[Neuroimaging] extract center of mass with nibabel/nilearn/numpy

Christopher Markiewicz markiewicz at stanford.edu
Sat May 16 08:30:31 EDT 2020

Assuming that you're using standard center of mass, and are content with them sometimes lying outside the region if it is nonconvex, then it should be pretty simple:

Retrieve the indices for a region with numpy.where and average in each dimension. That will give you the index (though possibly non integral). If you need it in world coordinates, nibabel's apply_affine function can be passed the atlas affine and COM index.


On May 15, 2020 21:36, Sam W <samfmri at gmail.com> wrote:
I have an atlas with voxel numbers between 1 and 40 that correspond to different ROIs. I would like to extract the center of mass of each ROI, is there a way to do this with nibabel/nilearn/numpy?
Best regards,
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