Hi JK,

You can use mri_extract_label:

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

Cheers,

/Eugenio

-- 

Juan Eugenio Iglesias

ERC Senior Research Fellow

Translational Imaging Group

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of 강준영 <episode9999@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, 19 December 2017 at 10:10
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Hippocampus subfield ROI

Deer Freesurfer Experts.

I'm currently working on hippocampus subfield parcellation in freesurfer version 6.0.0

In the previous version, freesurfer gave me CA1, CA3 and other subfields with separate mgz files so I could easily analyze them by AFNI separately. (make afni files for each subfields)

However, in the current version, it gives me a whole file hippoSflabels-T1.v1.mgz and I tried to extract a specific subfield information (e.g. CA1, subiculum) only but failed. How can I make separate volume files of hippocampus subfields out of the 'hippoSfLabels-T1.v1.mgz file?

I used 3dcalc function but got no idea to specify a region I'm interested in.

Please help me out guys.. 

Thanks!

Sincerely, 

Joonyoung Kang.