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
-------------------

* fMRIPrep documentation: https://fmriprep.org
* BIDS specification: https://bids.neuroimaging.io
* NiPreps project: https://www.nipreps.org

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