CREST fmriprep: recon-all error

[jdkent]

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 BETTER120041 \
-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

200315-12:00:45,49 nipype.workflow WARNING:
	 [Node] Error on "fmriprep_wf.single_subject_BETTER120041_wf.anat_preproc_wf.surface_recon_wf.autorecon1" (/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120041_wf/anat_preproc_wf/surface_recon_wf/autorecon1)
200315-12:00:47,231 nipype.workflow ERROR:
	 Node autorecon1 failed to run on host argon-lc-d7-21.hpc.
200315-12:00:47,265 nipype.workflow ERROR:
	 Saving crash info to /mnt/Projects/CREST/derivatives/fmriprep/sub-BETTER120041/log/20200315-115848_c2902e24-0ca3-4489-973d-6e710c7b75e1/crash-20200315-120047-ariveradompenciel-autorecon1-68b78db9-7c04-4959-b777-d6f8e47320dc.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/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:
recon-all -autorecon1 -i /mnt/Projects/CREST/sub-BETTER120041/anat/sub-BETTER120041_T1w.nii.gz -noskullstrip -openmp 10 -subjid sub-BETTER120041 -sd /mnt/Projects/CREST/derivatives/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 /mnt/Projects/CREST/derivatives/freesurfer
Actual FREESURFER_HOME /opt/freesurfer
Linux argon-lc-d7-21.hpc 3.10.0-862.14.4.el7.x86_64 #1 SMP Wed Sep 26 15:12:11 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
'/opt/freesurfer/bin/recon-all' -> '/mnt/Projects/CREST/derivatives/freesurfer/sub-BETTER120041/scripts/recon-all.local-copy'
/mnt/Projects/CREST/derivatives/freesurfer/sub-BETTER120041

 mri_convert /mnt/Projects/CREST/sub-BETTER120041/anat/sub-BETTER120041_T1w.nii.gz /mnt/Projects/CREST/derivatives/freesurfer/sub-BETTER120041/mri/orig/001.mgz 

mri_convert.bin /mnt/Projects/CREST/sub-BETTER120041/anat/sub-BETTER120041_T1w.nii.gz /mnt/Projects/CREST/derivatives/freesurfer/sub-BETTER120041/mri/orig/001.mgz 
niiRead(): error reading from /mnt/Projects/CREST/sub-BETTER120041/anat/sub-BETTER120041_T1w.nii.gz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /mnt/Projects/CREST/sub-BETTER120041/anat/sub-BETTER120041_T1w.nii.gz...
Linux argon-lc-d7-21.hpc 3.10.0-862.14.4.el7.x86_64 #1 SMP Wed Sep 26 15:12:11 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-BETTER120041 exited with ERRORS at Sun Mar 15 12:00:44 CDT 2020

For more details, see the log file /mnt/Projects/CREST/derivatives/freesurfer/sub-BETTER120041/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Standard error:

Return code: 1

Debugging

I tried running nib-ls on the anatomical file /Shared/vosslabhpc/Projects/CREST/sub-BETTER120041/anat/sub-BETTER120041_T1w.nii.gz
and it failed, which indicates the file was improperly copied/corrupted.

Potential Solution

Copy/create the anatomical file over again.