Getting Started

Loading the fMRIPrep Module

The SCC uses a module system to load and access software packages. Refer to our module page for more extensive documentation.

To see all versions of fMRIPrep available on the SCC, you can search for the package with the module command:

[scc4]$ module avail fmriprep

--------------------------- /share/module.8/imaging ----------------------------
   fmriprep/v20.2.5    fmriprep/23.1.4        fmriprep/25.2.5
   fmriprep/v21.0.1    fmriprep/23.2.3 (D)
   fmriprep/22.0.2     fmriprep/24.1.1

  Where:
   D:  Default Module

Note that fmriprep/23.2.3 is the default — the version you get if you do not name one — and that it is not the newest build. Pin an explicit version in every script so your analyses stay reproducible. Results are not identical across fMRIPrep versions, so never change version partway through a study.

To load a specific version of fMRIPrep (25.2.5):

[scc4]$ module load fmriprep/25.2.5

Confirm the load worked:

[scc4]$ fmriprep --version
fMRIPrep v25.2.5

The FreeSurfer License

fMRIPrep uses FreeSurfer, which normally requires you to register for a free license file and pass it with --fs-license-file.

On the SCC you do not need to do this. The fmriprep module is a wrapper that supplies a license automatically, so the examples in this guide never mention one. If you copy a command from the fMRIPrep documentation that sets --fs-license-file, you can drop that flag.

Your Input Data

Your data must be organized according to the BIDS standard. We recommend using the tools dcm2bids and yaxil to get your data into BIDS format. Please see these help pages for more information.

A flat DICOM directory of opaque .dcm filenames on the left, reorganized on the right into a BIDS dataset: my_dataset/ holding participants.tsv and one sub-<label>/ directory per participant, each split into anat/, func/ and dwi/ with descriptive names such as sub-01_task-rest_bold.nii.gz.

Raw DICOMs as they come off the scanner (left) reorganized into a BIDS dataset (right).