My understanding is the same. I've made my own ROI by hand drawing on the average subject and using various commands to map onto individual subjects. If you're doing resting analysis then you can check your general whole brain correlation results against the literature to see if your ROI performs well. It's not perfect, but it can give decent results.

Paul

Sent from my iPhone

On Mar 18, 2014, at 7:13 AM, Ella <ellahinton@hotmail.com> wrote:

Hi all,

I'm looking to create a mask for the hypothalamus on individual subjects. I've had a good look at the literature, and at the moment, am I right in thinking the automatic segmentation in Freesurfer doesn't currently include the hypothalamus?

thanks in advance
Ella

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