fMRIPrep (Containerised)

fMRIPrep is a robust, community-maintained preprocessing pipeline for functional MRI (fMRI) data. On this cluster, fMRIPrep is provided as a containerized BIDS-App using Apptainer.

This ensures a consistent, reproducible software environment and avoids the need for users to install or manage neuroimaging dependencies.

Software Overview

  • Application: fMRIPrep

  • Version: 25.1.2

  • Container runtime: Apptainer

  • Interface: BIDS-Apps compliant command line

  • Execution: SLURM batch jobs

Loading the Module

Load the fMRIPrep module before running any jobs:

module load fmriprep/25.1.2

This makes the fmriprep command available on your $PATH.

Basic Usage

The fMRIPrep command follows the standard BIDS-Apps interface:

fmriprep <bids_dir> <output_dir> <analysis_level> [options...]

Required arguments:

  • <bids_dir> – Path to the BIDS-formatted input dataset (read-only)

  • <output_dir> – Directory where outputs will be written

  • <analysis_level> – Processing level (usually participant)

Example:

fmriprep /projects/mygroup/bids \
         /projects/mygroup/derivatives/fmriprep \
         participant

Running with SLURM

fMRIPrep should be run on compute nodes using SLURM.

Example SLURM job script:

#!/bin/bash
#SBATCH --job-name=fmriprep
#SBATCH --cpus-per-task=16
#SBATCH --mem=64G
#SBATCH --time=12:00:00
#SBATCH --output=fmriprep_%j.out
#SBATCH --error=fmriprep_%j.err

module load fmriprep/25.1.2

export TEMPLATEFLOW_HOME=/opt/templateflow
export FS_LICENSE=/opt/freesurfer/license.txt

fmriprep /projects/mygroup/bids \
         /projects/mygroup/derivatives/fmriprep \
         participant \
         --participant-label sub-01

Environment Variables

The following environment variables may be set in your job script:

TEMPLATEFLOW_HOME

Path to a TemplateFlow cache directory. Using a shared cache avoids repeated downloads of templates.

FS_LICENSE

Path to a valid FreeSurfer license file. This is required when FreeSurfer-based steps are enabled.

Scratch / Working Directory

During execution, fMRIPrep uses a temporary working directory on the compute node (preferentially $SLURM_TMPDIR). This directory is created automatically by the wrapper script and does not require manual configuration.

Participant Selection

To run specific participants, use the --participant-label option:

fmriprep /projects/mygroup/bids \
         /projects/mygroup/derivatives/fmriprep \
         participant \
         --participant-label sub-01 sub-02

Checking the Installation

To verify that fMRIPrep is available:

module load fmriprep/25.1.2
fmriprep --help

This should display the fMRIPrep help text.

Further Information

If you encounter issues or have questions, please contact the Research Computing support team.