
PROGRAM: Genetic and functional Annotation Toolbox for the Human Connectome Project (HCP) Brain Atlas

VERSION: V1.0

PUBLICATION: Genetic and Functional Characterization of the areas in the Human Connectome Project Brain Atlas

AUTHORS: Zhaowen Liu, Edmund Rolls, Jie Zhang, Kamil Ugurbil, Jianfeng Feng

CONTACT: jianfeng.feng@warwick.ac.uk

DATE: 2017-3-01

DESCRIPTION: The toolbox provides genetic and functional annotations for the brain atlas provided in the paper 'Glasser, M.F., et al. A multi-modal parcellation of human cerebral cortex. Nature 536, 171-178 (2016).' 

USAGE: To run the toolbox, set the hcp_annotation folder as the current working directory in your Matlab workspace. Type 'hcp_annotation' in the command window to run the toolbox.

NOTES: The normalized region gene expression profiles are provided with the toolbox. The normalized region expression profiles were obtained by following procedures. 1. For a gene and an individual, expressions were normalized by extracting the median of the gene's expression across all samples belonging to the individual and then dividing by the median. This normalization procedure was performed for all genes and all the 6 individuals. 2. Then, all the samples were pooled together. The region expression value of a gene is the mean of all the samples that mapped to the region according to their MNI coordinates. Details are provided in our paper cited above.

ACKNOWLEDGEMENTS: The authors gratefully acknowledge the Allen Institute for Brain Science (for the genetic data); the Neurosynth Database (Yarkoni, T., Poldrack, R.A., Nichols, T.E., Van Essen, D.C. & Wager, T.D. Large-scale automated synthesis of human functional neuroimaging data. Nat Methods 8, 665-670 (2011)); and the Human Connectome Project.

