Summary of what happened:
For a project that previously used scripts/configurations/etc set up for fmriprep 1.3.2, using fmriprep 22.1.1, with some changes to options, results in various failures. The task data that has been through fmriprep 1.3.2 is not going to be reprocessed, but we need to put the resting state scans through the new version of fmriprep that produces different output. (Resting state scans have made it through the old version of fmriprep, but we plan on replacing that output).
Command used (and if a helper script was used, a link to the helper script or the command generated):
previously used (without error):
/opt/singularity/bin/singularity run --cleanenv -B \
"${PRIMARY_WORKING_DIR}ECDM$(echo ${SUBID} | cut -c 1-4)":/tmp \
/data/nil-bluearc/ccp-hcp/SingularityImages/fmriprep-1.3.2.simg \
--fs-license-file /tmp/.license/freesurfer/license.txt \
-w /tmp /tmp/BIDS /tmp/derivatives \
participant --participant_label "ECDM$(echo ${SUBID} | cut -c 1-4)" \
--output-space template fsaverage5 \
--template MNI152NLin2009cAsym \
--template-resampling-grid native \
--n-cpus 16 \
--omp-nthreads 4 \
--mem-mb 64000 -v
New, failing command, with modified options for slightly different output (recommended by lab member)
/opt/singularity/bin/singularity run --cleanenv -B \
"${PRIMARY_WORKING_DIR}ECDM$(echo ${SUBID} | cut -c 1-4)":/tmp \
/data/nil-bluearc/ccp-hcp/SingularityImages/fmriprep-22.1.1.simg \
--fs-license-file /tmp/.license/freesurfer/license.txt \
-w /tmp /tmp/BIDS /tmp/derivatives \
participant --participant_label "ECDM$(echo ${SUBID} | cut -c 1-4)" \
--output-spaces MNI152NLin6Asym:res-2 MNI152NLin2009cAsym \
--cifti-output \
--n-cpus 16 \
--omp-nthreads 4 \
--mem-mb 64000 -v
Version:
22.1.1
Environment (Docker, Singularity, custom installation):
singularity
Data formatted according to a validatable standard? Please provide the output of the validator:
BIDS; Previously, with the older version of fmriprep, we were able to process without a dataset_description.json file. In my current attempts at troubleshooting, noting a related error, I did some digging and realized that the new version of fmriprep expected that as mandatory, so I created one to see if it helped. The data now passes through the online validator tool without errors, only warnings about missing events, readme, and too few authors. That doesn’t seem to resolve the problems, though.
Relevant log outputs (up to 20 lines):
Some of the errors:
ECDM_fMRIPREP_Process_Rest_Only.sh: line 223: /scratch3/fMRIPrep_AFNI_Processing/ECDM/ECDM1000:/tmp: No such file or directory
a singularity error? (singularity versions haven’t changed)
Error for command "run": requires at least 1 arg(s), only received 0
Usage:
singularity [global options...] run [run options...] <container>
Run 'singularity run --help' for more detailed usage information.
Screenshots / relevant information:
My knowledge about neuro/BIDS/fmriprep is superficial at best; most of my work has been scriptifying containers that other people in our lab have made, and this feels like I’m going to have to take a deeper dive and better understand some things in order to troubleshoot. I believe the problem stems from differences in the different versions of fMRIPrep, and maybe some sort of difference in options that are passed, but it’s also possible that I might have made some other mistake in trying to adapt our old stuff to the new fmriprep version.