CREST fmriprep: another recon-all error #2
Description
Script/Job File
#!/bin/bash
#$ -pe smp 16
#$ -q UI
#$ -m bea
#$ -M [email protected]
#$ -o /Shared/vosslabhpc/Projects/CREST/code/fmriprep/out/
#$ -e /Shared/vosslabhpc/Projects/CREST/code/fmriprep/err/
OMP_NUM_THREADS=10
singularity run -H ${HOME}/singularity_home -B /Shared/vosslabhpc:/mnt \
/Shared/vosslabhpc/UniversalSoftware/SingularityContainers/fmriprep-1.2.1.simg \
/mnt/Projects/CREST/ /mnt/Projects/CREST/derivatives \
participant --participant_label BETTER120044 \
-w /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep \
--write-graph --mem_mb 35000 --omp-nthreads 10 --nthreads 16 --use-aroma \
--output-space template \
--template MNI152NLin2009cAsym \
--fs-license-file /mnt/UniversalSoftware/freesurfer_license.txt
Error Message
200308-19:04:37,644 nipype.workflow WARNING:
[Node] Error on "fmriprep_wf.single_subject_BETTER120044_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.tonative" (/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120044_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonative)
200308-19:04:38,854 nipype.workflow ERROR:
Node tonative failed to run on host argon-itf-cf49-34.hpc.
200308-19:04:38,859 nipype.workflow ERROR:
Saving crash info to /mnt/Projects/CREST/derivatives/fmriprep/sub-BETTER120044/log/20200308-100511_d66a5daa-772a-4968-b8d4-99daf24ea0a9/crash-20200308-190438-ariveradompenciel-tonative-78122109-9cd6-4992-a632-81babfdc0001.txt
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 471, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 555, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/freesurfer/base.py", line 144, in run
return super(FSCommand, self).run(**inputs)
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 522, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 1038, in _run_interface
self.raise_exception(runtime)
File "/usr/local/miniconda/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 975, in raise_exception
).format(**runtime.dictcopy()))
RuntimeError: Command:
mri_label2vol --regheader /mnt/Projects/CREST/derivatives/freesurfer/sub-BETTER120044/mri/aseg.mgz --seg /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120044_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonative/aseg.mgz --temp /mnt/Projects/CREST/derivatives/freesurfer/sub-BETTER120044/mri/rawavg.mgz --o /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120044_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonative/aseg_vol.nii.gz
Standard output:
Number of labels: 0
Annot File: (null)
Template Volume: /mnt/Projects/CREST/derivatives/freesurfer/sub-BETTER120044/mri/rawavg.mgz
Outut Volume: /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120044_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonative/aseg_vol.nii.gz
Registration File: (null)
Fill Threshold: 0
Label Vox Vol: 1
ProjType: (null)
ProjTypeId: 0
ProjStart: 0
ProjStop: 0
ProjDelta: 0.1
Subject: (null)
Hemi: (null)
UseNewASeg2Vol: 0
DoLabelStatVol 0
LabelCodeOffset 0
setenv SUBJECTS_DIR /opt/freesurfer/subjects
$Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $
Template RAS-to-Vox: --------
-1.00000 -0.00000 -0.00000 98.00000;
-0.00000 -0.00000 -1.00000 128.00000;
-0.00000 1.00000 -0.00000 128.00000;
-0.00000 -0.00000 -0.00000 1.00000;
Template Voxel Volume: 1
nHits Thresh: 0
Computing registration based on header
RegMat: --------
-1.00000 0.00000 0.00000 0.00000;
0.00000 0.00000 1.00000 0.00000;
0.00000 -1.00000 0.00000 0.00000;
0.00000 0.00000 0.00000 1.00000;
Label RAS-to-Vox: --------
1.00000 0.00000 0.00000 98.00000;
0.00000 1.00000 0.00000 128.00000;
0.00000 0.00000 1.00000 128.00000;
0.00000 0.00000 0.00000 1.00000;
ERROR: loading aseg /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120044_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonative/aseg.mgz
Standard error:
mghRead(/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120044_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonative/aseg.mgz): could not read 262144 bytes at slice 151
Return code: 1
Potential Solution
delete the working directory and run again: /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120044_wf/anat_preproc_wf/surface_recon_wf