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6. Parcellation mask

The JDE framework estimates HRF parcels-wide. This means that you need a parcellation mask to compute the estimation-detection. PyHRF provides some tools to generate parcellation masks and provides also a parcellation mask.

6.1. Willard atlas

The Willard atlas comes from Stanford.


To use it check where it is installed by using:

$ pyhrf_list_datafiles

and check for stanford_willard_parcellation_3x3x3mm.nii.gz file.

This parcellation mask has been created from the files distributed by Stanford (above website) with a voxel resolution of 3x3x3mm and a volume shape of 53x63x52 voxels.

The citation for the 499 fROI atlas, nicknamed the “Willard” atlas after the two creators, William Shirer and Bernard Ng, is the following publication:

Richiardi, J., Altmann, A., Milazzo, A.-C., Chang, C., Chakravarty, M. M., Banaschewski, T., … Tahmasebi, A. (2015). Correlated gene expression supports synchronous activity in brain networks. Science, 348(6240), 1241–1244.