MRIpostproc

Cognitive and Brain Health Laboratory 2026-19-5

Installation

install.packages("pak") 
pak::pak("CogBrainHealthLab/MRIpostproc")

Overview

This package contains tools:

• To post-process, export fMRI, ASL data into analyzable formats

  • CIFTItoFC : Generate FC matrices from XCP-D processed dtseries

  • CIFTItoFC_concat_ses : Generate FC matrices from XCP-D processed dtseries while concatenating multiple runs within each session

  • CIFTI_subj_avg : Compute the average FSLRv data across multiple runs for each subject

  • extractFS.ROI : Extract Destrieux atlas and ASEG ROIs from FreeSurfer's LHDestrieux.table, LHDestrieux.table and aseg.vol.table files

• To prepare data for preprocessing

  • modifyJSON : Edit .JSON files

  • editJSON_IntendedFor : Edit fmap's JSON files

• To assist downloading of HCP data from NIMH data archive

  • extract_links : Extract links from data manifests

  • extract_linksXCP : Extract links of XCP-d minimal inputs and FreeSurfer surface data from data manifests

• Quality control for preprocessed data

  • headmotion.fmriprep : Collate motion parameters from fMRIprep and generating bash script to delete fMRI volumes with excessive headmotion

  • headmotion.XCP : Collate motion parameters from XCP-D and generating bash script to delete fMRI volumes with excessive headmotion

  • asl.QC : Collate QC parameters from ASLprep