Example fmriprep Scripts¶

Example Single-Subject Job Script¶

This example script was written to process a single subject P01 from BIDS-formatted dataset D01 stored in $USER_DATA.

#!/bin/bash
#
#SBATCH --job-name=P01-fmriprep
#SBATCH --output=$USER_DATA/D01/jobs/out/P01-fmriprep-out.txt
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --partition=medium
#SBATCH --time=50:00:00
#SBATCH --mem-per-cpu=5G
#SBATCH --mail-type=FAIL

# Users should only need to change the dataset_dir and the participant below to run this script.

# set the path to the dataset directory. This is the parent to the BIDS-formatted nifti directory.
dataset_dir=$USER_DATA/D01

# set the name of the participant
participant=P01

# load the module
module load rc/fmriprep/20.2.3

# run fmriprep
fmriprep --work-dir $dataset_dir/workdir/ \
         --participant-label $participant \
         --output-spaces T1w \
         --fs-license-file $HOME/license.txt \
         --n-cpus 4 \
         --omp-nthreads 4 \
         --cifti-output 91k \
         $dataset_dir/nifti/ \
         $dataset_dir/nifti/derivatives \
         participant

The job requests 4 CPUs and 4 GBs of memory per CPU for 50 hours total on the medium partition.
The working directory was placed directly underneath the dataset directory
The output space of the BOLD images was set to native T1w space as opposed to a normalized template space.
The copied FreeSurfer license file was placed in my home directory and referenced in the script.
All outputs were requested to be in cifti-space (91k default)
The bids_dir, output_dir, and analysis_level were listed in that order after the options.

This script can be submitted to the scheduler using sbatch <script.sh> where script.sh is the full path of the script (or just the script name if the terminal working directory contains the script).

Example Array Job Script¶

SLURM job arrays are scripts made to easily replicate a job to be performed across multiple inputs (i.e. multiple participants) while not taxing the job scheduler. Read more about SLURM job arrays at their documentation.

This example script was written to process all subjects from the participants.tsv file in BIDS-formatted dataset D01.

#!/bin/bash
#
#SBATCH --job-name=fmriprep-%a
#SBATCH --output=fmriprep-%A-%a.txt
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --partition=medium
#SBATCH --time=50:00:00
#SBATCH --mem-per-cpu=5G
#SBATCH --mail-type=FAIL

# Users should only need to change the dataset_dir to run this script.

# set the path to the dataset directory. This is the parent to the BIDS-formatted nifti directory.
dataset_dir=$USER_DATA/D01

# set the path to the BIDS-formatted nifti directory
bidsdir=$dataset_dir/nifti/

# set the participant id from the participants.tsv file in the bidsdir
pid=$(awk "NR==$(($SLURM_ARRAY_TASK_ID+2)){print;exit}" $bidsdir/participants.tsv | cut -f 1)

# load the module
module load rc/fmriprep/20.2.3

# run fmriprep
fmriprep --work-dir $dataset_dir/workdir/ \
         --participant-label $pid \
         --output-spaces T1w \
         --fs-license-file $HOME/license.txt \
         --n-cpus 4 \
         --omp-nthreads 4 \
         --cifti-output 91k \
         $bidsdir \
         $bidsdir/derivatives \
         participant

This script will replicate the fmriprep command for participants in the participants.tsv file. When submitting this job, include the --array=<min>-<max> option in the sbatch command representing the index of the participants you want to run. The index is 0-based. For example, if you want to run the first 10 participants in the file, use --array=0-9, whereas if you want to run the 7th and 10th participant only, use --array=6,9.

This script can be placed in and run from a code folder placed under the main dataset directory to maintain BIDS compliance.