Something is wrong in your settings. Have you checked your attachment?
For this specific command I used:
---- COMMAND EXECUTED: ---------------------------------------------------------
( export TMPDIR=/lscratch/$SLURM_JOB_ID && export SINGULARITY_BINDPATH=/gs3,/gs4,/gs5,/gs6,/gs7,/gs8,/gs9,/gs10,/gs11,/spin1,/scratch,/fdb,/data,/lscratch && export SINGULARITYENV_TEMPLATEFLOW_HOME=/home/fmriprep/.cache/templateflow && mkdir -p $TMPDIR/out && mkdir -p $TMPDIR/wrk && singularity run --cleanenv -B /data/DSST/containers/TemplateFlow:/home/fmriprep/.cache/templateflow -B /home/dmoracze/.cache/fmriprep:/home/fmriprep/.cache/fmriprep /data/DSST/containers/fmriprep-1.5.0.simg /data/dmoracze/rawdata $TMPDIR/out participant --participant_label sub-M16 -w $TMPDIR/wrk --nthreads $SLURM_CPUS_PER_TASK --mem_mb $SLURM_MEM_PER_NODE --fs-license-file /home/dmoracze/license.txt --output-spaces func fsaverage6 MNI152NLin6Asym --longitudinal --use-aroma --error-on-aroma-warnings ; \ STATUS=$? rsync -ach $TMPDIR/out /scratch/dmoracze/derivatives ; chown -R :MLDSST /scratch/dmoracze/derivatives ; (exit $STATUS) )
Which uses the node’s temporary scratch (/lscratch), then once the processing is finished it copies the output to /scratch. I’ll check my settings to see what’s going on, but either way the preprocessing still has errors.
This very much looks like you did not successfully find a stable configuration for your system. Could you post a link to the documentation of your HPC?
As discussed previously (Longitudinal FMRIPrep) the choice of
--longitudinalwill define how your T1w will be averaged. Unless you are expecting large anatomical changes, I think you are better off without it.
That’s fair. I’d still like the option to make this work if possible.