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From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Erik O'Hanlon <erikohanlon@rcsi.ie>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, 29 May 2018 at 11:07
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] hippo subfields and amygdala

Hi FS experts,

I have run my analysis using the dev version and have all the necessary volume.txt files. As a secondary step, I want to use some of the subfields as seed volumes for tractography (using ExploreDTI). I have may diffusion data in the same space as the FS brain.mgz but am wondering how I should make the subfield masks so that they will be in the same coordinate space when exported as a nii file. If I use Freeview and load the brain.mgz and then the subfield volumes, is it simply a case of reducing the LUT to the specific subfield and then save that as a volume/mask ? Will that mask be in the same coordinate space and regsitered the brain.nii too.

Is it just a matter of doing this process numerous times in Freeview and each time simply changing the LUT corresponding to the specific ROI needed to get the masks I want to use for each subject.

Thanks for any information you can offer

Best regards

Erik