tl;dr: Running fmriprep via Docker, I get an error “FOV=289.000 > 256” with the suggestion to “Include the flag -cw256 with recon-all!” How do I input this into the docker command?
Hi all,
I am very new to anything outside of Windows and SPM, so please excuse me if my questions are on a very basic level. Over the last few days, I have tried familiarizing myself with the BIDS format and fmriprep. To this end, I have downloaded a dataset from openneuro.org, ds000157, just to test out how stuff works.
I have tried using fmriprep-docker to no avail, as when running fmriprep-docker I either get a “permission denied” from Docker, or, when using the “sudo” prefix, the command can not be found.
So, I moved on to “invoking Docker directly”, and after getting the Freesurfer license stuff to work, I received the outputs below. Any suggestions on how to proceed? Is maybe the dataset I have chosen incompatible?
Thank you very much!
FOV_error_terminal
~$ sudo docker run -ti --rm -v ~/Desktop/bidstest/reference/ds000157:/data:ro -v ~/Desktop/bidstest/reference/fmriprep:/out -v /usr/local/freesurfer/license.txt:/opt/freesurfer/license.txt poldracklab/fmriprep:latest /data /out/out participant --participant-label sub-01
180727-16:19:45,297 nipype.workflow IMPORTANT:
Running fMRIPREP version 1.1.2:
* BIDS dataset path: /data.
* Participant list: ['01'].
* Run identifier: 20180727-161945_8147aa85-24b6-4ead-94a3-88f03cb4659a.
34180727-16:19:46,83 nipype.workflow IMPORTANT:
Creating bold processing workflow for “/data/sub-01/func/sub-01_task-passiveimageviewing_bold.nii.gz” (0.05 GB / 375 TRs). Memory resampled/largemem=0.21/0.40 GB.
180727-16:19:46,233 nipype.workflow WARNING:
SDC: no fieldmaps found or they were ignored (/data/sub-01/func/sub-01_task-passiveimageviewing_bold.nii.gz).
180727-16:19:46,523 nipype.workflow IMPORTANT:
Creating BOLD surface-sampling workflow.
180727-16:19:53,592 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_reference_wf.validate” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_reference_wf/validate”.
180727-16:19:53,593 nipype.workflow INFO:
[Node] Running “validate” (“fmriprep.interfaces.images.ValidateImage”)
180727-16:19:53,601 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_01_wf.bidssrc” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/bidssrc”.
180727-16:19:53,603 nipype.workflow INFO:
[Node] Running “bidssrc” (“fmriprep.interfaces.bids.BIDSDataGrabber”)
180727-16:19:53,604 nipype.interface WARNING:
No ‘t2w’ images found for sub-
180727-16:19:53,604 nipype.interface WARNING:
No ‘flair’ images found for sub-
180727-16:19:53,604 nipype.interface WARNING:
No ‘fmap’ images found for sub-
180727-16:19:53,604 nipype.interface WARNING:
No ‘sbref’ images found for sub-
180727-16:19:53,604 nipype.interface WARNING:
No ‘roi’ images found for sub-
180727-16:19:53,607 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_reference_wf.validate”.180727-16:19:53,607 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_01_wf.bidssrc”.
180727-16:19:54,776 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_split” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_split”.
180727-16:19:54,777 nipype.workflow INFO:
[Node] Running “bold_split” (“nipype.interfaces.fsl.utils.Split”), a CommandLine Interface with command:
fslsplit /data/sub-01/func/sub-01_task-passiveimageviewing_bold.nii.gz -t
180727-16:19:55,415 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_reference_wf.gen_ref” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_reference_wf/gen_ref”.
180727-16:19:55,416 nipype.workflow INFO:
[Node] Running “gen_ref” (“niworkflows.interfaces.registration.EstimateReferenceImage”)
180727-16:19:55,451 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_template_wf.t1_template_dimensions” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1_template_dimensions”.
180727-16:19:55,453 nipype.workflow INFO:
[Node] Running “t1_template_dimensions” (“fmriprep.interfaces.images.TemplateDimensions”)
180727-16:19:55,622 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_template_wf.t1_template_dimensions”.
180727-16:19:55,854 nipype.interface INFO:
stderr 2018-07-27T16:19:55.854284:++ 3dvolreg: AFNI version=Debian-16.2.07~dfsg.1-5~nd16.04+1 (Jun 12 2017) [64-bit]
180727-16:19:55,854 nipype.interface INFO:
stderr 2018-07-27T16:19:55.854284:++ Authored by: RW Cox
180727-16:19:55,854 nipype.interface INFO:
stderr 2018-07-27T16:19:55.854699:++ Coarse del was 10, replaced with 3
180727-16:19:56,835 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.t1_name” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_derivatives_wf/t1_name”.
180727-16:19:56,836 nipype.workflow INFO:
[Node] Running “t1_name” (“nipype.interfaces.utility.wrappers.Function”)
180727-16:19:56,840 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.t1_name”.
180727-16:19:57,539 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_template_wf.t1_conform” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1_conform”.
180727-16:19:57,541 nipype.workflow INFO:
[Node] Setting-up “_t1_conform0” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0”.
180727-16:19:57,542 nipype.workflow INFO:
[Node] Running “_t1_conform0” (“fmriprep.interfaces.images.Conform”)
180727-16:19:58,127 nipype.workflow INFO:
[Node] Finished “_t1_conform0”.
180727-16:19:58,129 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_template_wf.t1_conform”.
180727-16:20:01,245 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.recon_config” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/recon_config”.
180727-16:20:01,246 nipype.workflow INFO:
[Node] Running “recon_config” (“fmriprep.interfaces.freesurfer.FSDetectInputs”)
180727-16:20:01,256 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.recon_config”.
180727-16:20:03,930 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_split”.
180727-16:20:04,236 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_mni_trans_wf.gen_ref” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_mni_trans_wf/gen_ref”.
180727-16:20:04,238 nipype.workflow INFO:
[Node] Running “gen_ref” (“niworkflows.interfaces.utils.GenerateSamplingReference”)
180727-16:20:04,510 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_mni_trans_wf.gen_ref”.
180727-16:20:06,184 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_01_wf.anat_preproc_wf.skullstrip_ants_wf.t1_skull_strip” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip”.
180727-16:20:06,186 nipype.workflow INFO:
[Node] Running “t1_skull_strip” (“nipype.interfaces.ants.segmentation.BrainExtraction”), a CommandLine Interface with command:
antsBrainExtraction.sh -a /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/t1_conform0/sub-01_T1w_ras.nii.gz -m /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip/T_template0_BrainCerebellumProbabilityMask.nii.gz -e /niworkflows_data/ants_oasis_template_ras/T_template0.nii.gz -d 3 -f /niworkflows_data/ants_oasis_template_ras/T_template0_BrainCerebellumRegistrationMask.nii.gz -s nii.gz -k 1 -o highres001 -q 1
180727-16:20:08,562 nipype.interface INFO:
stderr 2018-07-27T16:20:08.562258:++ Max displacement in automask = 0.20 (mm) at sub-brick 19
180727-16:20:08,562 nipype.interface INFO:
stderr 2018-07-27T16:20:08.562258:++ Max delta displ in automask = 0.12 (mm) at sub-brick 5
180727-16:20:09,266 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_reference_wf.gen_ref”.
180727-16:20:10,195 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_hmc_wf.mcflirt” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_hmc_wf/mcflirt”.
180727-16:20:10,198 nipype.workflow INFO:
[Node] Running “mcflirt” (“nipype.interfaces.fsl.preprocess.MCFLIRT”), a CommandLine Interface with command:
mcflirt -in /data/sub-01/func/sub-01_task-passiveimageviewing_bold.nii.gz -out /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_hmc_wf/mcflirt/sub-01_task-passiveimageviewing_bold_mcf.nii.gz -reffile /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_reference_wf/gen_ref/ref_image.nii.gz -mats -plots
180727-16:21:37,902 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_hmc_wf.mcflirt”.
180727-16:21:38,795 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_hmc_wf.normalize_motion” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_hmc_wf/normalize_motion”.
180727-16:21:38,796 nipype.workflow INFO:
[Node] Running “normalize_motion” (“niworkflows.interfaces.utils.NormalizeMotionParams”)
180727-16:21:38,804 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_hmc_wf.normalize_motion”.
180727-16:21:40,335 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_confounds_wf.fdisp” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_confounds_wf/fdisp”.
180727-16:21:40,337 nipype.workflow INFO:
[Node] Running “fdisp” (“nipype.algorithms.confounds.FramewiseDisplacement”)
180727-16:21:40,344 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_confounds_wf.fdisp”.
180727-16:21:42,276 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_mask” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_mask”.
180727-16:21:42,278 nipype.workflow INFO:
[Node] Running “n4_mask” (“fmriprep.interfaces.nilearn.MaskEPI”)
180727-16:21:42,678 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_mask”.
180727-16:21:44,292 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct”.
180727-16:21:44,294 nipype.workflow INFO:
[Node] Running “n4_correct” (“nipype.interfaces.ants.segmentation.N4BiasFieldCorrection”), a CommandLine Interface with command:
N4BiasFieldCorrection -d 3 --input-image /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_reference_wf/gen_ref/ref_image.nii.gz --mask-image /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_mask/ref_image_mask.nii.gz --output ref_image_corrected.nii.gz
180727-16:21:45,347 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct”.
180727-16:21:46,290 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass”.
180727-16:21:46,292 nipype.workflow INFO:
[Node] Running “skullstrip_first_pass” (“nipype.interfaces.fsl.preprocess.BET”), a CommandLine Interface with command:
bet /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_image_corrected.nii.gz /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_corrected_brain.nii.gz -f 0.20 -m
180727-16:21:48,48 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass”.
180727-16:21:48,291 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate”.
180727-16:21:48,293 nipype.workflow INFO:
[Node] Running “skullstrip_first_dilate” (“nipype.interfaces.fsl.maths.DilateImage”), a CommandLine Interface with command:
fslmaths -dt char /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_image_corrected_brain_mask_dil.nii.gz
180727-16:21:48,529 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate”.
180727-16:21:50,294 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask”.
180727-16:21:50,296 nipype.workflow INFO:
[Node] Running “skullstrip_first_mask” (“nipype.interfaces.fsl.maths.ApplyMask”), a CommandLine Interface with command:
fslmaths /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_corrected_brain.nii.gz -mas /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_image_corrected_brain_mask_dil.nii.gz /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_image_corrected_brain_masked.nii.gz
180727-16:21:50,375 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask”.
180727-16:21:52,295 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize”.
180727-16:21:52,298 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 /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize/ref_image_corrected_brain_masked.nii.gz
180727-16:21:53,32 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize”.
180727-16:21:54,372 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize”.
180727-16:21:54,374 nipype.workflow INFO:
[Node] Running “fixhdr_unifize” (“niworkflows.interfaces.utils.CopyXForm”)
180727-16:21:54,403 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize”.
180727-16:21:56,361 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass”.
180727-16:21:56,363 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 /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz
180727-16:21:56,493 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass”.
180727-16:21:58,911 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2”.
180727-16:21:58,913 nipype.workflow INFO:
[Node] Running “fixhdr_skullstrip2” (“niworkflows.interfaces.utils.CopyXForm”)
180727-16:21:58,936 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2”.
180727-16:22:00,321 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks”.
180727-16:22:00,324 nipype.workflow INFO:
[Node] Running “combine_masks” (“nipype.interfaces.fsl.maths.BinaryMaths”), a CommandLine Interface with command:
fslmaths /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_corrected_brain_mask.nii.gz -mul /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_corrected_brain_mask_maths.nii.gz
180727-16:22:00,415 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks”.
180727-16:22:02,323 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask”.
180727-16:22:02,325 nipype.workflow INFO:
[Node] Running “apply_mask” (“nipype.interfaces.fsl.maths.ApplyMask”), a CommandLine Interface with command:
fslmaths /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_corrected_brain_mask_maths.nii.gz /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz
180727-16:22:02,417 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask”.
180727-16:39:30,861 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_01_wf.anat_preproc_wf.skullstrip_ants_wf.t1_skull_strip”.
180727-16:39:31,362 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_hmc_wf.fsl2itk” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/func_preproc_task_passiveimageviewing_wf/bold_hmc_wf/fsl2itk”.
180727-16:39:31,373 nipype.workflow INFO:
[Node] Running “fsl2itk” (“fmriprep.interfaces.itk.MCFLIRT2ITK”)
180727-16:39:50,509 nipype.workflow INFO:
[Node] Finished “fmriprep_wf.single_subject_01_wf.func_preproc_task_passiveimageviewing_wf.bold_hmc_wf.fsl2itk”.
180727-16:39:51,405 nipype.workflow INFO:
[Node] Setting-up “fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon1” in “/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon1”.
180727-16:39:51,407 nipype.workflow INFO:
[Node] Running “autorecon1” (“nipype.interfaces.freesurfer.preprocess.ReconAll”), a CommandLine Interface with command:
recon-all -autorecon1 -i /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0/sub-01_T1w_ras.nii.gz -noskullstrip -openmp 7 -subjid sub-01 -sd /out/out/freesurfer
180727-16:40:02,247 nipype.workflow WARNING:
[Node] Error on “fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon1” (/root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon1)
Traceback (most recent call last):
File “/usr/local/miniconda/bin/fmriprep”, line 11, in
sys.exit(main())
File “/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py”, line 316, in main
fmriprep_wf.run(**plugin_settings)
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/workflows.py”, line 595, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/plugins/base.py”, line 162, in run
self._clean_queue(jobid, graph, result=result))
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/plugins/base.py”, line 224, in _clean_queue
raise RuntimeError("".join(result[‘traceback’]))
RuntimeError: Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/plugins/multiproc.py”, line 69, in run_node
result[‘result’] = node.run(updatehash=updatehash)
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py”, line 480, in run
result = self._run_interface(execute=True)
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py”, line 564, in _run_interface
return self._run_command(execute)
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py”, line 644, in _run_command
result = self._interface.run(cwd=outdir)
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base/core.py”, line 521, in run
runtime = self._run_interface(runtime)
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base/core.py”, line 1033, in _run_interface
self.raise_exception(runtime)
File “/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base/core.py”, line 970, in raise_exception
).format(**runtime.dictcopy()))
RuntimeError: Command:
recon-all -autorecon1 -i /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0/sub-01_T1w_ras.nii.gz -noskullstrip -openmp 7 -subjid sub-01 -sd /out/out/freesurfer
Standard output:
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
INFO: SUBJECTS_DIR is /out/out/freesurfer
Actual FREESURFER_HOME /opt/freesurfer
Linux 6c62d40f1789 4.15.0-29-generic #31-Ubuntu SMP Tue Jul 17 15:39:52 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
‘/opt/freesurfer/bin/recon-all’ -> ‘/out/out/freesurfer/sub-01/scripts/recon-all.local-copy’
/out/out/freesurfer/sub-01
mri_convert /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0/sub-01_T1w_ras.nii.gz /out/out/freesurfer/sub-01/mri/orig/001.mgz
mri_convert.bin /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0/sub-01_T1w_ras.nii.gz /out/out/freesurfer/sub-01/mri/orig/001.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /root/src/fmriprep/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0/sub-01_T1w_ras.nii.gz…
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.998482, -0.0535858, 0.0127173)
j_ras = (0.0550641, 0.975752, -0.21184)
k_ras = (-0.00105725, 0.212219, 0.977222)
writing to /out/out/freesurfer/sub-01/mri/orig/001.mgz…
#--------------------------------------------
#@# MotionCor Fri Jul 27 16:39:55 UTC 2018
Found 1 runs
/out/out/freesurfer/sub-01/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs…
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I’ll
copy the run to rawavg and continue.
cp /out/out/freesurfer/sub-01/mri/orig/001.mgz /out/out/freesurfer/sub-01/mri/rawavg.mgz
/out/out/freesurfer/sub-01
mri_convert /out/out/freesurfer/sub-01/mri/rawavg.mgz /out/out/freesurfer/sub-01/mri/orig.mgz --conform
mri_convert.bin /out/out/freesurfer/sub-01/mri/rawavg.mgz /out/out/freesurfer/sub-01/mri/orig.mgz --conform
WARNING ==================++++++++++++++++++++++++=======================================
The physical sizes are (175.00 mm, 288.00 mm, 288.00 mm), which cannot fit in 256^3 mm^3 volume.
The resulting volume will have 289 slices.
If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu).
==================================================++++++++++++++++++++++++===============
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /out/out/freesurfer/sub-01/mri/rawavg.mgz…
TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.998482, -0.0535858, 0.0127173)
j_ras = (0.0550641, 0.975752, -0.21184)
k_ras = (-0.00105725, 0.212219, 0.977222)
changing data type from float to uchar (noscale = 0)…
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /out/out/freesurfer/sub-01/mri/orig.mgz…
ERROR! FOV=289.000 > 256
Include the flag -cw256 with recon-all!
Inspect orig.mgz to ensure the head is fully visible.
Linux 6c62d40f1789 4.15.0-29-generic #31-Ubuntu SMP Tue Jul 17 15:39:52 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub-01 exited with ERRORS at Fri Jul 27 16:40:02 UTC 2018
For more details, see the log file /out/out/freesurfer/sub-01/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Standard error:
Return code: 1
Sentry is attempting to send 1 pending error messages
Waiting up to 10 seconds
Press Ctrl-C to quit