Hi Iglesias,

Kindly, we would like to know if there are any methods in Freesurfer that can help to segment that brain stem nucleus. I mean output the nucleus automatically as a small masks, so these small masks can be used in other analyses (e.g. fMRI)

I am thinking of creating masks for these nucleus depending on an atlas. I open the T1 image in Fslview and I create the mask for the nucleus of interest. But this is so hard, not accurate and time consuming. The reason for my question.

We highly appreciate any suggestion!

Best,

Mohamad