Evaluation code used in the brain parcellation survey "Human brain mapping: A systematic comparison of parcellation methods for the human cerebral cortex".
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atlas
README.md
adj_rand_index.m
compute_bic.py
count_unique_elements.m
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README.md

Brain Parcellation Survey: Evaluation Code

This repo holds the evaluation code (mainly written in Matlab) used in the brain parcellation survey "Human brain mapping: A systematic comparison of parcellation methods for the human cerebral cortex", in which a large-scale and systematic comparison is carried out between the state-of-the-art connectivity-driven, anatomical, and random parcellation methods.

Please cite the corresponding paper (if using the code) as:

Arslan, S., Ktena, S.I., Makropoulos, A., Robinson, E.C., Rueckert, D., Parisot, S., "Human brain mapping: A systematic comparison of parcellation methods for the human cerebral cortex", NeuroImage (2017), http://dx.doi.org/10.1016/j.neuroimage.2017.04.014

Some useful links you may want to see before using the code

Survey page: https://biomedia.doc.ic.ac.uk/brain-parcellation-survey/

Download parcellations from: https://imperialcollegelondon.box.com/s/g5q0kyvpqdha5jgofhmiov9ws1ao0hi0

Preprint of manuscript: https://www.doc.ic.ac.uk/~sa1013/pub/2017-neuroimage-brain-parcellation-survey.pdf

Data reference manual: https://biomedia.doc.ic.ac.uk/wp-content/uploads/sites/95/2017/04/Reference-Manual.pdf

Usage

Simply follow in-file instructions. Reading the Data and Experimental Setup sections in the article may also help understand the code better.

Data

Generation and evaluation of parcellations are carried out using the publicly available datasets from the Human Connectome Project (HCP). Some functions may be dependent on the HCP data structures and require you to download certain files. However, each script can also be adapted to any other dataset, by following the steps throughout the codes. If you would like to use the HCP data, it can be downloaded from https://db.humanconnectome.org

Contact

Forward any questions to name.surname@imperial.ac.uk

To stay up-to-date with the survey follow me on https://twitter.com/salimarslan