ReHo and fALFF processing

This github page stores the code used to process the fMRI data to calcualte ReHo and fALFF values

Main steps, and corresponding code:

1. Preprocessing and calculation of fALFF and ReHo using CPAC
   • ABIDE_CPAC, especially the CPAC config file (CPAC_config_ABIDEI.yml and CPAC_config_ABIDEII.yml)
2. Registration and segmentation
   • EPI_registraion/ABIDE1_EPI_registration_parallel.sh
   • EPI_registraion/ABIDE1_EPI_registration_parallel.sh
3. Compute regional stats
   • EPI_registraion/compute_stats.py
4. Removal of subjects with poor alignment to MNI
   • notebooks/remove_poor_alignment_and_add_meta.ipynb
5. Removal of subjects with high motion
   • notebooks/motion_based_scan_selection_and_culling.ipynb
6. Site correction
   • /archive/bioinformatics/DLLab/AlexTreacher/src/autism_DCG/github/site_norm/calc_global_and_site_means.py
   • /archive/bioinformatics/DLLab/AlexTreacher/src/autism_DCG/github/site_norm/equalize_global_all.py

Dependencies

You will need python3, Matlab, CPAC and FSL to run this code.