Freesurfer error FOV > 256

freesurfer
fmriprep

#1

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


#2

The input data looks very unusual. Lots of empty space above the head - very suboptimal FOV

I have never run into such data before - indeed adding an option to pass cw256 to recon-all would fix. I’ll open an issue, but in the interest of setting priorities: are you interested in processing this particular dataset or just picked it at random to play with BIDS data?


#3

GitHub issue: https://github.com/poldracklab/fmriprep/issues/1225


#4

Hi Chris, thanks for your very quick reply. I actually just randomly picked it to experiment with it, so just luck of the draw. I have now downloaded another set of data and will continue with that one.
BTW, how can I pass cw256 to recon-all from the docker command?


#5

This functionality is currently not supported.


#6

Hi, Chris,
I also encountered similar problem with my own data when using recon function (with --fs-no-reconall, I could finish the preprocessing)

Here is the log from recon-all.log:

Mon Mar 11 00:13:28 UTC 2019
/out/out/freesurfer/sub-001
/opt/freesurfer/bin/recon-all
-autorecon1 -i /data/sub-001/ses-d1/anat/sub-001_ses-d1_T1w.nii.gz -noskullstrip -cw256 -hires -openmp 7 -subjid sub-001 -sd /out/out/freesurfer -expert /work/fmriprep_wf/single_subject_001_wf/anat_preproc_wf/surface_recon_wf/autorecon1/expert.opts
subjid sub-001
setenv SUBJECTS_DIR /out/out/freesurfer
FREESURFER_HOME /opt/freesurfer
Actual FREESURFER_HOME /opt/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
Linux 3e5932778b80 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 09:33:07 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 8192 kbytes
coredumpsize unlimited
memoryuse unlimited
vmemoryuse unlimited
descriptors 1048576
memorylocked 16384 kbytes
maxproc unlimited
maxlocks unlimited
maxsignal 63302
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited

          total        used        free      shared  buff/cache   available

Mem: 16284864 4278568 2888448 294604 9117848 11211380
Swap: 7812092 456192 7355900

########################################
program versions used
$Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $
$Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $
mri_convert.bin -all-info
ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
FLIRT version 5.5
$Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $
mri_convert.bin --version
stable6
ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
Program nu_correct, built from:
Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34
ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/11-00:13:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:28-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
$Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $

ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
$Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $

ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/03/11-00:13:29-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: root Machine: 3e5932778b80 Platform: Linux PlatformVersion: 4.15.0-46-generic CompilerName: GCC CompilerVersion: 40400
#######################################
GCADIR /opt/freesurfer/average
GCA RB_all_2016-05-10.vc700.gca
GCASkull RB_all_withskull_2016-05-10.vc700.gca
AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif
GCSDIR /opt/freesurfer/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
#######################################
-cw256 option is now persistent (remove with -clean-cw256)
/out/out/freesurfer/sub-001

mri_convert /data/sub-001/ses-d1/anat/sub-001_ses-d1_T1w.nii.gz /out/out/freesurfer/sub-001/mri/orig/001.mgz

mri_convert.bin /data/sub-001/ses-d1/anat/sub-001_ses-d1_T1w.nii.gz /out/out/freesurfer/sub-001/mri/orig/001.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/sub-001/ses-d1/anat/sub-001_ses-d1_T1w.nii.gz…
TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (1, 1.94477e-16, -1.10357e-16)
j_ras = (-2e-16, 0.998622, -0.0524728)
k_ras = (1e-16, 0.0524728, 0.998622)
writing to /out/out/freesurfer/sub-001/mri/orig/001.mgz…
#--------------------------------------------
#@# MotionCor Mon Mar 11 00:13:41 UTC 2019
Found 1 runs
/out/out/freesurfer/sub-001/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-001/mri/orig/001.mgz /out/out/freesurfer/sub-001/mri/rawavg.mgz

/out/out/freesurfer/sub-001

mri_convert /out/out/freesurfer/sub-001/mri/rawavg.mgz /out/out/freesurfer/sub-001/mri/orig.mgz --conform_min

mri_convert.bin /out/out/freesurfer/sub-001/mri/rawavg.mgz /out/out/freesurfer/sub-001/mri/orig.mgz --conform_min
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /out/out/freesurfer/sub-001/mri/rawavg.mgz…
TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (1, 1.94477e-16, -1.10357e-16)
j_ras = (-2e-16, 0.998622, -0.0524728)
k_ras = (1e-16, 0.0524728, 0.998622)
changing data type from float to uchar (noscale = 0)…
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /out/out/freesurfer/sub-001/mri/orig.mgz…


ERROR! FOV=259.201 > 256
Include the flag -cw256 with recon-all!
Inspect orig.mgz to ensure the head is fully visible.


Linux 3e5932778b80 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 09:33:07 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-001 exited with ERRORS at Mon Mar 11 00:13:54 UTC 2019

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


#7

Are you reusing an old working directory?


#8

Hi, Oscar,

Thanks for your response!
Can you specify a bit? I am not sure that I fully understand what “an old working directory” means.

Below is my code:

docker run --rm -it \
-v /media/hcp4715/USB1/Data/RepDopa/BIDS_test/Nifti:/data:ro \
-v /media/hcp4715/USB1/Data/RepDopa/BIDS_test/Nifti/derivatives:/out \
-v /media/hcp4715/OS/host/freesurf_license/license.txt:/license/license.txt \
-v /media/hcp4715/study/fmriprep_tmp:/work \
poldracklab/fmriprep:1.3.1 \
/data /out/out \
participant --participant-label 001 \
-w /work \
--fs-license-file /license/license.txt

#9

No worries, the question is whether you have some old fmriprep run on /media/hcp4715/study/fmriprep_tmp. Since you are passing that to be mounted at /work and then the working directory is set there -w /work, it could be the case that you are running an old instance of the interfaces (although I must say this is very unlikely).


#10

Hey, Oscar,

That’s not likely the case, because I already emptied the folder before I run.


#11

Thanks, I’ll double check this on our end. Stay tuned!


#12

Update: sMRIPrep does add the -cw256 flag when running this dataset. I’ll find out why fMRIPrep (which imports the surface reconstruction workflow from sMRIPrep) is not picking it up.


#13

@hcp4715 It seems to work for me. I’m running:

docker run -it --rm -u $( id -u ) \
       -v $HOME/.freesurfer6.txt:/opt/fslicense.txt:ro \
       -v $HOME/datalad/ds000157:/data:ro \
       -v $PWD:/tmp -w /tmp \
       poldracklab/fmriprep:1.3.1 \
       /data out/ participant \
      --participant-label 01 --omp-nthreads 8 --nthreads 10 \
      -vv --fs-license /opt/fslicense.txt

And I get:

$ cat work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon1/command.txt
recon-all -autorecon1 -i /tmp/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 -cw256 -openmp 8 -subjid sub-01 -sd /tmp/out/freesurfer

As you’ll see, the -cw256 argument is properly set. I think the old arguments are cached somewhere, so please start fresh wiping out both work and out directories.

Please let us know whether that worked for you.


#14

Hi, Oscar,

I ran the analysis again. Yes, the -cw256 argument was also there in the recon-all.log. but still I got the same error.
Does that means my data has problem?

Below are the crash log:

Node: fmriprep_wf.single_subject_001_wf.anat_preproc_wf.surface_recon_wf.autorecon1
Working directory: /tmp/fmriprep_wf/single_subject_001_wf/anat_preproc_wf/surface_recon_wf/autorecon1

Node inputs:

FLAIR_file = <undefined>
T1_files = ['/data/sub-001/ses-d1/anat/sub-001_ses-d1_T1w.nii.gz']
T2_file = <undefined>
args = <undefined>
big_ventricles = <undefined>
brainstem = <undefined>
directive = autorecon1
environ = {}
expert = <undefined>
flags = ['-noskullstrip', '-cw256']
hemi = <undefined>
hippocampal_subfields_T1 = <undefined>
hippocampal_subfields_T2 = <undefined>
hires = True
mprage = <undefined>
mri_aparc2aseg = <undefined>
mri_ca_label = <undefined>
mri_ca_normalize = <undefined>
mri_ca_register = <undefined>
mri_edit_wm_with_aseg = <undefined>
mri_em_register = <undefined>
mri_fill = <undefined>
mri_mask = <undefined>
mri_normalize = <undefined>
mri_pretess = <undefined>
mri_remove_neck = <undefined>
mri_segment = <undefined>
mri_segstats = <undefined>
mri_tessellate = <undefined>
mri_watershed = <undefined>
mris_anatomical_stats = <undefined>
mris_ca_label = <undefined>
mris_fix_topology = <undefined>
mris_inflate = -n 50
mris_make_surfaces = <undefined>
mris_register = <undefined>
mris_smooth = <undefined>
mris_sphere = <undefined>
mris_surf2vol = <undefined>
mrisp_paint = <undefined>
openmp = 8
parallel = <undefined>
subject_id = sub-001
subjects_dir = /tmp/out/freesurfer
talairach = <undefined>
use_FLAIR = <undefined>
use_T2 = <undefined>
xopts = <undefined>

Traceback (most recent call last):
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 473, in run
    result = self._run_interface(execute=True)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 557, in _run_interface
    return self._run_command(execute)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 637, 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/nipype/interfaces/base/core.py", line 758, in _run_interface
    self.raise_exception(runtime)
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 695, in raise_exception
    ).format(**runtime.dictcopy()))
RuntimeError: Command:
recon-all -autorecon1 -i /data/sub-001/ses-d1/anat/sub-001_ses-d1_T1w.nii.gz -noskullstrip -cw256 -hires -openmp 8 -subjid sub-001 -sd /tmp/out/freesurfer -expert /tmp/fmriprep_wf/single_subject_001_wf/anat_preproc_wf/surface_recon_wf/autorecon1/expert.opts
Standard output:
INFO: hi-res volumes are conformed to the min voxel size
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 /tmp/out/freesurfer
Actual FREESURFER_HOME /opt/freesurfer
Linux 5c08ef032aee 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 09:33:07 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
'/opt/freesurfer/bin/recon-all' -> '/tmp/out/freesurfer/sub-001/scripts/recon-all.local-copy'
-cw256 option is now persistent (remove with -clean-cw256)
/tmp/out/freesurfer/sub-001

 mri_convert /data/sub-001/ses-d1/anat/sub-001_ses-d1_T1w.nii.gz /tmp/out/freesurfer/sub-001/mri/orig/001.mgz 

mri_convert.bin /data/sub-001/ses-d1/anat/sub-001_ses-d1_T1w.nii.gz /tmp/out/freesurfer/sub-001/mri/orig/001.mgz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/sub-001/ses-d1/anat/sub-001_ses-d1_T1w.nii.gz...
TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (1, 1.94477e-16, -1.10357e-16)
j_ras = (-2e-16, 0.998622, -0.0524728)
k_ras = (1e-16, 0.0524728, 0.998622)
writing to /tmp/out/freesurfer/sub-001/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Tue Mar 12 13:15:36 UTC 2019
Found 1 runs
/tmp/out/freesurfer/sub-001/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 /tmp/out/freesurfer/sub-001/mri/orig/001.mgz /tmp/out/freesurfer/sub-001/mri/rawavg.mgz 

/tmp/out/freesurfer/sub-001

 mri_convert /tmp/out/freesurfer/sub-001/mri/rawavg.mgz /tmp/out/freesurfer/sub-001/mri/orig.mgz --conform_min 

mri_convert.bin /tmp/out/freesurfer/sub-001/mri/rawavg.mgz /tmp/out/freesurfer/sub-001/mri/orig.mgz --conform_min 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /tmp/out/freesurfer/sub-001/mri/rawavg.mgz...
TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (1, 1.94477e-16, -1.10357e-16)
j_ras = (-2e-16, 0.998622, -0.0524728)
k_ras = (1e-16, 0.0524728, 0.998622)
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
Reslicing using trilinear interpolation 
writing to /tmp/out/freesurfer/sub-001/mri/orig.mgz...

****************************************
ERROR! FOV=259.201 > 256
Include the flag -cw256 with recon-all!
Inspect orig.mgz to ensure the head is fully visible.
****************************************

Linux 5c08ef032aee 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 09:33:07 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-001 exited with ERRORS at Tue Mar 12 13:15:49 UTC 2019

For more details, see the log file /tmp/out/freesurfer/sub-001/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Standard error:

Return code: 1

#15

Hi @hcp4715 this looks like worth posting on FreeSurfer’s mailing list. I think this is not fMRIPrep’s fault. Before escalating the issue, could we wait for @effigies to double check I’m right?


#16

It looks like -cw256 and -hires are mutually exclusive.

From recon-all:

    case "-hires":
      set HiRes = 1;
      set ConformMin = 1;
      echo "INFO: hi-res volumes are conformed to the min voxel size"
      # per testing by Natalia Zaretskaya, Mar 2015, the flags which
      # normally disable the aseg steps are no longer necessary (which
      # means aseg.mgz can be created with hi-res data).
      breaksw

...

  if($ConformMin) then
    set cmd = ($cmd --conform_min)
  else
    set cmd = ($cmd --conform)
    if($DoConformWidth256 || -e $subjdir/tmp/cw256) then
      # force conform width to 256
      set cmd = ($cmd --cw256)
      # see note just below on when -cw256 is necessary (ie, when FOV > 256)
    endif
  endif

So feel free to report it as a bug to the list, but you’re unlikely to find a simple resolution. I think your best options are (a) --no-submm-recon, if you don’t care about using the extra resolution; or (b) cropping your original image to a suitably small FoV.


#17

Hi, Chris,

I tried the first approach, used codes, but got the same error.
Did I use the --no-submm-recon incorrectly?

docker run --rm -it \
-v /media/hcp4715/USB1/Data/RepDopa/BIDS_test/Nifti:/data:ro \
-v /media/hcp4715/USB1/Data/RepDopa/BIDS_test/Nifti/derivatives:/out \
-v /media/hcp4715/OS/host/freesurf_license/license.txt:/license/license.txt:ro \
-v /media/hcp4715/study/tmp:/tmp \
poldracklab/fmriprep:1.3.1 \
/data /out/ \
participant --participant-label 001 \
--omp-nthreads 8 --nthreads 6 \
-w /tmp \
-vv --fs-license /license/license.txt
--no-submm-recon

Error log:

RuntimeError: Command:
recon-all -autorecon1 -i /data/sub-001/ses-d1/anat/sub-001_ses-d1_T1w.nii.gz -noskullstrip -cw256 -hires -openmp 8 -subjid sub-001 -sd /out/freesurfer -expert /tmp/fmriprep_wf/single_subject_001_wf/anat_preproc_wf/surface_recon_wf/autorecon1/expert.opts
Standard output:
INFO: hi-res volumes are conformed to the min voxel size
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/freesurfer
Actual FREESURFER_HOME /opt/freesurfer
Linux c06a4a912929 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 09:33:07 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
'/opt/freesurfer/bin/recon-all' -> '/out/freesurfer/sub-001/scripts/recon-all.local-copy'
-cw256 option is now persistent (remove with -clean-cw256)
/out/freesurfer/sub-001

 mri_convert /data/sub-001/ses-d1/anat/sub-001_ses-d1_T1w.nii.gz /out/freesurfer/sub-001/mri/orig/001.mgz 

mri_convert.bin /data/sub-001/ses-d1/anat/sub-001_ses-d1_T1w.nii.gz /out/freesurfer/sub-001/mri/orig/001.mgz 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /data/sub-001/ses-d1/anat/sub-001_ses-d1_T1w.nii.gz...
TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (1, 1.94477e-16, -1.10357e-16)
j_ras = (-2e-16, 0.998622, -0.0524728)
k_ras = (1e-16, 0.0524728, 0.998622)
writing to /out/freesurfer/sub-001/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Thu Mar 14 01:05:48 UTC 2019
Found 1 runs
/out/freesurfer/sub-001/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/freesurfer/sub-001/mri/orig/001.mgz /out/freesurfer/sub-001/mri/rawavg.mgz 

/out/freesurfer/sub-001

 mri_convert /out/freesurfer/sub-001/mri/rawavg.mgz /out/freesurfer/sub-001/mri/orig.mgz --conform_min 

mri_convert.bin /out/freesurfer/sub-001/mri/rawavg.mgz /out/freesurfer/sub-001/mri/orig.mgz --conform_min 
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /out/freesurfer/sub-001/mri/rawavg.mgz...
TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (1, 1.94477e-16, -1.10357e-16)
j_ras = (-2e-16, 0.998622, -0.0524728)
k_ras = (1e-16, 0.0524728, 0.998622)
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram 
Reslicing using trilinear interpolation 
writing to /out/freesurfer/sub-001/mri/orig.mgz...

****************************************
ERROR! FOV=259.201 > 256
Include the flag -cw256 with recon-all!
Inspect orig.mgz to ensure the head is fully visible.
****************************************

Linux c06a4a912929 4.15.0-46-generic #49-Ubuntu SMP Wed Feb 6 09:33:07 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-001 exited with ERRORS at Thu Mar 14 01:06:01 UTC 2019

#18

Hi @hcp4715, I think the likely problem is here:

With no slash at the end of the next-to-last line, the last line is not part of the command, hence why you’re still seeing -hires in the recon-all command.

Also, I suspect you’re already doing this, but just in case, be sure to delete the subject directory (/media/hcp4715/USB1/Data/RepDopa/BIDS_test/Nifti/derivatives/freesurfer/sub-001), to ensure that a clean recon-all is run.


#19

thanks for spotting this error!
Now the code is running (already more than 8 hours)!!

PS: I asked my colleague about the FOV of the T1 image of my data (224 * 320 * 320, checked from MRIcron), he told me that it need to be reslice to 260.


#20

If your study is actively acquiring more data, you may want to look into your protocol and optimize the FoV prescription, as you are acquiring a fair volume of just noise.

Other than that, I don’t think you should reslice the images at all. Maybe crop out Y and Z to 255 (if you crop to 260 you still won’t be able to use the high resolution recon-all). Please do not reslice the data, just crop the data array and update the affine information if necessary.