Pre-processing MRI data

This repository contains the code for pre-processing MRI data. The codes are highly customized for the data we have. However, the codes can be used as a reference for pre-processing MRI data.

Requirements

R and python are required to run the codes. Additionally, we utilize a lot of containers including heudiconv, mriqc and fmriprep. Please refer to the BIDS documentation for more information.

Usage

Pre-processing is done with the following steps:

1. Convert DICOM files to BIDS format: ./preprocess/perform_heudiconv.R. Run ./preprocess/perform_heudiconv.R -h for more information.
2. Run MRIQC: ./preprocess/perform_mriqc.R. Run ./preprocess/perform_mriqc.R -h for more information.
3. Run pre-processing for functional data (i.e., fmriprep): ./preprocess/perform_fmriprep.R. Run ./preprocess/perform_fmriprep.R -h for more information.

Notes

The repository is organized into the following structure:

• Data Folders:
  • Folder sourcedata: contains the DICOM files.
  • Folder rawdata: contains the BIDS format data.
  • Folder bids_db: contains the database of BIDS Layout. This is used to speed up the pre-processing.
  • Folder derivatives: contains the pre-processed data.
  • Folder backup: contains backup data which are deemed obsolete.
  • Folder tmp: contains the temporary files generated during the pre-processing (mostly will be deleted after the pre-processing automatically).
  • Folder logs: contains the log files generated during the pre-processing by the cluster.
• Code Folders:
  • Folder R: contains the R scripts to do the pre-processing.
  • Folder preprocess: contains the end point script to do the pre-processing.
  • Folder template: contains the template files (you can find the shell and python templates here) to do the pre-processing.

fMRIprep

For storage considerations, we specified the outspaces as:

• MNI152NLin6Asym: we do not include MNI152NLin2009cAsym.
• anat: T1 weighted non-standard space.
• fsaverage6: freesurfer's surface based space.
• fsLR: aka CIFTI output.

TODO

ICA-AROMA was removed from fmriprep since 23.1.0, and a custom ICA-AROMA workflow is required.