fmriprep: Autorecon1 Crashing #286 on fmriprep:22.0.0rc1
What happened?
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node autorecon1. No func data created. Saw the bug #286 but the problem persists.
What command did you use?
I used docker swarm and also tried with docker
docker run -ti --rm \
-v /MRI_DATA/nyspi/patensasc/rawdata:/input:ro \
-v /MRI_DATA/nyspi/patensasc/derivatives:/output \
-v /MRI_DATA/freesurferlicense.txt:/opt/freesurfer/license.txt:ro \
nipreps/fmriprep:22.0.0rc1 \
/data /out \
participant --participant-label patensasc0085 --output-spaces T1w MNI152NLin2009cAsym:res-2 --cifti-output --output-layout legacy > /MRI_DATA/nyspi/patensasc/derivatives/fmriprep/logs/patensasc85.log 2>&1
What version of fMRIPrep are you running?
22.0.0rc1
How are you running fMRIPrep?
Docker
Is your data BIDS valid?
Yes
Are you reusing any previously computed results?
No
Please copy and paste any relevant log output.
[juan@doctor 20220622-194930_b6c9a7c4-f8c0-42c1-9d24-c2bb21870bee]$ cayt crash-20220622-202601-root-autorecon1-280d52fd-362d-4982-983c-78bdc47b4a87.txt
cayt: Command not found.
[juan@doctor 20220622-194930_b6c9a7c4-f8c0-42c1-9d24-c2bb21870bee]$ cat crash-20220622-202601-root-autorecon1-280d52fd-362d-4982-983c-78bdc47b4a87.txt
Node: fmriprep_22_0_wf.single_subject_patensasc0085_wf.anat_preproc_wf.surface_recon_wf.autorecon1
Working directory: /tmp/work/fmriprep_22_0_wf/single_subject_patensasc0085_wf/anat_preproc_wf/surface_recon_wf/autorecon1
Node inputs:
FLAIR_file = <undefined>
T1_files = <undefined>
T2_file = <undefined>
args = <undefined>
big_ventricles = <undefined>
brainstem = <undefined>
directive = autorecon1
environ = {}
expert = <undefined>
flags = <undefined>
hemi = <undefined>
hippocampal_subfields_T1 = <undefined>
hippocampal_subfields_T2 = <undefined>
hires = <undefined>
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 = <undefined>
mris_make_surfaces = <undefined>
mris_register = <undefined>
mris_smooth = <undefined>
mris_sphere = <undefined>
mris_surf2vol = <undefined>
mrisp_paint = <undefined>
openmp = 8
parallel = <undefined>
steps = <undefined>
subject_id = recon_all
subjects_dir = <undefined>
talairach = <undefined>
use_FLAIR = <undefined>
use_T2 = <undefined>
xopts = <undefined>
Traceback (most recent call last):
File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 524, in run
result = self._run_interface(execute=True)
File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 642, in _run_interface
return self._run_command(execute)
File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 750, in _run_command
raise NodeExecutionError(
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node autorecon1.
RuntimeError: subprocess exited with code 1.
Additional information / screenshots
]
About this issue
- Original URL
- State: closed
- Created 2 years ago
- Comments: 27 (9 by maintainers)
Thanks Chris Data went through
From: Chris Markiewicz @.> Sent: Thursday, July 28, 2022 7:45 AM To: nipreps/fmriprep @.> Cc: Sanchez, Juan (NYSPI) @.>; Mention @.> Subject: Re: [nipreps/fmriprep] Autorecon1 Crashing #286 on fmriprep:22.0.0rc1 (Issue #2801)
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ds000221 anatomicals, I think, are MP2RAGE: https://openneuro.org/datasets/ds000221/versions/1.0.0/file-display/sub-010001:ses-02:anat:sub-010001_ses-02_acq-mp2rage_T1w.nii.gzhttps://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fopenneuro.org%2Fdatasets%2Fds000221%2Fversions%2F1.0.0%2Ffile-display%2Fsub-010001%3Ases-02%3Aanat%3Asub-010001_ses-02_acq-mp2rage_T1w.nii.gz&data=05|01|Juan.Sanchez%40nyspi.columbia.edu|3aabe53e067440c2c1e808da708eab79|f46cb8ea79004d108ceb80e8c1c81ee7|0|0|637946056529503267|Unknown|TWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D|3000|||&sdata=gu5eXSMi3Nf19%2BdZmtSBqHgurYYDkB1NG605dn8DrDA%3D&reserved=0
Handling these is an open problem (nipreps/smriprep#18https://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnipreps%2Fsmriprep%2Fissues%2F18&data=05|01|Juan.Sanchez%40nyspi.columbia.edu|3aabe53e067440c2c1e808da708eab79|f46cb8ea79004d108ceb80e8c1c81ee7|0|0|637946056529503267|Unknown|TWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D|3000|||&sdata=cku2FTj0Xpm9i0RUhnpySUflx%2BxDwoTiJyowYb2VXQo%3D&reserved=0) and out-of-scope for this issue.
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Hi, I opened the original smriprep issue. I just learned tha
getfullpathfrom FS is also not imported and may be called by recon-all, leading to an error.