Li Jingwei
Li Jingwei v0.6.5 - FixPublicationDetail_Wu2017_Schaefer2018

* These two papers are published now. Publication details are updated.

This change addresses the need by:

* Wu2017_RegistrationFusion users & Schaefer2018_LocalGlobal users
Latest commit 0967679 Aug 17, 2018



Resting state fMRI data from 1489 subjects were registered using surface-based alignment. A gradient weighted markov random field approach was employed to identify cortical parcels ranging from 100 to 1000 parcels. More details can be found in Schaefer et al. 2018.

Parcellations Release

The parcellations are available at multiple resolution (100 parcels to 1000 parcels), and can be found under the Parcellations folder. To use the parcellations without the trouble of downloading our entire repository, you can just click on this link: download Schaefer2018_Parcellations

Specifically, there are three subfolders corresponding to three different spaces Freesurfer5.3, MNI and HCP.

The parcellations were first computed in Freesurfer fsaverage6 space and sampled to fsaverage5 and fsaverage space. The parcellations were also projected to HCP fslr32k and FSL MNI space. Each parcel is matched to a corresponding network in the 7 and 17 network parcellation by Yeo et al. 2011.(The organization of the human cerebral cortex estimated by intrinsic functional connectivity).

Here we provide a visualization of the 400 parcel parcellation in fslr32k space, parcels were colored to match Yeo 7/17 network parcellation:

Code Release

The code utilized in this study is under Code folder. Specifically, the Code folder includes:

  • CBIG_gwMRF_build_data_and_perform_clustering.m -- The wrapper function that generates input data format from fMRI data and perform clustering.

  • lib folder -- This folder contains all other functions that will be called by the wrapper function.

  • -- You can check this file to find out more about our clustering code.


We provide example code for you run as well as example results for you to compare under examples folder. Please refer to examples/ for more information.

Download stand-alone repository

Since the whole Github repository is too big, we provide a stand-alone version of only this project and its dependencies. To download this stand-alone repository, visit this link:

Download whole repository

Except for this project, if you want to use the code for other stable projects from out lab as well, you need to download the whole repository.

To download the version of the code that is last tested, you can either


  • run the following command, if you have Git installed
git checkout -b Schaefer2018_LocalGlobal v0.6.5-FixPublicationDetail_Wu2017_Schaefer2018


  • Release v0.3.0 (21/07/2017): release the parcellations in MNI, fsLR and fsaverage space

  • Release v0.3.1 (07/09/2017): update utilities code

  • Release v0.3.2 (14/09/2017): fix a labeling bug in cifti files

  • Release v0.4.8 (30/01/2018): release clustering code

  • Release v0.4.12 (09/04/2018):

    1. Move example subjects from $CBIG_CODE_DIR/data/example_data/${subj_ID} to $CBIG_CODE_DIR/data/example_data/Corr_HNU/${subj_ID}.

    2. The example subjects are re-processed by a newer version of our preprocessing pipeline (v0.4.9). Hence results in ./Code/examples are updated.

    3. Update some files.

  • Release v0.6.3 (17/07/2018):

    1. Release Schaefer2018 300 parcels and 500 parcels parcellation.

    2. Add unit test scripts to unit_tests folder.

    3. Update, add links for people to directly download the Parcellations and this project's standalone repository: Standalone_Schaefer2018_LocalGlobal.

  • Release v0.6.5 (17/08/2018):

    1. Move examples folder from $CBIG_CODE_DIR/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/Code/examples to $CBIG_CODE_DIR/stable_projects/brain_parcellation/Schaefer2018_LocalGlobal/examples.

    2. Update publication details in README files.

    3. Fix a bug related to creating Standalone_Schaefer2018_LocalGlobal.

Bugs and Questions

Please contact Alexander Schaefer at and Thomas Yeo at