calculating the cortical thickness of the ROIs defined by a desired atlas

[maryamsadeghi357]

Hi everyone. I need to calculate the gray matter volume and cortical thickness of the ROIs defined by some atlases, like Craddock400, rather than the DKT atlas, for the parcellation. Is it possible to do this by ANTsPyNet (or other software or codes) and how?

[ntustison]

We don't have the Craddock400 atlas as part of the ANTsXNet functionality as we do the DKT atlas. However, I'm guessing that other people have propagated those labels to an individual T1 and you could do what they do to get your ROI-specific gray matter volumes. If you do that, you can generate the cortical thickness image using antspynet.cortical_thickness(...) example here and easily get the ROI thickness measurements.

[maryamsadeghi357]

Thank you, Nick, for your reply. How can I propagate the labels and calculate the GMV?

[ntustison]

If I'm not mistaken, the Craddock400 atlas was developed for fMRI analysis and so I'd be skeptical that it would even be a good candidate for gray matter volume estimates. If I were you, I would find a paper that actually uses it for that purpose and mimic what they do.