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.