WilliamFCB
commented
10 months ago Hi @dmd, did you figure it out? I am not a mriqc expert, but I could see in the error that your input file could not be found/identified
The 'in_file' trait of a _AddProvenanceInputSpec instance must be a pathlike object or string representing an existing file, but a value of '/data/skohut/data/p50/sub-ss102/ses-12baseline/func/sub-ss102_ses-12baseline_task-rest_bold.nii' <class 'str'> was specified.
Maybe 23.1.0 somehow evaluates relevant input differently than 23.0.1? I leave that up to the experts ...
Anyway, I typically run things in slurm using sbatch and loop through subjects. The call below using 23.1.0 works fine for me.
Cheers William
mriqc_sif="${SCRIPTS_DIR}/mriqc.23.1.0.sif"
mem=18 #gb
sub_label=${sub/sub-}
ses_label=${ses/ses-}
catch_error singularity run --cleanenv --contain \ -B ${TOOLS_DIR} \ -B ${SCRIPTS_DIR} \ -B ${BIDS_TMP_DIR}:/data_in \ -B ${DERIV_DIR}:/data_out \ -B ${WORK_DIR}:/work \ -B /tmp:/tmp \ ${mriqc_sif} \ /data_in \ /data_out \ participant \ -w /work \ --participant-label ${sub} \ --session-id ${ses_label} \ --mem_gb ${mem} \ --float32 \ --nprocs ${SLURM_CPUS_PER_TASK} \ --ants-nthreads ${SLURM_CPUS_PER_TASK} \ --verbose-reports \ --no-sub \ --write-graph \ --notrack \ -vv
dmd
effigies
What happened?
Using:
mriqc immediately fails: 23.1.0.txt
Using the exact same command line but with 23.0.1:
mriqc completes successfully.
What command did you use?
What version of the software are you running?
23.1.0
How are you running this software?
Singularity
Is your data BIDS valid?
Yes
Are you reusing any previously computed results?
No
Please copy and paste any relevant log output.
No response
Additional information / screenshots
No response