Run ICA-AROMA on existing output

1

Hello

I am running fmriprep 20.2.4 with the following command on compute canada:

singularity run --cleanenv -B /home -B /project -B /scratch -B /localscratch /dir1/fmriprep_new.simg /dir1/MRIBIDS /dir1/PROCESSED participant --participant-label ${subject} --notrack --use-aroma --aroma-melodic-dimensionality 80 --nthreads 1 --omp-nthreads 4 --output-space T1w MNI152NLin6Asym fsnative fsaverage -vvv --error-on-aroma-warnings --fs-subjects-dir /dir1/PROCESSED/freesurfer --fs-license-file /dir2/license.txt --work-dir $SLURM_TMPDIR

However, the pipeline was aborted for certain subjects due to out-of-memory error at the ICA-AROMA step. All other output files are there. Is there a simple way to only run the ICA-AROMA without have to redo the initial part of the pipeline?

#SBATCH --array=1-267
#SBATCH --cpus-per-task=8
#SBATCH --time=0-12:00
#SBATCH --mem=20G

Thank you for the info!
Julie

2

As long as you use the same work-dir and don’t remove the contents inside, previous outputs will be used to prevent unnecessary reprocessing.

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