running "_ds_surfs7" ("smriprep.interfaces.DerivativesDataSink") 190415-23:07:23,562 nipype.workflow INFO: [Node] Finished "_ds_surfs7". 190415-23:07:23,562 nipype.workflow INFO: [Job 296] Completed (_ds_surfs7). 190415-23:07:23,633 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 6.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_2_mni 190415-23:07:23,707 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_surfs" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/ds_surfs". 190415-23:07:23,712 nipype.workflow INFO: [Node] Setting-up "_ds_surfs0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/ds_surfs/mapflow/_ds_surfs0". 190415-23:07:23,719 nipype.workflow INFO: [Node] Running "_ds_surfs0" ("smriprep.interfaces.DerivativesDataSink") 190415-23:07:23,869 nipype.workflow INFO: [Node] Finished "_ds_surfs0". 190415-23:07:23,871 nipype.workflow INFO: [Node] Setting-up "_ds_surfs1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/ds_surfs/mapflow/_ds_surfs1". 190415-23:07:23,878 nipype.workflow INFO: [Node] Running "_ds_surfs1" ("smriprep.interfaces.DerivativesDataSink") 190415-23:07:24,18 nipype.workflow INFO: [Node] Finished "_ds_surfs1". 190415-23:07:24,21 nipype.workflow INFO: [Node] Setting-up "_ds_surfs2" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/ds_surfs/mapflow/_ds_surfs2". 190415-23:07:24,29 nipype.workflow INFO: [Node] Running "_ds_surfs2" ("smriprep.interfaces.DerivativesDataSink") 190415-23:07:24,235 nipype.workflow INFO: [Node] Finished "_ds_surfs2". 190415-23:07:24,237 nipype.workflow INFO: [Node] Setting-up "_ds_surfs3" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/ds_surfs/mapflow/_ds_surfs3". 190415-23:07:24,247 nipype.workflow INFO: [Node] Running "_ds_surfs3" ("smriprep.interfaces.DerivativesDataSink") 190415-23:07:24,429 nipype.workflow INFO: [Node] Finished "_ds_surfs3". 190415-23:07:24,432 nipype.workflow INFO: [Node] Setting-up "_ds_surfs4" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/ds_surfs/mapflow/_ds_surfs4". 190415-23:07:24,441 nipype.workflow INFO: [Node] Running "_ds_surfs4" ("smriprep.interfaces.DerivativesDataSink") 190415-23:07:24,626 nipype.workflow INFO: [Node] Finished "_ds_surfs4". 190415-23:07:24,628 nipype.workflow INFO: [Node] Setting-up "_ds_surfs5" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/ds_surfs/mapflow/_ds_surfs5". 190415-23:07:24,646 nipype.workflow INFO: [Node] Running "_ds_surfs5" ("smriprep.interfaces.DerivativesDataSink") 190415-23:07:24,802 nipype.workflow INFO: [Node] Finished "_ds_surfs5". 190415-23:07:24,804 nipype.workflow INFO: [Node] Setting-up "_ds_surfs6" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/ds_surfs/mapflow/_ds_surfs6". 190415-23:07:24,811 nipype.workflow INFO: [Node] Running "_ds_surfs6" ("smriprep.interfaces.DerivativesDataSink") 190415-23:07:24,989 nipype.workflow INFO: [Node] Finished "_ds_surfs6". 190415-23:07:24,991 nipype.workflow INFO: [Node] Setting-up "_ds_surfs7" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/ds_surfs/mapflow/_ds_surfs7". 190415-23:07:24,998 nipype.workflow INFO: [Node] Running "_ds_surfs7" ("smriprep.interfaces.DerivativesDataSink") 190415-23:07:25,171 nipype.workflow INFO: [Node] Finished "_ds_surfs7". 190415-23:07:25,195 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_surfs". 190415-23:07:25,195 nipype.workflow INFO: [Job 254] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_surfs). 190415-23:07:25,633 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 6.77/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_2_mni 190415-23:52:13,560 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_2_mni". 190415-23:52:15,183 nipype.workflow INFO: [Job 141] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.t1_2_mni). 190415-23:52:15,186 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 10 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-23:52:15,258 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.bbregister" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/bbregister". 190415-23:52:15,264 nipype.workflow INFO: [Node] Running "bbregister" ("niworkflows.interfaces.freesurfer.PatchedBBRegisterRPT"), a CommandLine Interface with command: bbregister --t2 --6 --init-reg /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/mri_coreg/registration.lta --lta /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked_bbreg_sub-NC080001.lta --reg /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked_bbreg_sub-NC080001.dat --o /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked_bbreg.nii.gz --mov /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked.nii.gz --s sub-NC080001 190415-23:52:17,186 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 11 jobs ready. Free memory (GB): 0.00/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.bbregister 190415-23:52:49,238 nipype.interface INFO: stdout 2019-04-15T23:52:49.238010: 190415-23:52:49,238 nipype.interface INFO: stdout 2019-04-15T23:52:49.238010:Matrix from LTA: 190415-23:52:49,238 nipype.interface INFO: stdout 2019-04-15T23:52:49.238010: 0.99971 -0.02420 0.00090 2.60037; 190415-23:52:49,238 nipype.interface INFO: stdout 2019-04-15T23:52:49.238010: 0.00295 0.15839 0.98737 -4.00560; 190415-23:52:49,238 nipype.interface INFO: stdout 2019-04-15T23:52:49.238010:-0.02403 -0.98708 0.15842 -0.63927; 190415-23:52:49,239 nipype.interface INFO: stdout 2019-04-15T23:52:49.238010: 0.00000 0.00000 0.00000 1.00000; 190415-23:52:49,355 nipype.interface INFO: stdout 2019-04-15T23:52:49.355594: 190415-23:52:49,355 nipype.interface INFO: stdout 2019-04-15T23:52:49.355594:/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked.nii.gz /out/freesurfer/sub-NC080001/mri/brainmask.mgz 190415-23:52:49,355 nipype.interface INFO: stdout 2019-04-15T23:52:49.355594:movvol /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked.nii.gz 190415-23:52:49,356 nipype.interface INFO: stdout 2019-04-15T23:52:49.355594:targvol /out/freesurfer/sub-NC080001/mri/brainmask.mgz 190415-23:52:49,356 nipype.interface INFO: stdout 2019-04-15T23:52:49.355594:outvol /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked_warped.nii.gz 190415-23:52:49,356 nipype.interface INFO: stdout 2019-04-15T23:52:49.355594:regfile /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked_bbreg_sub-NC080001.lta 190415-23:52:49,356 nipype.interface INFO: stdout 2019-04-15T23:52:49.355594:invert 0 190415-23:52:49,356 nipype.interface INFO: stdout 2019-04-15T23:52:49.355594:tal 0 190415-23:52:49,356 nipype.interface INFO: stdout 2019-04-15T23:52:49.355594:talres 2 190415-23:52:49,356 nipype.interface INFO: stdout 2019-04-15T23:52:49.355594:regheader 0 190415-23:52:49,356 nipype.interface INFO: stdout 2019-04-15T23:52:49.355594:noresample 0 190415-23:52:49,356 nipype.interface INFO: stdout 2019-04-15T23:52:49.355594:interp nearest (0) 190415-23:52:49,356 nipype.interface INFO: stdout 2019-04-15T23:52:49.355594:precision float (3) 190415-23:52:49,357 nipype.interface INFO: stdout 2019-04-15T23:52:49.355594:Gdiag_no -1 190415-23:52:49,357 nipype.interface INFO: stdout 2019-04-15T23:52:49.355594:Synth 0 190415-23:52:49,357 nipype.interface INFO: stdout 2019-04-15T23:52:49.355594:SynthSeed 1555666351 190415-23:52:49,357 nipype.interface INFO: stdout 2019-04-15T23:52:49.355594: 190415-23:52:49,357 nipype.interface INFO: stdout 2019-04-15T23:52:49.355594:Final tkRAS-to-tkRAS Matrix is: 190415-23:52:49,357 nipype.interface INFO: stdout 2019-04-15T23:52:49.355594: 0.99971 -0.02420 0.00090 2.60039; 190415-23:52:49,357 nipype.interface INFO: stdout 2019-04-15T23:52:49.355594: 0.00295 0.15839 0.98737 -4.00559; 190415-23:52:49,357 nipype.interface INFO: stdout 2019-04-15T23:52:49.355594:-0.02403 -0.98708 0.15842 -0.63925; 190415-23:52:49,357 nipype.interface INFO: stdout 2019-04-15T23:52:49.355594: 0.00000 0.00000 0.00000 1.00000; 190415-23:52:49,357 nipype.interface INFO: stdout 2019-04-15T23:52:49.355594: 190415-23:52:49,357 nipype.interface INFO: stdout 2019-04-15T23:52:49.355594: 190415-23:52:49,358 nipype.interface INFO: stdout 2019-04-15T23:52:49.355594:Vox2Vox Matrix is: 190415-23:52:49,358 nipype.interface INFO: stdout 2019-04-15T23:52:49.355594: 0.29082 0.00026 0.00704 -6.91640; 190415-23:52:49,358 nipype.interface INFO: stdout 2019-04-15T23:52:49.355594:-0.00699 0.04609 0.28715 -9.57322; 190415-23:52:49,358 nipype.interface INFO: stdout 2019-04-15T23:52:49.355594:-0.00064 -0.21465 0.03443 38.77849; 190415-23:52:49,358 nipype.interface INFO: stdout 2019-04-15T23:52:49.355594: 0.00000 0.00000 0.00000 1.00000; 190415-23:52:49,883 nipype.interface INFO: stdout 2019-04-15T23:52:49.883390: 190415-23:52:49,883 nipype.interface INFO: stdout 2019-04-15T23:52:49.883390:Resampling 190415-23:52:49,883 nipype.interface INFO: stdout 2019-04-15T23:52:49.883390:Output registration matrix is identity 190415-23:52:49,883 nipype.interface INFO: stdout 2019-04-15T23:52:49.883390: 190415-23:52:49,883 nipype.interface INFO: stdout 2019-04-15T23:52:49.883390:mri_vol2vol done 190415-23:53:02,481 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.bbregister". 190415-23:53:03,194 nipype.workflow INFO: [Job 120] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.bbregister). 190415-23:53:03,198 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 13 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-23:53:03,269 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.reports" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/reports". 190415-23:53:03,271 nipype.workflow INFO: [Node] Running "reports" ("nipype.interfaces.utility.base.Merge") 190415-23:53:03,274 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.reports". 190415-23:53:03,274 nipype.workflow INFO: [Job 121] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.reports). 190415-23:53:03,336 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.transforms" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/transforms". 190415-23:53:03,338 nipype.workflow INFO: [Node] Running "transforms" ("nipype.interfaces.utility.base.Merge") 190415-23:53:03,342 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.transforms". 190415-23:53:03,343 nipype.workflow INFO: [Job 122] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.transforms). 190415-23:53:03,412 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_reports_wf.ds_t1_2_mni_report" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_reports_wf/ds_t1_2_mni_report". 190415-23:53:03,414 nipype.workflow INFO: [Node] Running "ds_t1_2_mni_report" ("smriprep.interfaces.DerivativesDataSink") 190415-23:53:03,418 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_reports_wf.ds_t1_2_mni_report". 190415-23:53:03,418 nipype.workflow INFO: [Job 142] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_reports_wf.ds_t1_2_mni_report). 190415-23:53:03,487 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_mni" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/ds_t1_mni". 190415-23:53:03,489 nipype.workflow INFO: [Node] Running "ds_t1_mni" ("smriprep.interfaces.DerivativesDataSink") 190415-23:53:04,600 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_mni". 190415-23:53:04,600 nipype.workflow INFO: [Job 143] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_mni). 190415-23:53:04,664 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_mni_inv_warp" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/ds_t1_mni_inv_warp". 190415-23:53:04,667 nipype.workflow INFO: [Node] Running "ds_t1_mni_inv_warp" ("smriprep.interfaces.DerivativesDataSink") 190415-23:53:07,664 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_mni_inv_warp". 190415-23:53:07,664 nipype.workflow INFO: [Job 144] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_mni_inv_warp). 190415-23:53:07,729 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_mni_warp" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/ds_t1_mni_warp". 190415-23:53:07,731 nipype.workflow INFO: [Node] Running "ds_t1_mni_warp" ("smriprep.interfaces.DerivativesDataSink") 190415-23:53:11,4 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_mni_warp". 190415-23:53:11,4 nipype.workflow INFO: [Job 145] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_t1_mni_warp). 190415-23:53:11,69 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.aparc_mni_tfm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/aparc_mni_tfm". 190415-23:53:11,72 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.aseg_mni_tfm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/aseg_mni_tfm". 190415-23:53:11,74 nipype.workflow INFO: [Node] Running "aparc_mni_tfm" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/tonii/aparc+aseg_vol_out.nii.gz --interpolation MultiLabel --output aparc+aseg_vol_out_trans.nii.gz --reference-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/gen_ref/tpl-MNI152NLin2009cAsym_res-01_T1w_reference.nii.gz --transform /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/t1_2_mni/ants_t1_to_mniComposite.h5190415-23:53:11,74 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_mask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/mni_mask". 190415-23:53:11,76 nipype.workflow INFO: [Node] Running "aseg_mni_tfm" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonii/aseg_vol_out.nii.gz --interpolation MultiLabel --output aseg_vol_out_trans.nii.gz --reference-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/gen_ref/tpl-MNI152NLin2009cAsym_res-01_T1w_reference.nii.gz --transform /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/t1_2_mni/ants_t1_to_mniComposite.h5 190415-23:53:11,77 nipype.workflow INFO: [Node] Running "mni_mask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/refine/sub-NC080001_T1w_ras_maths_corrected_rbrainmask.nii.gz --interpolation MultiLabel --output sub-NC080001_T1w_ras_maths_corrected_rbrainmask_trans.nii.gz --reference-image /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz --transform /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/t1_2_mni/ants_t1_to_mniComposite.h5 190415-23:53:11,81 nipype.workflow INFO: [MultiProc] Running 6 tasks, and 2 jobs ready. Free memory (GB): 5.97/8.77, Free processors: 0/6. Currently running: * _mni_tpms1 * _mni_tpms0 * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_seg * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_mask * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.aseg_mni_tfm * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.aparc_mni_tfm 190415-23:53:11,83 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_seg" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/mni_seg". 190415-23:53:11,84 nipype.workflow INFO: [Node] Setting-up "_mni_tpms1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/mni_tpms/mapflow/_mni_tpms1". 190415-23:53:11,86 nipype.workflow INFO: [Node] Setting-up "_mni_tpms0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/mni_tpms/mapflow/_mni_tpms0". 190415-23:53:11,87 nipype.workflow INFO: [Node] Running "mni_seg" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/t1_seg/sub-NC080001_T1w_ras_maths_corrected_masked_seg.nii.gz --interpolation MultiLabel --output sub-NC080001_T1w_ras_maths_corrected_masked_seg_trans.nii.gz --reference-image /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz --transform /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/t1_2_mni/ants_t1_to_mniComposite.h5 190415-23:53:11,89 nipype.workflow INFO: [Node] Running "_mni_tpms1" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/t1_seg/sub-NC080001_T1w_ras_maths_corrected_masked_prob_1.nii.gz --interpolation Linear --output sub-NC080001_T1w_ras_maths_corrected_masked_prob_1_trans.nii.gz --reference-image /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz --transform /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/t1_2_mni/ants_t1_to_mniComposite.h5 190415-23:53:11,90 nipype.workflow INFO: [Node] Running "_mni_tpms0" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/t1_seg/sub-NC080001_T1w_ras_maths_corrected_masked_prob_0.nii.gz --interpolation Linear --output sub-NC080001_T1w_ras_maths_corrected_masked_prob_0_trans.nii.gz --reference-image /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz --transform /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/t1_2_mni/ants_t1_to_mniComposite.h5 190415-23:53:13,703 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.aseg_mni_tfm". 190415-23:53:13,722 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.aparc_mni_tfm". 190415-23:53:14,357 nipype.workflow INFO: [Node] Finished "_mni_tpms1". 190415-23:53:14,415 nipype.workflow INFO: [Node] Finished "_mni_tpms0". 190415-23:53:15,86 nipype.workflow INFO: [Job 146] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.aparc_mni_tfm). 190415-23:53:15,87 nipype.workflow INFO: [Job 148] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.aseg_mni_tfm). 190415-23:53:15,88 nipype.workflow INFO: [Job 297] Completed (_mni_tpms0). 190415-23:53:15,89 nipype.workflow INFO: [Job 298] Completed (_mni_tpms1). 190415-23:53:15,91 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 4 jobs ready. Free memory (GB): 8.37/8.77, Free processors: 4/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_seg * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_mask 190415-23:53:15,160 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.func_derivatives_wf.ds_bold_aparc_mni" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/func_derivatives_wf/ds_bold_aparc_mni". 190415-23:53:15,162 nipype.workflow INFO: [Node] Running "ds_bold_aparc_mni" ("fmriprep.interfaces.DerivativesDataSink") 190415-23:53:15,239 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.func_derivatives_wf.ds_bold_aparc_mni". 190415-23:53:15,239 nipype.workflow INFO: [Job 147] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.func_derivatives_wf.ds_bold_aparc_mni). 190415-23:53:15,303 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.func_derivatives_wf.ds_bold_aseg_mni" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/func_derivatives_wf/ds_bold_aseg_mni". 190415-23:53:15,306 nipype.workflow INFO: [Node] Running "ds_bold_aseg_mni" ("fmriprep.interfaces.DerivativesDataSink") 190415-23:53:15,396 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.func_derivatives_wf.ds_bold_aseg_mni". 190415-23:53:15,396 nipype.workflow INFO: [Job 149] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.func_derivatives_wf.ds_bold_aseg_mni). 190415-23:53:15,457 nipype.workflow INFO: [Node] Setting-up "_mni_tpms2" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/mni_tpms/mapflow/_mni_tpms2". 190415-23:53:15,460 nipype.workflow INFO: [Node] Running "_mni_tpms2" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/t1_seg/sub-NC080001_T1w_ras_maths_corrected_masked_prob_2.nii.gz --interpolation Linear --output sub-NC080001_T1w_ras_maths_corrected_masked_prob_2_trans.nii.gz --reference-image /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz --transform /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/t1_2_mni/ants_t1_to_mniComposite.h5 190415-23:53:17,90 nipype.workflow INFO: [MultiProc] Running 3 tasks, and 2 jobs ready. Free memory (GB): 8.17/8.77, Free processors: 3/6. Currently running: * _mni_tpms2 * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_seg * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_mask 190415-23:53:17,197 nipype.workflow INFO: [Node] Setting-up "_lta_ras2ras1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/lta_ras2ras/mapflow/_lta_ras2ras1". 190415-23:53:17,199 nipype.workflow INFO: [Node] Setting-up "_lta_ras2ras0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/lta_ras2ras/mapflow/_lta_ras2ras0". 190415-23:53:17,199 nipype.workflow INFO: [Node] Running "_lta_ras2ras1" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command: lta_convert --inlta /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/mri_coreg/registration.lta --outlta /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/lta_ras2ras/mapflow/_lta_ras2ras1/out.lta 190415-23:53:17,202 nipype.workflow INFO: [Node] Running "_lta_ras2ras0" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command: lta_convert --inlta /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked_bbreg_sub-NC080001.lta --outlta /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/lta_ras2ras/mapflow/_lta_ras2ras0/out.lta 190415-23:53:17,276 nipype.workflow INFO: [Node] Finished "_lta_ras2ras1". 190415-23:53:17,289 nipype.workflow INFO: [Node] Finished "_lta_ras2ras0". 190415-23:53:18,389 nipype.workflow INFO: [Node] Finished "_mni_tpms2". 190415-23:53:19,91 nipype.workflow INFO: [Job 299] Completed (_mni_tpms2). 190415-23:53:19,92 nipype.workflow INFO: [Job 300] Completed (_lta_ras2ras0). 190415-23:53:19,93 nipype.workflow INFO: [Job 301] Completed (_lta_ras2ras1). 190415-23:53:19,95 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 2 jobs ready. Free memory (GB): 8.37/8.77, Free processors: 4/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_seg * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_mask 190415-23:53:19,158 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.lta_ras2ras" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/lta_ras2ras". 190415-23:53:19,161 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_tpms" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/mni_tpms". 190415-23:53:19,163 nipype.workflow INFO: [Node] Setting-up "_lta_ras2ras0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/lta_ras2ras/mapflow/_lta_ras2ras0". 190415-23:53:19,164 nipype.workflow INFO: [Node] Cached "_lta_ras2ras0" - collecting precomputed outputs 190415-23:53:19,165 nipype.workflow INFO: [Node] "_lta_ras2ras0" found cached. 190415-23:53:19,165 nipype.workflow INFO: [Node] Setting-up "_mni_tpms0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/mni_tpms/mapflow/_mni_tpms0". 190415-23:53:19,167 nipype.workflow INFO: [Node] Cached "_mni_tpms0" - collecting precomputed outputs 190415-23:53:19,167 nipype.workflow INFO: [Node] "_mni_tpms0" found cached. 190415-23:53:19,167 nipype.workflow INFO: [Node] Setting-up "_lta_ras2ras1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/lta_ras2ras/mapflow/_lta_ras2ras1". 190415-23:53:19,168 nipype.workflow INFO: [Node] Setting-up "_mni_tpms1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/mni_tpms/mapflow/_mni_tpms1". 190415-23:53:19,169 nipype.workflow INFO: [Node] Cached "_lta_ras2ras1" - collecting precomputed outputs 190415-23:53:19,169 nipype.workflow INFO: [Node] Cached "_mni_tpms1" - collecting precomputed outputs 190415-23:53:19,169 nipype.workflow INFO: [Node] "_mni_tpms1" found cached. 190415-23:53:19,169 nipype.workflow INFO: [Node] "_lta_ras2ras1" found cached. 190415-23:53:19,170 nipype.workflow INFO: [Node] Setting-up "_mni_tpms2" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/mni_tpms/mapflow/_mni_tpms2". 190415-23:53:19,172 nipype.workflow INFO: [Node] Cached "_mni_tpms2" - collecting precomputed outputs 190415-23:53:19,172 nipype.workflow INFO: [Node] "_mni_tpms2" found cached. 190415-23:53:19,172 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.lta_ras2ras". 190415-23:53:19,174 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_tpms". 190415-23:53:21,96 nipype.workflow INFO: [Job 123] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.lta_ras2ras). 190415-23:53:21,97 nipype.workflow INFO: [Job 242] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_tpms). 190415-23:53:21,100 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 2 jobs ready. Free memory (GB): 8.37/8.77, Free processors: 4/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_seg * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_mask 190415-23:53:21,160 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.compare_transforms" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/compare_transforms". 190415-23:53:21,162 nipype.workflow INFO: [Node] Running "compare_transforms" ("nipype.interfaces.utility.wrappers.Function") 190415-23:53:21,164 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_mni_tpms" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/ds_mni_tpms". 190415-23:53:21,167 nipype.workflow INFO: [Node] Running "ds_mni_tpms" ("smriprep.interfaces.DerivativesDataSink") 190415-23:53:21,180 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.compare_transforms". 190415-23:53:24,173 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_mni_tpms". 190415-23:53:24,173 nipype.workflow INFO: [Job 243] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_mni_tpms). 190415-23:53:24,232 nipype.workflow INFO: [Job 124] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.compare_transforms). 190415-23:53:24,235 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 2 jobs ready. Free memory (GB): 8.37/8.77, Free processors: 4/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_seg * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_mask Captured warning (): In future, it will be an error for 'np.bool_' scalars to be interpreted as an index 190415-23:53:24,298 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.select_report" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/select_report". 190415-23:53:24,299 nipype.workflow INFO: [Node] Running "select_report" ("nipype.interfaces.utility.base.Select") 190415-23:53:24,303 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.select_report". 190415-23:53:24,303 nipype.workflow INFO: [Job 125] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.select_report). 190415-23:53:24,365 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.select_transform" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/select_transform". 190415-23:53:24,368 nipype.workflow INFO: [Node] Running "select_transform" ("nipype.interfaces.utility.base.Select") 190415-23:53:24,372 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.select_transform". 190415-23:53:24,372 nipype.workflow INFO: [Job 127] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.select_transform). 190415-23:53:26,235 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 2 jobs ready. Free memory (GB): 8.37/8.77, Free processors: 4/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_seg * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_mask 190415-23:53:26,297 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.ds_report_reg" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/ds_report_reg". 190415-23:53:26,299 nipype.workflow INFO: [Node] Running "ds_report_reg" ("fmriprep.interfaces.DerivativesDataSink") 190415-23:53:26,304 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.ds_report_reg". 190415-23:53:26,304 nipype.workflow INFO: [Job 126] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.ds_report_reg). 190415-23:53:26,366 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.lta_concat" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/lta_concat". 190415-23:53:26,369 nipype.workflow INFO: [Node] Running "lta_concat" ("niworkflows.interfaces.freesurfer.PatchedConcatenateLTA"), a CommandLine Interface with command: mri_concatenate_lta /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked_bbreg_sub-NC080001.lta /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/fsnative_2_t1_xfm/T1_robustreg.lta out.lta 190415-23:53:26,442 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.lta_concat". 190415-23:53:28,237 nipype.workflow INFO: [Job 128] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.lta_concat). 190415-23:53:28,240 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 2 jobs ready. Free memory (GB): 8.37/8.77, Free processors: 4/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_seg * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_mask 190415-23:53:28,297 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.lta2fsl_inv" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/lta2fsl_inv". 190415-23:53:28,299 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.lta2fsl_fwd" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/lta2fsl_fwd". 190415-23:53:28,300 nipype.workflow INFO: [Node] Running "lta2fsl_inv" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command: lta_convert --inlta /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/lta_concat/out.lta --invert --outfsl /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/lta2fsl_inv/out.mat 190415-23:53:28,301 nipype.workflow INFO: [Node] Running "lta2fsl_fwd" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command: lta_convert --inlta /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/lta_concat/out.lta --outfsl /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/lta2fsl_fwd/out.mat 190415-23:53:28,380 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.lta2fsl_inv". 190415-23:53:28,386 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.lta2fsl_fwd". 190415-23:53:30,240 nipype.workflow INFO: [Job 129] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.lta2fsl_inv). 190415-23:53:30,242 nipype.workflow INFO: [Job 130] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.lta2fsl_fwd). 190415-23:53:30,244 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 2 jobs ready. Free memory (GB): 8.37/8.77, Free processors: 4/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_seg * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_mask 190415-23:53:30,303 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.fsl2itk_inv" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/fsl2itk_inv". 190415-23:53:30,305 nipype.workflow INFO: [Node] Running "fsl2itk_inv" ("nipype.interfaces.c3.C3dAffineTool"), a CommandLine Interface with command: c3d_affine_tool -ref /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz -src /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/applyrefined/sub-NC080001_T1w_ras_maths_corrected_masked.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/lta2fsl_inv/out.mat -fsl2ras -oitk /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/fsl2itk_inv/affine.txt 190415-23:53:30,309 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.fsl2itk_fwd" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/fsl2itk_fwd". 190415-23:53:30,312 nipype.workflow INFO: [Node] Running "fsl2itk_fwd" ("nipype.interfaces.c3.C3dAffineTool"), a CommandLine Interface with command: c3d_affine_tool -ref /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/applyrefined/sub-NC080001_T1w_ras_maths_corrected_masked.nii.gz -src /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/lta2fsl_fwd/out.mat -fsl2ras -oitk /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/fsl2itk_fwd/affine.txt 190415-23:53:30,625 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.fsl2itk_inv". 190415-23:53:30,629 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.fsl2itk_fwd". 190415-23:53:32,245 nipype.workflow INFO: [Job 156] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.fsl2itk_inv). 190415-23:53:32,247 nipype.workflow INFO: [Job 159] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_reg_wf.bbreg_wf.fsl2itk_fwd). 190415-23:53:32,249 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 9 jobs ready. Free memory (GB): 8.37/8.77, Free processors: 4/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_seg * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_mask 190415-23:53:32,309 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.carpetplot_wf.mrg_xfms" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/carpetplot_wf/mrg_xfms". 190415-23:53:32,311 nipype.workflow INFO: [Node] Running "mrg_xfms" ("nipype.interfaces.utility.base.Merge") 190415-23:53:32,314 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.carpetplot_wf.mrg_xfms". 190415-23:53:32,316 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.merge_xforms" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/merge_xforms". 190415-23:53:32,318 nipype.workflow INFO: [Node] Running "merge_xforms" ("nipype.interfaces.utility.base.Merge") 190415-23:53:32,321 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.merge_xforms". 190415-23:53:32,321 nipype.workflow INFO: [Job 160] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.merge_xforms). 190415-23:53:32,386 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.mask_t1w_tfm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/mask_t1w_tfm".190415-23:53:32,386 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.merge_xforms" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/merge_xforms". 190415-23:53:32,389 nipype.workflow INFO: [Node] Running "merge_xforms" ("nipype.interfaces.utility.base.Merge") 190415-23:53:32,393 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.merge_xforms". 190415-23:53:32,393 nipype.workflow INFO: [Job 188] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.merge_xforms). 190415-23:53:32,394 nipype.workflow INFO: [Node] Running "mask_t1w_tfm" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_valid_corrected_brain_mask_maths.nii.gz --interpolation MultiLabel --output ref_image_valid_corrected_brain_mask_maths_trans.nii.gz --reference-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/gen_ref/sub-NC080001_T1w_ras_maths_corrected_masked_reference.nii.gz --transform /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/fsl2itk_fwd/affine.txt 190415-23:53:32,457 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.mask_merge_tfms" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/mask_merge_tfms". 190415-23:53:32,459 nipype.workflow INFO: [Node] Running "mask_merge_tfms" ("nipype.interfaces.utility.base.Merge") 190415-23:53:32,462 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.mask_merge_tfms". 190415-23:53:32,462 nipype.workflow INFO: [Job 195] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.mask_merge_tfms). 190415-23:53:32,527 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.wm_tfm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/wm_tfm". 190415-23:53:32,530 nipype.workflow INFO: [Node] Running "wm_tfm" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/wm_roi/sub-NC080001_T1w_ras_maths_corrected_masked_prob_2_roi.nii.gz --interpolation NearestNeighbor --output sub-NC080001_T1w_ras_maths_corrected_masked_prob_2_roi_trans.nii.gz --reference-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_valid_corrected_brain_mask_maths.nii.gz --transform /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/fsl2itk_inv/affine.txt 190415-23:53:32,532 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.tcc_tfm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/tcc_tfm". 190415-23:53:32,535 nipype.workflow INFO: [Node] Running "tcc_tfm" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/csf_roi/sub-NC080001_T1w_ras_maths_corrected_rbrainmask_eroded.nii.gz --interpolation NearestNeighbor --output sub-NC080001_T1w_ras_maths_corrected_rbrainmask_eroded_trans.nii.gz --reference-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_valid_corrected_brain_mask_maths.nii.gz --transform /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/fsl2itk_inv/affine.txt 190415-23:53:32,695 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.wm_tfm". 190415-23:53:32,707 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.tcc_tfm". 190415-23:53:33,216 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.mask_t1w_tfm". 190415-23:53:34,214 nipype.workflow INFO: [Job 157] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.carpetplot_wf.mrg_xfms). 190415-23:53:34,216 nipype.workflow INFO: [Job 175] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.mask_t1w_tfm). 190415-23:53:34,216 nipype.workflow INFO: [Job 216] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.wm_tfm). 190415-23:53:34,217 nipype.workflow INFO: [Job 219] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.tcc_tfm). 190415-23:53:34,220 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 9 jobs ready. Free memory (GB): 8.37/8.77, Free processors: 4/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_seg * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_mask 190415-23:53:34,280 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.carpetplot_wf.resample_parc" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/carpetplot_wf/resample_parc". 190415-23:53:34,280 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 190415-23:53:34,282 nipype.workflow INFO: [Node] Running "resample_parc" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /opt/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_desc-carpet_dseg.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-01_desc-carpet_dseg_trans.nii.gz --reference-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_valid_corrected_brain_mask_maths.nii.gz --transform /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/fsl2itk_inv/affine.txt --transform /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/t1_2_mni/ants_t1_to_mniInverseComposite.h5 190415-23:53:34,283 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/mask_t1w_tfm/ref_image_valid_corrected_brain_mask_maths_trans.nii.gz -kernel sphere 3.0000 -dilF /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/ref_image_valid_corrected_brain_mask_maths_trans_dil.nii.gz 190415-23:53:34,288 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.mask_mni_tfm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/mask_mni_tfm". 190415-23:53:34,291 nipype.workflow INFO: [Node] Running "mask_mni_tfm" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_valid_corrected_brain_mask_maths.nii.gz --interpolation MultiLabel --output ref_image_valid_corrected_brain_mask_maths_trans.nii.gz --reference-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/gen_ref/tpl-MNI152NLin2009cAsym_res-01_T1w_reference.nii.gz --transform /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/t1_2_mni/ants_t1_to_mniComposite.h5 --transform /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/fsl2itk_fwd/affine.txt 190415-23:53:34,300 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.wm_msk" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/wm_msk". 190415-23:53:34,302 nipype.workflow INFO: [Node] Running "wm_msk" ("nipype.interfaces.utility.wrappers.Function") 190415-23:53:34,331 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.wm_msk". 190415-23:53:34,396 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190415-23:53:35,657 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.carpetplot_wf.resample_parc". 190415-23:53:36,98 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.mask_mni_tfm". 190415-23:53:36,218 nipype.workflow INFO: [Job 158] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.carpetplot_wf.resample_parc). 190415-23:53:36,219 nipype.workflow INFO: [Job 176] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate). 190415-23:53:36,220 nipype.workflow INFO: [Job 196] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.mask_mni_tfm). 190415-23:53:36,221 nipype.workflow INFO: [Job 217] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.wm_msk). 190415-23:53:36,223 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 7 jobs ready. Free memory (GB): 8.37/8.77, Free processors: 4/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_seg * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_mask 190415-23:53:36,289 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.func_derivatives_wf.ds_bold_mask_mni" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/func_derivatives_wf/ds_bold_mask_mni". 190415-23:53:36,291 nipype.workflow INFO: [Node] Running "ds_bold_mask_mni" ("fmriprep.interfaces.DerivativesDataSink") 190415-23:53:36,368 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.func_derivatives_wf.ds_bold_mask_mni". 190415-23:53:36,369 nipype.workflow INFO: [Job 197] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.func_derivatives_wf.ds_bold_mask_mni). 190415-23:53:36,430 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 190415-23:53:36,431 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.tcc_msk" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/tcc_msk". 190415-23:53:36,434 nipype.workflow INFO: [Node] Running "tcc_msk" ("nipype.interfaces.utility.wrappers.Function") 190415-23:53:36,434 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/mask_mni_tfm/ref_image_valid_corrected_brain_mask_maths_trans.nii.gz -kernel sphere 3.0000 -dilF /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/ref_image_valid_corrected_brain_mask_maths_trans_dil.nii.gz 190415-23:53:36,438 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.acc_tfm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/acc_tfm". 190415-23:53:36,438 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.csf_tfm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/csf_tfm". 190415-23:53:36,441 nipype.workflow INFO: [Node] Running "csf_tfm" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/csf_roi/sub-NC080001_T1w_ras_maths_corrected_masked_prob_0_roi.nii.gz --interpolation NearestNeighbor --output sub-NC080001_T1w_ras_maths_corrected_masked_prob_0_roi_trans.nii.gz --reference-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_valid_corrected_brain_mask_maths.nii.gz --transform /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/fsl2itk_inv/affine.txt 190415-23:53:36,441 nipype.workflow INFO: [Node] Running "acc_tfm" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/acc_roi/sub-NC080001_T1w_ras_maths_corrected_masked_prob_0_tpmsum_roi.nii.gz --interpolation NearestNeighbor --output sub-NC080001_T1w_ras_maths_corrected_masked_prob_0_tpmsum_roi_trans.nii.gz --reference-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_valid_corrected_brain_mask_maths.nii.gz --transform /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_reg_wf/bbreg_wf/fsl2itk_inv/affine.txt 190415-23:53:36,458 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.tcc_msk". 190415-23:53:36,608 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190415-23:53:36,635 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.csf_tfm". 190415-23:53:36,641 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.acc_tfm". 190415-23:53:38,219 nipype.workflow INFO: [Job 198] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate). 190415-23:53:38,221 nipype.workflow INFO: [Job 220] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.tcc_msk). 190415-23:53:38,222 nipype.workflow INFO: [Job 222] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.csf_tfm). 190415-23:53:38,224 nipype.workflow INFO: [Job 228] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.acc_tfm). 190415-23:53:38,227 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 5 jobs ready. Free memory (GB): 8.37/8.77, Free processors: 4/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_seg * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_mask 190415-23:53:38,293 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.csf_msk" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/csf_msk". 190415-23:53:38,294 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.tcompcor" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/tcompcor". 190415-23:53:38,295 nipype.workflow INFO: [Node] Running "csf_msk" ("nipype.interfaces.utility.wrappers.Function") 190415-23:53:38,296 nipype.workflow INFO: [Node] Running "tcompcor" ("niworkflows.interfaces.patches.RobustTCompCor") 190415-23:53:38,308 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.acc_msk" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/acc_msk". 190415-23:53:38,310 nipype.workflow INFO: [Node] Running "acc_msk" ("nipype.interfaces.utility.wrappers.Function") 190415-23:53:38,325 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.csf_msk". 190415-23:53:38,344 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.acc_msk". /usr/local/miniconda/lib/python3.7/site-packages/nipype/algorithms/confounds.py:1037: FutureWarning: `rcond` parameter will change to the default of machine precision times ``max(M, N)`` where M and N are the input matrix dimensions. To use the future default and silence this warning we advise to pass `rcond=None`, to keep using the old, explicitly pass `rcond=-1`. betas = np.linalg.lstsq(X, data.T)[0] 190415-23:53:39,223 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.tcompcor". 190415-23:53:40,221 nipype.workflow INFO: [Job 221] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.tcompcor). 190415-23:53:40,223 nipype.workflow INFO: [Job 223] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.csf_msk). 190415-23:53:40,224 nipype.workflow INFO: [Job 229] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.acc_msk). 190415-23:53:40,226 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 5 jobs ready. Free memory (GB): 8.37/8.77, Free processors: 4/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_seg * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_mask 190415-23:53:40,284 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.merge_rois" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/merge_rois". 190415-23:53:40,286 nipype.workflow INFO: [Node] Running "merge_rois" ("nipype.interfaces.utility.base.Merge") 190415-23:53:40,289 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.merge_rois". 190415-23:53:40,289 nipype.workflow INFO: [Job 224] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.merge_rois). 190415-23:53:40,351 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.merge_compcor" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/merge_compcor". 190415-23:53:40,353 nipype.workflow INFO: [Node] Running "merge_compcor" ("nipype.interfaces.utility.base.Merge") 190415-23:53:40,356 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.merge_compcor". 190415-23:53:40,356 nipype.workflow INFO: [Job 230] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.merge_compcor). 190415-23:53:40,423 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.acompcor" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/acompcor". 190415-23:53:40,425 nipype.workflow INFO: [Node] Running "acompcor" ("niworkflows.interfaces.patches.RobustACompCor") /usr/local/miniconda/lib/python3.7/site-packages/nipype/algorithms/confounds.py:1037: FutureWarning: `rcond` parameter will change to the default of machine precision times ``max(M, N)`` where M and N are the input matrix dimensions. To use the future default and silence this warning we advise to pass `rcond=None`, to keep using the old, explicitly pass `rcond=-1`. betas = np.linalg.lstsq(X, data.T)[0] 190415-23:53:41,166 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.acompcor". 190415-23:53:42,223 nipype.workflow INFO: [Job 233] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.acompcor). 190415-23:53:42,226 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 4 jobs ready. Free memory (GB): 8.37/8.77, Free processors: 4/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_seg * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_mask 190415-23:53:42,287 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.signals" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/signals". 190415-23:53:42,289 nipype.workflow INFO: [Node] Running "signals" ("niworkflows.interfaces.images.SignalExtraction") 190415-23:53:42,289 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.rois_plot" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/rois_plot". 190415-23:53:42,292 nipype.workflow INFO: [Node] Running "rois_plot" ("niworkflows.interfaces.masks.ROIsPlot") 190415-23:53:43,170 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.signals". /usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index return _nd_image.find_objects(input, max_label) /usr/local/miniconda/lib/python3.7/site-packages/matplotlib/contour.py:1173: UserWarning: No contour levels were found within the data range. warnings.warn("No contour levels were found" /usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index return _nd_image.find_objects(input, max_label) /usr/local/miniconda/lib/python3.7/site-packages/matplotlib/contour.py:1173: UserWarning: No contour levels were found within the data range. warnings.warn("No contour levels were found" /usr/local/miniconda/lib/python3.7/site-packages/matplotlib/contour.py:1173: UserWarning: No contour levels were found within the data range. warnings.warn("No contour levels were found" /usr/local/miniconda/lib/python3.7/site-packages/matplotlib/contour.py:1173: UserWarning: No contour levels were found within the data range. warnings.warn("No contour levels were found" /usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index return _nd_image.find_objects(input, max_label) 190415-23:53:44,229 nipype.workflow INFO: [Job 225] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.signals). 190415-23:53:44,239 nipype.workflow INFO: [MultiProc] Running 3 tasks, and 3 jobs ready. Free memory (GB): 8.21/8.77, Free processors: 3/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.rois_plot * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_seg * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_mask 190415-23:53:44,311 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.concat" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/concat". 190415-23:53:44,316 nipype.workflow INFO: [Node] Running "concat" ("fmriprep.interfaces.confounds.GatherConfounds") 190415-23:53:44,374 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.concat". 190415-23:53:44,375 nipype.workflow INFO: [Job 234] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.concat). /usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index return _nd_image.find_objects(input, max_label) /usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index return _nd_image.find_objects(input, max_label) /usr/local/miniconda/lib/python3.7/site-packages/matplotlib/contour.py:1173: UserWarning: No contour levels were found within the data range. warnings.warn("No contour levels were found" /usr/local/miniconda/lib/python3.7/site-packages/matplotlib/contour.py:1173: UserWarning: No contour levels were found within the data range. warnings.warn("No contour levels were found" /usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index return _nd_image.find_objects(input, max_label) /usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index return _nd_image.find_objects(input, max_label) /usr/local/miniconda/lib/python3.7/site-packages/matplotlib/contour.py:1173: UserWarning: No contour levels were found within the data range. warnings.warn("No contour levels were found" /usr/local/miniconda/lib/python3.7/site-packages/matplotlib/contour.py:1173: UserWarning: No contour levels were found within the data range. warnings.warn("No contour levels were found" /usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index return _nd_image.find_objects(input, max_label) /usr/local/miniconda/lib/python3.7/site-packages/matplotlib/contour.py:1173: UserWarning: No contour levels were found within the data range. warnings.warn("No contour levels were found" /usr/local/miniconda/lib/python3.7/site-packages/matplotlib/contour.py:1173: UserWarning: No contour levels were found within the data range. warnings.warn("No contour levels were found" /usr/local/miniconda/lib/python3.7/site-packages/matplotlib/contour.py:1173: UserWarning: No contour levels were found within the data range. warnings.warn("No contour levels were found" /usr/local/miniconda/lib/python3.7/site-packages/scipy/ndimage/measurements.py:272: DeprecationWarning: In future, it will be an error for 'np.bool_' scalars to be interpreted as an index return _nd_image.find_objects(input, max_label) 190415-23:53:46,233 nipype.workflow INFO: [MultiProc] Running 3 tasks, and 5 jobs ready. Free memory (GB): 8.21/8.77, Free processors: 3/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.rois_plot * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_seg * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_mask 190415-23:53:46,303 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.func_derivatives_wf.ds_confounds" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/func_derivatives_wf/ds_confounds". 190415-23:53:46,305 nipype.workflow INFO: [Node] Running "ds_confounds" ("fmriprep.interfaces.DerivativesDataSink") 190415-23:53:46,329 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.func_derivatives_wf.ds_confounds". 190415-23:53:46,329 nipype.workflow INFO: [Job 235] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.func_derivatives_wf.ds_confounds). 190415-23:53:46,394 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.summary" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/summary". 190415-23:53:46,396 nipype.workflow INFO: [Node] Running "summary" ("fmriprep.interfaces.reports.FunctionalSummary") 190415-23:53:46,400 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.summary". 190415-23:53:46,400 nipype.workflow INFO: [Job 236] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.summary). 190415-23:53:46,471 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.carpetplot_wf.conf_plot" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/carpetplot_wf/conf_plot". 190415-23:53:46,473 nipype.workflow INFO: [Node] Running "conf_plot" ("fmriprep.interfaces.confounds.FMRISummary") 190415-23:53:46,628 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.rois_plot". 190415-23:53:48,234 nipype.workflow INFO: [Job 231] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.rois_plot). 190415-23:53:48,238 nipype.workflow INFO: [MultiProc] Running 3 tasks, and 4 jobs ready. Free memory (GB): 8.27/8.77, Free processors: 3/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.carpetplot_wf.conf_plot * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_seg * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_mask 190415-23:53:48,316 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.ds_report_bold_rois" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_confounds_wf/ds_report_bold_rois". 190415-23:53:48,318 nipype.workflow INFO: [Node] Running "ds_report_bold_rois" ("fmriprep.interfaces.DerivativesDataSink") 190415-23:53:48,323 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.ds_report_bold_rois". 190415-23:53:48,323 nipype.workflow INFO: [Job 232] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_confounds_wf.ds_report_bold_rois). 190415-23:53:48,390 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.ds_report_summary" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/ds_report_summary". 190415-23:53:48,392 nipype.workflow INFO: [Node] Running "ds_report_summary" ("fmriprep.interfaces.DerivativesDataSink") 190415-23:53:48,396 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.ds_report_summary". 190415-23:53:48,397 nipype.workflow INFO: [Job 237] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.ds_report_summary). 190415-23:53:48,689 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.carpetplot_wf.conf_plot". 190415-23:53:50,238 nipype.workflow INFO: [Job 238] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.carpetplot_wf.conf_plot). 190415-23:53:50,240 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 3 jobs ready. Free memory (GB): 8.37/8.77, Free processors: 4/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_seg * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_mask 190415-23:53:50,303 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.carpetplot_wf.ds_report_bold_conf" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/carpetplot_wf/ds_report_bold_conf". 190415-23:53:50,305 nipype.workflow INFO: [Node] Running "ds_report_bold_conf" ("fmriprep.interfaces.DerivativesDataSink") 190415-23:53:50,309 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.carpetplot_wf.ds_report_bold_conf". 190415-23:53:50,309 nipype.workflow INFO: [Job 239] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.carpetplot_wf.ds_report_bold_conf). 190415-23:53:52,241 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 2 jobs ready. Free memory (GB): 8.37/8.77, Free processors: 4/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_seg * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_mask 190415-23:54:41,945 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_mask". 190415-23:54:42,247 nipype.workflow INFO: [Job 150] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_mask). 190415-23:54:42,250 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 8.57/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_seg 190415-23:54:42,314 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_mni_mask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/ds_mni_mask". 190415-23:54:42,317 nipype.workflow INFO: [Node] Running "ds_mni_mask" ("smriprep.interfaces.DerivativesDataSink") 190415-23:54:42,733 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_mni_mask". 190415-23:54:42,733 nipype.workflow INFO: [Job 151] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_mni_mask). 190415-23:54:42,821 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_to_t1w_transform" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_to_t1w_transform". 190415-23:54:42,835 nipype.workflow INFO: [Node] Running "bold_to_t1w_transform" ("niworkflows.interfaces.itk.MultiApplyTransforms") 190415-23:54:44,250 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 1 jobs ready. Free memory (GB): 7.08/8.77, Free processors: 0/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_to_t1w_transform * fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_seg 190415-23:54:48,459 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_seg". 190415-23:54:50,253 nipype.workflow INFO: [Job 244] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.mni_seg). 190415-23:54:50,257 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 7.28/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_to_t1w_transform 190415-23:54:50,325 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.lut_mni_seg" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/lut_mni_seg". 190415-23:54:50,328 nipype.workflow INFO: [Node] Running "lut_mni_seg" ("nipype.interfaces.utility.wrappers.Function") 190415-23:54:50,581 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.lut_mni_seg". 190415-23:54:52,257 nipype.workflow INFO: [Job 245] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.lut_mni_seg). 190415-23:54:52,260 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 7.28/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_to_t1w_transform 190415-23:54:52,337 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_mni_seg" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/anat_derivatives_wf/ds_mni_seg". 190415-23:54:52,339 nipype.workflow INFO: [Node] Running "ds_mni_seg" ("smriprep.interfaces.DerivativesDataSink") 190415-23:54:53,993 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_mni_seg". 190415-23:54:53,993 nipype.workflow INFO: [Job 246] Completed (fmriprep_wf.single_subject_NC080001_wf.anat_preproc_wf.anat_derivatives_wf.ds_mni_seg). 190415-23:54:54,260 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 7.28/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_to_t1w_transform 190415-23:55:14,756 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_to_t1w_transform". 190415-23:55:16,259 nipype.workflow INFO: [Job 161] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_to_t1w_transform). 190415-23:55:16,262 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 2 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-23:55:16,358 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.merge" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/merge". 190415-23:55:16,362 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_to_mni_transform" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_to_mni_transform". 190415-23:55:16,371 nipype.workflow INFO: [Node] Running "bold_to_mni_transform" ("niworkflows.interfaces.itk.MultiApplyTransforms") 190415-23:55:16,373 nipype.workflow INFO: [Node] Running "merge" ("fmriprep.interfaces.nilearn.Merge") 190415-23:55:18,263 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 0 jobs ready. Free memory (GB): 7.18/8.77, Free processors: 0/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_to_mni_transform * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.merge 190415-23:55:21,828 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.merge". 190415-23:55:22,266 nipype.workflow INFO: [Job 162] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.merge). 190415-23:55:22,270 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 7.28/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_to_mni_transform 190415-23:55:22,340 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.resampling_xfm" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/resampling_xfm". 190415-23:55:22,343 nipype.workflow INFO: [Node] Running "resampling_xfm" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command: lta_convert --inlta identity.nofile --outlta /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/resampling_xfm/out.lta --src /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/merge/vol0000_xform-00000_merged.nii --trg /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-NC080001_T1w_ras_maths_corrected.nii.gz 190415-23:55:22,427 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.resampling_xfm". 190415-23:55:24,270 nipype.workflow INFO: [Job 163] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.resampling_xfm). 190415-23:55:24,273 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 7.28/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_to_mni_transform 190415-23:55:24,336 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.set_xfm_source" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/set_xfm_source". 190415-23:55:24,339 nipype.workflow INFO: [Node] Running "set_xfm_source" ("niworkflows.interfaces.freesurfer.PatchedConcatenateLTA"), a CommandLine Interface with command: mri_concatenate_lta -out_type 1 /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/resampling_xfm/out.lta /tmp/work/fmriprep_wf/single_subject_NC080001_wf/anat_preproc_wf/surface_recon_wf/t1_2_fsnative_xfm/out.lta out_concat.lta 190415-23:55:24,428 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.set_xfm_source". 190415-23:55:26,274 nipype.workflow INFO: [Job 164] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.set_xfm_source). 190415-23:55:26,277 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 7.28/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_to_mni_transform 190415-23:55:26,347 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.rename_src" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/rename_src". 190415-23:55:26,350 nipype.workflow INFO: [Node] Setting-up "_rename_src0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/rename_src/mapflow/_rename_src0". 190415-23:55:26,352 nipype.workflow INFO: [Node] Running "_rename_src0" ("nipype.interfaces.utility.base.Rename") 190415-23:55:26,356 nipype.workflow INFO: [Node] Finished "_rename_src0". 190415-23:55:26,357 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.rename_src". 190415-23:55:26,357 nipype.workflow INFO: [Job 165] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.rename_src). 190415-23:55:26,428 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.validate" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/validate". 190415-23:55:26,431 nipype.workflow INFO: [Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage") 190415-23:55:26,435 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.validate". 190415-23:55:28,276 nipype.workflow INFO: [Job 172] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.validate). 190415-23:55:28,279 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 7.28/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_to_mni_transform 190415-23:55:28,351 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.sampler" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/_hemi_rh/sampler". 190415-23:55:28,357 nipype.workflow INFO: [Node] Setting-up "_sampler0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/_hemi_rh/sampler/mapflow/_sampler0". 190415-23:55:28,361 nipype.workflow INFO: [Node] Running "_sampler0" ("nipype.interfaces.freesurfer.utils.SampleToSurface"), a CommandLine Interface with command: mri_vol2surf --cortex --hemi rh --interp trilinear --o /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/_hemi_rh/sampler/mapflow/_sampler0/rh.fsaverage5.gii --srcsubject sub-NC080001 --reg /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/set_xfm_source/out_concat.lta --projfrac-avg 0.000 1.000 0.200 --mov /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/rename_src/mapflow/_rename_src0/fsaverage5.nii --trgsubject fsaverage5 190415-23:55:30,280 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 2 jobs ready. Free memory (GB): 6.98/8.77, Free processors: 0/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.sampler * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_to_mni_transform 190415-23:55:48,761 nipype.workflow INFO: [Node] Finished "_sampler0". 190415-23:55:48,763 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.sampler". 190415-23:55:50,267 nipype.workflow INFO: [Job 166] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.sampler). 190415-23:55:50,271 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 7.28/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_to_mni_transform 190415-23:55:50,341 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.sampler" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/_hemi_lh/sampler". 190415-23:55:50,352 nipype.workflow INFO: [Node] Setting-up "_sampler0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/_hemi_lh/sampler/mapflow/_sampler0". 190415-23:55:50,362 nipype.workflow INFO: [Node] Running "_sampler0" ("nipype.interfaces.freesurfer.utils.SampleToSurface"), a CommandLine Interface with command: mri_vol2surf --cortex --hemi lh --interp trilinear --o /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/_hemi_lh/sampler/mapflow/_sampler0/lh.fsaverage5.gii --srcsubject sub-NC080001 --reg /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/set_xfm_source/out_concat.lta --projfrac-avg 0.000 1.000 0.200 --mov /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/rename_src/mapflow/_rename_src0/fsaverage5.nii --trgsubject fsaverage5 190415-23:55:52,272 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 1 jobs ready. Free memory (GB): 6.98/8.77, Free processors: 0/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.sampler * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_to_mni_transform 190415-23:56:10,678 nipype.workflow INFO: [Node] Finished "_sampler0". 190415-23:56:10,680 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.sampler". 190415-23:56:12,269 nipype.workflow INFO: [Job 167] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.sampler). 190415-23:56:12,275 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 7.28/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_to_mni_transform 190415-23:56:12,335 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.merger" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/merger". 190415-23:56:12,337 nipype.workflow INFO: [Node] Running "merger" ("nipype.interfaces.utility.base.Merge") 190415-23:56:12,340 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.merger". 190415-23:56:12,341 nipype.workflow INFO: [Job 168] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.merger). 190415-23:56:12,404 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.gen_ref" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/gen_ref". 190415-23:56:12,405 nipype.workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") 190415-23:56:12,687 nipype.interface INFO: stderr 2019-04-15T23:56:12.687101:++ 3dvolreg: AFNI version=Debian-16.2.07~dfsg.1-5~nd16.04+1 (Jun 12 2017) [64-bit] 190415-23:56:12,692 nipype.interface INFO: stderr 2019-04-15T23:56:12.691984:++ Authored by: RW Cox 190415-23:56:12,692 nipype.interface INFO: stderr 2019-04-15T23:56:12.691984:++ Coarse del was 10, replaced with 3 190415-23:56:14,273 nipype.workflow INFO: [MultiProc] Running 2 tasks, and 1 jobs ready. Free memory (GB): 6.28/8.77, Free processors: 0/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.gen_ref * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_to_mni_transform 190415-23:56:23,797 nipype.interface INFO: stderr 2019-04-15T23:56:23.797386:++ Max displacement in automask = 0.08 (mm) at sub-brick 17 190415-23:56:23,797 nipype.interface INFO: stderr 2019-04-15T23:56:23.797386:++ Max delta displ in automask = 0.07 (mm) at sub-brick 2 190415-23:56:24,276 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.gen_ref". 190415-23:56:24,280 nipype.workflow INFO: [Job 173] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.gen_ref). 190415-23:56:24,283 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 7.28/8.77, Free processors: 1/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_to_mni_transform 190415-23:56:24,360 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.validate_ref" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/validate_ref". 190415-23:56:24,361 nipype.workflow INFO: [Node] Running "validate_ref" ("niworkflows.interfaces.images.ValidateImage") 190415-23:56:24,371 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.validate_ref". 190415-23:56:25,847 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_to_mni_transform". 190415-23:56:26,286 nipype.workflow INFO: [Job 189] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_to_mni_transform). 190415-23:56:26,288 nipype.workflow INFO: [Job 174] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.validate_ref). 190415-23:56:26,291 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 4 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-23:56:26,351 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.check_hdr" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/check_hdr". 190415-23:56:26,353 nipype.workflow INFO: [Node] Running "check_hdr" ("niworkflows.interfaces.images.MatchHeader") 190415-23:56:26,368 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.check_hdr". 190415-23:56:26,368 nipype.workflow INFO: [Job 177] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.check_hdr). 190415-23:56:26,455 nipype.workflow INFO: [Node] Setting-up "_update_metadata0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/update_metadata/mapflow/_update_metadata0". 190415-23:56:26,456 nipype.workflow INFO: [Node] Setting-up "_update_metadata1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/update_metadata/mapflow/_update_metadata1". 190415-23:56:26,457 nipype.workflow INFO: [Node] Running "_update_metadata0" ("niworkflows.interfaces.surf.GiftiSetAnatomicalStructure") 190415-23:56:26,458 nipype.workflow INFO: [Node] Running "_update_metadata1" ("niworkflows.interfaces.surf.GiftiSetAnatomicalStructure") 190415-23:56:26,482 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.merge" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/merge". 190415-23:56:26,491 nipype.workflow INFO: [Node] Running "merge" ("fmriprep.interfaces.nilearn.Merge") /usr/local/miniconda/lib/python3.7/site-packages/nibabel/gifti/gifti.py:760: ResourceWarning: unclosed file <_io.BufferedReader name='/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/_hemi_lh/sampler/mapflow/_sampler0/lh.fsaverage5.gii'> parser.parse(fptr=file_map['image'].get_prepare_fileobj('rb')) /usr/local/miniconda/lib/python3.7/site-packages/nibabel/filebasedimages.py:334: ResourceWarning: unclosed file <_io.BufferedWriter name='/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/update_metadata/mapflow/_update_metadata0/lh.fsaverage5.gii'> self.to_file_map() 190415-23:56:26,931 nipype.workflow INFO: [Node] Finished "_update_metadata0". 190415-23:56:26,932 nipype.workflow INFO: [Node] Finished "_update_metadata1". 190415-23:56:28,289 nipype.workflow INFO: [Job 302] Completed (_update_metadata0). 190415-23:56:28,290 nipype.workflow INFO: [Job 303] Completed (_update_metadata1). 190415-23:56:28,292 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 8.47/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.merge 190415-23:56:28,356 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.update_metadata" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/update_metadata". 190415-23:56:28,358 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190415-23:56:28,359 nipype.workflow INFO: [Node] Setting-up "_update_metadata0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/update_metadata/mapflow/_update_metadata0". 190415-23:56:28,360 nipype.workflow INFO: [Node] Cached "_update_metadata0" - collecting precomputed outputs 190415-23:56:28,361 nipype.workflow INFO: [Node] "_update_metadata0" found cached. 190415-23:56:28,361 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection -d 3 --input-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/gen_ref/ref_image.nii.gz --mask-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/check_hdr/ref_image_valid_corrected_brain_mask_maths_trans_dil_hdr.nii.gz --output ref_image_corrected.nii.gz 190415-23:56:28,362 nipype.workflow INFO: [Node] Setting-up "_update_metadata1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_surf_wf/update_metadata/mapflow/_update_metadata1". 190415-23:56:28,363 nipype.workflow INFO: [Node] Cached "_update_metadata1" - collecting precomputed outputs 190415-23:56:28,363 nipype.workflow INFO: [Node] "_update_metadata1" found cached. 190415-23:56:28,365 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.update_metadata". 190415-23:56:29,96 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190415-23:56:30,293 nipype.workflow INFO: [Job 169] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_surf_wf.update_metadata). 190415-23:56:30,294 nipype.workflow INFO: [Job 178] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct). 190415-23:56:30,296 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 8.47/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.merge 190415-23:56:30,367 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190415-23:56:30,369 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_image_corrected.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_corrected_brain.nii.gz -f 0.20 -m 190415-23:56:31,476 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190415-23:56:32,297 nipype.workflow INFO: [Job 179] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass). 190415-23:56:32,300 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 3 jobs ready. Free memory (GB): 8.47/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.merge 190415-23:56:32,365 nipype.workflow INFO: [Node] Setting-up "_name_surfs0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/func_derivatives_wf/name_surfs/mapflow/_name_surfs0". 190415-23:56:32,366 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190415-23:56:32,367 nipype.workflow INFO: [Node] Running "_name_surfs0" ("niworkflows.interfaces.surf.GiftiNameSource") 190415-23:56:32,369 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_image_corrected_brain_mask_dil.nii.gz 190415-23:56:32,371 nipype.workflow INFO: [Node] Finished "_name_surfs0". 190415-23:56:32,371 nipype.workflow INFO: [Job 304] Completed (_name_surfs0). 190415-23:56:32,437 nipype.workflow INFO: [Node] Setting-up "_name_surfs1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/func_derivatives_wf/name_surfs/mapflow/_name_surfs1". 190415-23:56:32,438 nipype.workflow INFO: [Node] Running "_name_surfs1" ("niworkflows.interfaces.surf.GiftiNameSource") 190415-23:56:32,442 nipype.workflow INFO: [Node] Finished "_name_surfs1". 190415-23:56:32,442 nipype.workflow INFO: [Job 305] Completed (_name_surfs1). 190415-23:56:32,571 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190415-23:56:34,267 nipype.workflow INFO: [Job 180] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate). 190415-23:56:34,270 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 8.47/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.merge 190415-23:56:34,329 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.func_derivatives_wf.name_surfs" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/func_derivatives_wf/name_surfs". 190415-23:56:34,332 nipype.workflow INFO: [Node] Setting-up "_name_surfs0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/func_derivatives_wf/name_surfs/mapflow/_name_surfs0". 190415-23:56:34,333 nipype.workflow INFO: [Node] Cached "_name_surfs0" - collecting precomputed outputs 190415-23:56:34,334 nipype.workflow INFO: [Node] "_name_surfs0" found cached. 190415-23:56:34,335 nipype.workflow INFO: [Node] Setting-up "_name_surfs1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/func_derivatives_wf/name_surfs/mapflow/_name_surfs1". 190415-23:56:34,336 nipype.workflow INFO: [Node] Cached "_name_surfs1" - collecting precomputed outputs 190415-23:56:34,336 nipype.workflow INFO: [Node] "_name_surfs1" found cached. 190415-23:56:34,338 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.func_derivatives_wf.name_surfs". 190415-23:56:34,338 nipype.workflow INFO: [Job 170] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.func_derivatives_wf.name_surfs). 190415-23:56:34,403 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 190415-23:56:34,408 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_corrected_brain.nii.gz -mas /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_image_corrected_brain_mask_dil.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_image_corrected_brain_masked.nii.gz 190415-23:56:34,491 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190415-23:56:36,272 nipype.workflow INFO: [Job 181] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask). 190415-23:56:36,275 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 2 jobs ready. Free memory (GB): 8.47/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.merge 190415-23:56:36,343 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize". 190415-23:56:36,345 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize/ref_image_corrected_brain_masked.nii.gz 190415-23:56:36,861 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize". 190415-23:56:38,86 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.merge". 190415-23:56:38,279 nipype.workflow INFO: [Job 190] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.merge). 190415-23:56:38,281 nipype.workflow INFO: [Job 182] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize). 190415-23:56:38,284 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 5 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-23:56:38,346 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 190415-23:56:38,348 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190415-23:56:38,352 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.func_derivatives_wf.ds_bold_mni" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/func_derivatives_wf/ds_bold_mni". 190415-23:56:38,353 nipype.workflow INFO: [Node] Running "ds_bold_mni" ("fmriprep.interfaces.DerivativesDataSink") 190415-23:56:38,376 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190415-23:56:53,801 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.func_derivatives_wf.ds_bold_mni". 190415-23:56:53,801 nipype.workflow INFO: [Job 191] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.func_derivatives_wf.ds_bold_mni). 190415-23:56:53,864 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.validate" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/validate". 190415-23:56:53,866 nipype.workflow INFO: [Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage") 190415-23:56:53,867 nipype.workflow INFO: [Node] Setting-up "_ds_bold_surfs0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/func_derivatives_wf/ds_bold_surfs/mapflow/_ds_bold_surfs0". 190415-23:56:53,869 nipype.workflow INFO: [Node] Running "_ds_bold_surfs0" ("fmriprep.interfaces.DerivativesDataSink") 190415-23:56:53,886 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.validate". 190415-23:56:54,129 nipype.workflow INFO: [Node] Finished "_ds_bold_surfs0". 190415-23:56:54,129 nipype.workflow INFO: [Job 306] Completed (_ds_bold_surfs0). 190415-23:56:54,194 nipype.workflow INFO: [Node] Setting-up "_ds_bold_surfs1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/func_derivatives_wf/ds_bold_surfs/mapflow/_ds_bold_surfs1". 190415-23:56:54,196 nipype.workflow INFO: [Node] Running "_ds_bold_surfs1" ("fmriprep.interfaces.DerivativesDataSink") 190415-23:56:54,447 nipype.workflow INFO: [Node] Finished "_ds_bold_surfs1". 190415-23:56:54,447 nipype.workflow INFO: [Job 307] Completed (_ds_bold_surfs1). 190415-23:56:54,509 nipype.workflow INFO: [Job 183] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize). 190415-23:56:54,511 nipype.workflow INFO: [Job 192] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.validate). 190415-23:56:54,514 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 3 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-23:56:54,579 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.func_derivatives_wf.ds_bold_surfs" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/func_derivatives_wf/ds_bold_surfs". 190415-23:56:54,583 nipype.workflow INFO: [Node] Setting-up "_ds_bold_surfs0" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/func_derivatives_wf/ds_bold_surfs/mapflow/_ds_bold_surfs0". 190415-23:56:54,587 nipype.workflow INFO: [Node] Running "_ds_bold_surfs0" ("fmriprep.interfaces.DerivativesDataSink") 190415-23:56:54,844 nipype.workflow INFO: [Node] Finished "_ds_bold_surfs0". 190415-23:56:54,846 nipype.workflow INFO: [Node] Setting-up "_ds_bold_surfs1" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/func_derivatives_wf/ds_bold_surfs/mapflow/_ds_bold_surfs1". 190415-23:56:54,850 nipype.workflow INFO: [Node] Running "_ds_bold_surfs1" ("fmriprep.interfaces.DerivativesDataSink") 190415-23:56:55,94 nipype.workflow INFO: [Node] Finished "_ds_bold_surfs1". 190415-23:56:55,97 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.func_derivatives_wf.ds_bold_surfs". 190415-23:56:55,97 nipype.workflow INFO: [Job 171] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.func_derivatives_wf.ds_bold_surfs). 190415-23:56:55,162 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 190415-23:56:55,163 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.gen_ref" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/gen_ref". 190415-23:56:55,164 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 190415-23:56:55,164 nipype.workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") 190415-23:56:55,275 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190415-23:56:55,998 nipype.interface INFO: stderr 2019-04-15T23:56:55.998107:++ 3dvolreg: AFNI version=Debian-16.2.07~dfsg.1-5~nd16.04+1 (Jun 12 2017) [64-bit] 190415-23:56:55,998 nipype.interface INFO: stderr 2019-04-15T23:56:55.998107:++ Authored by: RW Cox 190415-23:56:55,999 nipype.interface INFO: stderr 2019-04-15T23:56:55.998862:++ Coarse del was 10, replaced with 4 190415-23:56:56,511 nipype.workflow INFO: [Job 184] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass). 190415-23:56:56,514 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 7.77/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.gen_ref 190415-23:56:56,575 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 190415-23:56:56,577 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190415-23:56:56,595 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190415-23:56:58,514 nipype.workflow INFO: [Job 185] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2). 190415-23:56:58,517 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 7.77/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.gen_ref 190415-23:56:58,578 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks". 190415-23:56:58,580 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_corrected_brain_mask.nii.gz -mul /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_corrected_brain_mask_maths.nii.gz 190415-23:56:58,654 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190415-23:57:00,517 nipype.workflow INFO: [Job 186] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks). 190415-23:57:00,519 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 1 jobs ready. Free memory (GB): 7.77/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.gen_ref 190415-23:57:00,581 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask". 190415-23:57:00,583 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_corrected_brain_mask_maths.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 190415-23:57:00,656 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190415-23:57:02,519 nipype.workflow INFO: [Job 187] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask). 190415-23:57:02,521 nipype.workflow INFO: [MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 7.77/8.77, Free processors: 5/6. Currently running: * fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.gen_ref 190415-23:57:11,97 nipype.interface INFO: stderr 2019-04-15T23:57:11.097912:++ Max displacement in automask = 0.08 (mm) at sub-brick 17 190415-23:57:11,98 nipype.interface INFO: stderr 2019-04-15T23:57:11.097912:++ Max delta displ in automask = 0.08 (mm) at sub-brick 2 190415-23:57:11,791 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.gen_ref". 190415-23:57:12,504 nipype.workflow INFO: [Job 193] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.gen_ref). 190415-23:57:12,508 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-23:57:12,574 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.validate_ref" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/validate_ref". 190415-23:57:12,575 nipype.workflow INFO: [Node] Running "validate_ref" ("niworkflows.interfaces.images.ValidateImage") 190415-23:57:12,589 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.validate_ref". 190415-23:57:14,507 nipype.workflow INFO: [Job 194] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.validate_ref). 190415-23:57:14,511 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-23:57:14,572 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.check_hdr" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/check_hdr". 190415-23:57:14,574 nipype.workflow INFO: [Node] Running "check_hdr" ("niworkflows.interfaces.images.MatchHeader") 190415-23:57:14,598 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.check_hdr". 190415-23:57:14,598 nipype.workflow INFO: [Job 199] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.check_hdr). 190415-23:57:16,511 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-23:57:16,574 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190415-23:57:16,576 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection -d 3 --input-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/gen_ref/ref_image.nii.gz --mask-image /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/check_hdr/ref_image_valid_corrected_brain_mask_maths_trans_dil_hdr.nii.gz --output ref_image_corrected.nii.gz 190415-23:57:17,582 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190415-23:57:18,512 nipype.workflow INFO: [Job 200] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct). 190415-23:57:18,516 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 2 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-23:57:18,581 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.func_derivatives_wf.ds_bold_mni_ref" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/func_derivatives_wf/ds_bold_mni_ref". 190415-23:57:18,583 nipype.workflow INFO: [Node] Running "ds_bold_mni_ref" ("fmriprep.interfaces.DerivativesDataSink") 190415-23:57:18,706 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.func_derivatives_wf.ds_bold_mni_ref". 190415-23:57:18,706 nipype.workflow INFO: [Job 201] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.func_derivatives_wf.ds_bold_mni_ref). 190415-23:57:18,768 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190415-23:57:18,770 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_image_corrected.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_corrected_brain.nii.gz -f 0.20 -m 190415-23:57:19,794 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190415-23:57:20,515 nipype.workflow INFO: [Job 202] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass). 190415-23:57:20,519 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-23:57:20,581 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190415-23:57:20,583 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_image_corrected_brain_mask_dil.nii.gz 190415-23:57:20,873 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190415-23:57:22,521 nipype.workflow INFO: [Job 203] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate). 190415-23:57:22,525 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-23:57:22,587 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 190415-23:57:22,589 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_corrected_brain.nii.gz -mas /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_image_corrected_brain_mask_dil.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_image_corrected_brain_masked.nii.gz 190415-23:57:22,681 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190415-23:57:24,525 nipype.workflow INFO: [Job 204] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask). 190415-23:57:24,529 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-23:57:24,590 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize". 190415-23:57:24,592 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize/ref_image_corrected_brain_masked.nii.gz 190415-23:57:25,468 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize". 190415-23:57:26,530 nipype.workflow INFO: [Job 205] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize). 190415-23:57:26,534 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-23:57:26,595 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 190415-23:57:26,596 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190415-23:57:26,637 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190415-23:57:28,533 nipype.workflow INFO: [Job 206] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize). 190415-23:57:28,536 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-23:57:28,598 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 190415-23:57:28,600 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 190415-23:57:28,721 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190415-23:57:30,542 nipype.workflow INFO: [Job 207] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass). 190415-23:57:30,545 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-23:57:30,607 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 190415-23:57:30,609 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190415-23:57:30,632 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190415-23:57:32,545 nipype.workflow INFO: [Job 208] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2). 190415-23:57:32,548 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-23:57:32,610 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks". 190415-23:57:32,612 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_corrected_brain_mask.nii.gz -mul /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_corrected_brain_mask_maths.nii.gz 190415-23:57:32,657 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190415-23:57:34,516 nipype.workflow INFO: [Job 209] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks). 190415-23:57:34,520 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 1 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. 190415-23:57:34,582 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask". 190415-23:57:34,584 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_corrected_brain_mask_maths.nii.gz /tmp/work/fmriprep_wf/single_subject_NC080001_wf/func_preproc_task_rest_wf/bold_mni_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 190415-23:57:34,667 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190415-23:57:36,524 nipype.workflow INFO: [Job 210] Completed (fmriprep_wf.single_subject_NC080001_wf.func_preproc_task_rest_wf.bold_mni_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask). 190415-23:57:36,527 nipype.workflow INFO: [MultiProc] Running 0 tasks, and 0 jobs ready. Free memory (GB): 8.77/8.77, Free processors: 6/6. Error in atexit._run_exitfuncs: Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/concurrent/futures/process.py", line 101, in _python_exit thread_wakeup.wakeup() File "/usr/local/miniconda/lib/python3.7/concurrent/futures/process.py", line 89, in wakeup self._writer.send_bytes(b"") File "/usr/local/miniconda/lib/python3.7/multiprocessing/connection.py", line 183, in send_bytes self._check_closed() File "/usr/local/miniconda/lib/python3.7/multiprocessing/connection.py", line 136, in _check_closed raise OSError("handle is closed") OSError: handle is closed Sentry is attempting to send 0 pending error messages Waiting up to 2.0 seconds Press Ctrl-C to quit ChenYuans-MacBook-Pro:~ noelkuo$