MCIP: Multimodal Connectivity-based Individualized Parcellation

This is the code for paper: Multimodal connectivity-based individualized parcellation and analysis for humans and rhesus monkeys

MCIP simultaneously optimizes a single subject’s within-region homogeneity with the fusion of functional and anatomical connectivity, spatial continuity, and the similarity to a reference atlas.

How to use it

MATLAB Dependencies

• Reading GIfTI files in MATLAB: https://www.gllmflndn.com/software/matlab/gifti/
• Reading CIfTI files in MATLAB: https://github.com/Washington-University/cifti-matlab
• GCoptimization - software for energy minimization with graph cuts: https://github.com/nsubtil/gco-v3.0

Data preparation

Set rfMRI_dir as your rfMRI data directory, dMRI_dir as your dMRI data directory, and out_dir as your output directory in batch_mcip.sh.

Revise ref_atlas_file, LUT_file, and neighbor_file in batch_mcip.sh, if you want to use another reference atlas. neighbor_file can be automatically generated during the program running.

Using

Run the code with a batch of subjects using Slurm: sbatch -a 1-${N} batch_mcip.sh $sub_list, in which $sub_list is a .txt file containing subject ID.

If you do not use Slurm, please change sub_num=... to be a for loop.