Fmriprep is an fMRI data preprocessing pipeline that produces an output that can be submitted to a variety of group-level analyses, including task-based and resting-state fMRI, graph theoretical metrics, and surface or volume-based statistics. Some of the preprocessing steps performed by fmriprep include coregistration, normalization, unwarping, noise component extraction, segmentation, and skullstripping.

References:

• Esteban O, Markiewicz CJ, Blair RW, Moodie CA, Isik AI, Erramuzpe A, Kent JD, Goncalves M, DuPre E, Snyder M, Oya H, Ghosh SS, Wright J, Durnez J, Poldrack RA, Gorgolewski KJ. fMRIPrep: a robust preprocessing pipeline for functional MRI. Nat Methods. 2019 Jan;16(1):111-116.

• Fmriprep Documentation
• Github page

• Module Name: fmriprep (see the modules page for more information)

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load fmriprep

[user@cn3144 ~]$ fmriprep -h
usage: fmriprep [-h] [--skip_bids_validation]
                [--participant-label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
                [--session-label SESSION_LABEL [SESSION_LABEL ...]] [-t TASK_ID]
                [--echo-idx ECHO_IDX]
                [--subject-anatomical-reference {first-lex,unbiased,sessionwise}]
                [--bids-filter-file FILE] [-d PACKAGE=PATH [PACKAGE=PATH ...]]
                [--bids-database-dir PATH] [--nprocs NPROCS] [--omp-nthreads OMP_NTHREADS]
                [--mem MEMORY_MB] [--low-mem] [--use-plugin FILE] [--sloppy] [--anat-only]
                [--level {minimal,resampling,full}] [--boilerplate-only] [--reports-only]
[...]
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. fmriprep.sh). For example (using test data below):

#!/bin/bash
#SBATCH --job-name=fmriprep
#SBATCH --gres=lscratch:20
#SBATCH --exclusive
#SBATCH --mem=32g
#SBATCH --time=72:00:00

module load fmriprep/20.2.1

tar -C /lscratch/${SLURM_JOB_ID} -xf /usr/local/apps/fmriprep/TEST_DATA/ds001.tar.gz

fmriprep /lscratch/${SLURM_JOB_ID}/ds001 /lscratch/${SLURM_JOB_ID}/fmriprep.out.ds001 \
         participant --participant_label sub-01 -w /lscratch/${SLURM_JOB_ID} \
         --notrack --use-aroma

Submit this job using the Slurm sbatch command.

sbatch fmriprep.sh

Create a swarmfile (e.g. fmriprep.swarm). For example:

fmriprep /data/${USER}/BIDS-dataset/ds001/ /data/$USER/BIDS-dataset/fmriprep.out.ds001 \
         participant --participant_label sub-01 -w /lscratch/${SLURM_JOB_ID} \
         --use-aroma --notrack
fmriprep /data/${USER}/BIDS-dataset/ds002/ /data/$USER/BIDS-dataset/fmriprep.out.ds002 \
         participant --participant_label sub-02 -w /lscratch/${SLURM_JOB_ID} \
         --use-aroma --notrack
fmriprep /data/${USER}/BIDS-dataset/ds003/ /data/$USER/BIDS-dataset/fmriprep.out.ds003 \
         participant --participant_label sub-03 -w /lscratch/${SLURM_JOB_ID} \
         --use-aroma --notrack 

Submit this job using the swarm command.

swarm -f fmriprep.swarm [--gres=lscratch:#] [-g #] -t auto --module fmriprep