Hi Louis, thanks! I am still not sure whether or not structures such as the hippocampus and the amygdala are considered part of the cortex by freesurfer (they are referred to as `subcortical` but I think an anatomist would say they are in fact part of the cerebral cortex), and whether it makes sense to also calculate thickness for them, or just volume as detailed in the wiki page.

--Francesco

On 25 March 2014 18:59, Louis Nicholas Vinke <vinke@nmr.mgh.harvard.edu> wrote:

Hi Francesco,
This wiki page has pretty good definitions for the morphometry
stats. Let us know if you want to clarify anything though.

https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats

-Louis

On Tue, 25 Mar 2014, Francesco Puccettone wrote:

> Hello,
>
> I've read that cortical thickness analyses are limited to the cortex and cannot be used to examine subcortical grey
> matter. But does "subcortical grey matter" refer to deep gray matter structures such as the hippocampus, the basal
> ganglia or the nucleus accumbens - all of which are still technically part of the "cerebral cortex" - or does it in
> fact refer to gray matter nuclei surrounded by white matter, for which it would not be possible to model a white & a
> pial surface?
>
> Thank you!
> Francesco
>
>

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