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_gather_counfounds : Original files don't match #382

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g-bond opened this issue Mar 24, 2022 · 0 comments · Fixed by #403
Closed

_gather_counfounds : Original files don't match #382

g-bond opened this issue Mar 24, 2022 · 0 comments · Fixed by #403

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@g-bond
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g-bond commented Mar 24, 2022

Hello,
I'm running the qsiprep-0.15.3 singularity image to reprocess some subjects.
Error is thrown from qsiprep/interfaces/confounds.py.

Here's the qsub call
qsub -cwd -l h_vmem=64.0G,s_vmem=64.0G -l gpu=1 -pe threaded 8 \ -j y -o /cbica/projects/anxiousMisery/qsiprep_work_dirs/postQC_reruns/qsiprep_${sub}_\$JOB_ID.o \ run_qsiprep.sh \ ${data_root} ${sub} /cbica/projects/anxiousMisery/qsiprep_work_dirs/postQC_reruns/qsiprep_${sub}_\$JOB_ID

Here's the script run_qsiprep.sh that's being submitted
data_root=${1}
sub=${2}
workdir=${3}

img=/software/singularity/qsiprep-0.15.3.sif
fs_license=/software/freesurfer/license.txt
niidir=/data/raw
outdir=/data/derivatives/postQC_reruns/qsiprep
sliceInfo=/cbica/projects/anxiousMisery/data/slspec/slspec.txt
cudaInfo=/usr/local/cuda-10.2

singularity run --nv --cleanenv \ -B ${data_root}:/data,${sliceInfo}:/data/slspec/slspec.txt,${cudaInfo}:/usr/local/cuda \ ${img} ${niidir} ${outdir} participant \ --fs-license-file ${fs_license} --notrack \ --nthreads 8 --omp-nthreads 8 \ -w ${workdir} --skip_bids_validation \ --verbose --eddy-config eddy_params_prisma_cuda.json \ --participant-label ${sub} --mem-mb 58000 \ --distortion-group-merge concat --output-resolution 1.5

No issues are encountered until the confounds are concatenated.
Here's the crash report :
crash-20220322-151218-anxiousmisery-concat-4fae89d2-9994-4961-a873-26f6b136a459.txt

This occurs for each subject that we tested under these new settings.
I'd appreciate any help with figuring out what's going wrong.
I haven't been able to understand what the issue is.

Please let me know if the inclusion of any more information could be helpful.

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