Getting Started

Loading the MRIQC 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 MRIQC available on the SCC, you can search for the package with the module command:

[scc4]$ module avail mriqc

--------------------------- /share/module.8/imaging ----------------------------
   mriqc/22.0.6 (D)    mriqc/24.0.0

  Where:
   D:  Default Module

Note that mriqc/22.0.6 is the default — the version you get if you do not name one. We recommend pinning an explicit version in every script so your analyses stay reproducible.

To load a specific version of MRIQC (24.0.0):

[scc4]$ module load mriqc/24.0.0

Confirm the load worked:

[scc4]$ mriqc --version
MRIQC v24.1.0.dev0+g3fe90466.d20240417

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).