Freesurfer error FOV > 256

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

1 Like

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?

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

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?

This functionality is currently not supported.

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

Are you reusing an old working directory?

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

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).

Hey, Oscar,

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

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

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.

@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.

1 Like

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

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?

1 Like

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.

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

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.

2 Likes

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.

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.