This is the code for paper: Multimodal connectivity-based individualized parcellation and analysis for humans and rhesus monkeys Now published on IEEE Transcations on Medical Imaging: https://ieeexplore.ieee.org/document/10508267
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.
![image](https://private-user-images.githubusercontent.com/41955813/248475351-89a14cc1-cd61-4e45-921e-f61aeaad0fce.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.x5NOJooWH5QkdOF9yZJ3PAfXk9Jo8BH430rzfbVf2zY)
- 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
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.
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.
MCIP-derived individualized parcellations based on Glasser atlas and Brannetome atlas for HCP subjects is available on https://drive.google.com/file/d/1H0mV6Z4icdO9QSda7lPx0TgCO_1c_Dm8/view?usp=drive_link
@ARTICLE{10508267, author={Cui, Yue and Li, Chengyi and Lu, Yuheng and Ma, Liang and Cheng, Luqi and Cao, Long and Yu, Shan and Jiang, Tianzi}, journal={IEEE Transactions on Medical Imaging}, title={Multimodal Connectivity-based Individual Parcellation and Analysis for Humans and Rhesus Monkeys}, year={2024}, volume={}, number={}, pages={1-1}, keywords={Pipelines;Surface topography;Animals;Brain modeling;Task analysis;Surface reconstruction;Reliability;Brain atlas;diffusion tractography;individual parcellation;multimodal fusion;resting-state functional connectivity;rhesus monkey}, doi={10.1109/TMI.2024.3392946}}