190904-15:11:47,601 nipype.workflow IMPORTANT: Running fMRIPREP version 1.5.0rc1: * BIDS dataset path: /gpfs/ysm/scratch60/oad4/RV_BidsConversion. * Participant list: ['1343']. * Run identifier: 20190904-151142_c4d5c9df-ae56-43aa-b108-af5ad13fbeb2. 190904-15:11:50,741 nipype.workflow IMPORTANT: Creating bold processing workflow for "/gpfs/ysm/scratch60/oad4/RV_BidsConversion/sub-1343/ses-1/func/sub-1343_ses-1_task--rest_bold.nii.gz" (0.50 GB / 460 TRs). Memory resampled/largemem=1.98/4.26 GB. 190904-15:11:50,770 nipype.workflow IMPORTANT: No single-band-reference found for sub-1343_ses-1_task--rest_bold.nii.gz 190904-15:11:52,731 nipype.workflow IMPORTANT: Slice-timing correction will be included. 190904-15:11:52,749 nipype.workflow WARNING: SDC: no fieldmaps found or they were ignored (/gpfs/ysm/scratch60/oad4/RV_BidsConversion/sub-1343/ses-1/func/sub-1343_ses-1_task--rest_bold.nii.gz). 190904-15:11:53,565 nipype.workflow IMPORTANT: Creating BOLD surface-sampling workflow. 190904-15:11:56,174 nipype.workflow IMPORTANT: Creating bold processing workflow for "/gpfs/ysm/scratch60/oad4/RV_BidsConversion/sub-1343/ses-1/func/sub-1343_ses-1_task-_bold.nii.gz" (1.20 GB / 1104 TRs). Memory resampled/largemem=4.79/17.99 GB. 190904-15:11:56,204 nipype.workflow IMPORTANT: No single-band-reference found for sub-1343_ses-1_task-_bold.nii.gz 190904-15:11:57,817 nipype.workflow IMPORTANT: Slice-timing correction will be included. 190904-15:11:57,835 nipype.workflow WARNING: SDC: no fieldmaps found or they were ignored (/gpfs/ysm/scratch60/oad4/RV_BidsConversion/sub-1343/ses-1/func/sub-1343_ses-1_task-_bold.nii.gz). 190904-15:11:58,523 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_1206_wf.func_preproc_ses_1_task_rest_wf.bold_hmc_wf.mcflirt". 190904-15:11:58,684 nipype.workflow IMPORTANT: Creating BOLD surface-sampling workflow. 190904-15:12:07,638 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* 1.5.0rc1 (@fmriprep1; @fmriprep2; RRID:SCR_016216), which is based on *Nipype* 1.2.0 (@nipype1; @nipype2; RRID:SCR_002502). Anatomical data preprocessing : A total of 2 T1-weighted (T1w) images were found within the input BIDS dataset. All of them were corrected for intensity non-uniformity (INU) with `N4BiasFieldCorrection` [@n4], distributed with ANTs 2.2.0 [@ants, RRID:SCR_004757]. The T1w-reference was then skull-stripped with a *Nipype* implementation of the `antsBrainExtraction.sh` workflow (from ANTs), using OASIS30ANTs as target 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]. A T1w-reference map was computed after registration of 2 T1w images (after INU-correction) using `mri_robust_template` [FreeSurfer 6.0.1, @fs_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]. Volume-based spatial normalization to two standard spaces (MNI152NLin2009cAsym, MNI152NLin6Asym) was performed through nonlinear registration with `antsRegistration` (ANTs 2.2.0), using brain-extracted versions of both T1w reference and the T1w template. The following templates were selected for spatial normalization: *ICBM 152 Nonlinear Asymmetrical template version 2009c* [@mni152nlin2009casym, RRID:SCR_008796; TemplateFlow ID: MNI152NLin2009cAsym], *FSL's MNI ICBM 152 non-linear 6th Generation Asymmetric Average Brain Stereotaxic Registration Model* [@mni152nlin6asym, RRID:SCR_002823; TemplateFlow ID: MNI152NLin6Asym]. Functional data preprocessing : For each of the 2 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 six degrees of freedom. 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]. BOLD runs were slice-time corrected using `3dTshift` from AFNI 20160207 [@afni, RRID:SCR_005927]. The BOLD time-series, were resampled to surfaces on the following spaces: *fsaverage5*. *Grayordinates* files [@hcppipelines], which combine surface-sampled data and volume-sampled data, were also generated. 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 into several standard spaces, correspondingly generating the following *spatially-normalized, preprocessed BOLD runs*: MNI152NLin2009cAsym, MNI152NLin6Asym. First, a reference volume and its skull-stripped version were generated using a custom methodology of *fMRIPrep*. Automatic removal of motion artifacts using independent component analysis [ICA-AROMA, @aroma] was performed on the *preprocessed BOLD on MNI space* time-series after removal of non-steady state volumes and spatial smoothing with an isotropic, Gaussian kernel of 6mm FWHM (full-width half-maximum). Corresponding "non-aggresively" denoised runs were produced after such smoothing. Additionally, the "aggressive" noise-regressors were collected and placed in the corresponding confounds file. 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). 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, 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). Components are also calculated separately within the WM and CSF masks. For each CompCor decomposition, the *k* components with the largest singular values are retained, such that the retained components' time series are sufficient to explain 50 percent of variance across the nuisance mask (CSF, WM, combined, or temporal). The remaining components are dropped from consideration. The head-motion estimates calculated in the correction step were also placed within the corresponding confounds file. The confound time series derived from head motion estimates and global signals were expanded with the inclusion of temporal derivatives and quadratic terms for each [@confounds_satterthwaite_2013]. Frames that exceeded a threshold of 0.5 mm FD or 1.5 standardised DVARS were annotated as motion outliers. 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 output 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* 0.5.2 [@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"). ### Copyright Waiver The above boilerplate text was automatically generated by fMRIPrep with the express intention that users should copy and paste this text into their manuscripts *unchanged*. It is released under the [CC0](https://creativecommons.org/publicdomain/zero/1.0/) license. ### References 190904-15:12:21,50 nipype.workflow WARNING: Some nodes exceed the total amount of memory available (29.30GB). 190904-15:12:22,765 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_1343_wf.func_preproc_ses_1_task__rest_wf.func_derivatives_wf.raw_sources" in "/gpfs/ysm/scratch60/oad4/work_RV/fmriprep_wf/single_subject_1343_wf/func_preproc_ses_1_task__rest_wf/func_derivatives_wf/raw_sources". 190904-15:12:22,769 nipype.workflow INFO: [Node] Running "raw_sources" ("nipype.interfaces.utility.wrappers.Function") 190904-15:12:22,775 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_1343_wf.func_preproc_ses_1_task__rest_wf.func_derivatives_wf.raw_sources". 190904-15:12:22,797 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_1343_wf.func_preproc_ses_1_task__wf.func_derivatives_wf.raw_sources" in "/gpfs/ysm/scratch60/oad4/work_RV/fmriprep_wf/single_subject_1343_wf/func_preproc_ses_1_task__wf/func_derivatives_wf/raw_sources". 190904-15:12:22,800 nipype.workflow INFO: [Node] Running "raw_sources" ("nipype.interfaces.utility.wrappers.Function") 190904-15:12:22,805 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_1343_wf.func_preproc_ses_1_task__wf.func_derivatives_wf.raw_sources". 190904-15:12:27,413 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_1343_wf.anat_preproc_wf.brain_extraction_wf.res_tmpl" in "/gpfs/ysm/scratch60/oad4/work_RV/fmriprep_wf/single_subject_1343_wf/anat_preproc_wf/brain_extraction_wf/res_tmpl". 190904-15:12:27,413 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_1343_wf.anat_preproc_wf.brain_extraction_wf.lap_tmpl" in "/gpfs/ysm/scratch60/oad4/work_RV/fmriprep_wf/single_subject_1343_wf/anat_preproc_wf/brain_extraction_wf/lap_tmpl". 190904-15:12:27,416 nipype.workflow INFO: [Node] Running "res_tmpl" ("niworkflows.interfaces.ants.ResampleImageBySpacing"), a CommandLine Interface with command: ResampleImageBySpacing 3 /home/oad4/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz tpl-OASIS30ANTs_res-01_T1w_resampled.nii.gz 4 4 4 1 190904-15:12:27,416 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 /home/oad4/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz 1.5 1 190904-15:12:27,497 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_1343_wf.func_preproc_ses_1_task__rest_wf.bold_reference_wf.validate" in "/gpfs/ysm/scratch60/oad4/work_RV/fmriprep_wf/single_subject_1343_wf/func_preproc_ses_1_task__rest_wf/bold_reference_wf/validate". 190904-15:12:27,500 nipype.workflow INFO: [Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage") 190904-15:12:27,534 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_1343_wf.func_preproc_ses_1_task__wf.bold_reference_wf.validate" in "/gpfs/ysm/scratch60/oad4/work_RV/fmriprep_wf/single_subject_1343_wf/func_preproc_ses_1_task__wf/bold_reference_wf/validate". 190904-15:12:27,536 nipype.workflow INFO: [Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage") 190904-15:12:27,776 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_1343_wf.bidssrc" in "/gpfs/ysm/scratch60/oad4/work_RV/fmriprep_wf/single_subject_1343_wf/bidssrc". 190904-15:12:27,779 nipype.workflow INFO: [Node] Running "bidssrc" ("niworkflows.interfaces.bids.BIDSDataGrabber") 190904-15:12:27,780 nipype.interface WARNING: No "t2w" images found for sub- 190904-15:12:27,780 nipype.interface WARNING: No "flair" images found for sub- 190904-15:12:27,780 nipype.interface WARNING: No "fmap" images found for sub- 190904-15:12:27,781 nipype.interface WARNING: No "sbref" images found for sub- 190904-15:12:27,781 nipype.interface WARNING: No "roi" images found for sub- 190904-15:12:27,809 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_1343_wf.bidssrc". 190904-15:12:29,559 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_1343_wf.anat_preproc_wf.brain_extraction_wf.res_tmpl". 190904-15:12:35,51 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_1343_wf.anat_preproc_wf.anat_template_wf.t1_template_dimensions" in "/gpfs/ysm/scratch60/oad4/work_RV/fmriprep_wf/single_subject_1343_wf/anat_preproc_wf/anat_template_wf/t1_template_dimensions". 190904-15:12:35,57 nipype.workflow INFO: [Node] Running "t1_template_dimensions" ("niworkflows.interfaces.images.TemplateDimensions") 190904-15:12:35,398 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_1343_wf.anat_preproc_wf.anat_template_wf.t1_template_dimensions". 190904-15:12:35,519 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_1343_wf.bids_info" in "/gpfs/ysm/scratch60/oad4/work_RV/fmriprep_wf/single_subject_1343_wf/bids_info". 190904-15:12:35,523 nipype.workflow INFO: [Node] Running "bids_info" ("niworkflows.interfaces.bids.BIDSInfo") 190904-15:12:36,170 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_1343_wf.anat_preproc_wf.brain_extraction_wf.lap_tmpl". 190904-15:12:38,455 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_1343_wf.anat_preproc_wf.brain_extraction_wf.mrg_tmpl" in "/gpfs/ysm/scratch60/oad4/work_RV/fmriprep_wf/single_subject_1343_wf/anat_preproc_wf/brain_extraction_wf/mrg_tmpl". 190904-15:12:38,459 nipype.workflow INFO: [Node] Running "mrg_tmpl" ("nipype.interfaces.utility.base.Merge") 190904-15:12:38,464 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_1343_wf.anat_preproc_wf.brain_extraction_wf.mrg_tmpl". 190904-15:12:38,632 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_1343_wf.anat_preproc_wf.anat_derivatives_wf.raw_sources" in "/gpfs/ysm/scratch60/oad4/work_RV/fmriprep_wf/single_subject_1343_wf/anat_preproc_wf/anat_derivatives_wf/raw_sources". 190904-15:12:38,636 nipype.workflow INFO: [Node] Running "raw_sources" ("nipype.interfaces.utility.wrappers.Function") 190904-15:12:38,641 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_1343_wf.anat_preproc_wf.anat_derivatives_wf.raw_sources". 190904-15:12:38,643 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_1343_wf.anat_preproc_wf.anat_derivatives_wf.t1_name" in "/gpfs/ysm/scratch60/oad4/work_RV/fmriprep_wf/single_subject_1343_wf/anat_preproc_wf/anat_derivatives_wf/t1_name". 190904-15:12:38,646 nipype.workflow INFO: [Node] Running "t1_name" ("nipype.interfaces.utility.wrappers.Function") 190904-15:12:38,652 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_1343_wf.anat_preproc_wf.anat_derivatives_wf.t1_name". 190904-15:12:39,438 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_1343_wf.bids_info". 190904-15:12:41,223 nipype.workflow WARNING: [Node] Error on "fmriprep_wf.single_subject_1343_wf.summary" (/gpfs/ysm/scratch60/oad4/work_RV/fmriprep_wf/single_subject_1343_wf/summary) 190904-15:12:41,225 nipype.workflow ERROR: Node summary failed to run on host c14n07.farnam.hpc.yale.internal. 190904-15:12:41,229 nipype.workflow ERROR: Saving crash info to /gpfs/ysm/scratch60/oad4/RV_output/fmriprep/sub-1343/log/20190904-151142_c4d5c9df-ae56-43aa-b108-af5ad13fbeb2/crash-20190904-151241-oad4-summary-46e6f5ba-ed05-4db2-aacd-d61283171714.txt Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 316, in _send_procs_to_workers self.procs[jobid].run(updatehash=updatehash) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 472, in run result = self._run_interface(execute=True) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 563, in _run_interface return self._run_command(execute) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 643, in _run_command result = self._interface.run(cwd=outdir) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 375, in run runtime = self._run_interface(runtime) File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/interfaces/reports.py", line 100, in _run_interface return super(SubjectSummary, self)._run_interface(runtime) File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/interfaces/reports.py", line 64, in _run_interface segment = self._generate_segment() File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/interfaces/reports.py", line 124, in _generate_segment for series in bold_series) File "/usr/local/miniconda/lib/python3.7/collections/__init__.py", line 566, in __init__ self.update(*args, **kwds) File "/usr/local/miniconda/lib/python3.7/collections/__init__.py", line 653, in update _count_elements(self, iterable) File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/interfaces/reports.py", line 124, in for series in bold_series) TypeError: 'NoneType' object is not subscriptable 190904-15:12:43,766 nipype.workflow INFO: [Node] Setting-up "_t1_conform1" in "/gpfs/ysm/scratch60/oad4/work_RV/fmriprep_wf/single_subject_1343_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform1". 190904-15:12:43,769 nipype.workflow INFO: [Node] Setting-up "_t1_conform0" in "/gpfs/ysm/scratch60/oad4/work_RV/fmriprep_wf/single_subject_1343_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0". 190904-15:12:43,769 nipype.workflow INFO: [Node] Running "_t1_conform1" ("niworkflows.interfaces.images.Conform") 190904-15:12:43,771 nipype.workflow INFO: [Node] Running "_t1_conform0" ("niworkflows.interfaces.images.Conform") 190904-15:12:49,452 nipype.workflow INFO: [Node] Finished "_t1_conform0". 190904-15:12:50,971 nipype.workflow INFO: [Node] Finished "_t1_conform1". 190904-15:12:54,241 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_1343_wf.func_preproc_ses_1_task__rest_wf.bold_reference_wf.validate". 190904-15:13:31,128 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_1343_wf.func_preproc_ses_1_task__wf.bold_reference_wf.validate". 190904-15:18:14,764 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_1206_wf.func_preproc_ses_1_task__wf.bold_hmc_wf.mcflirt".