Hi Erik,
If you render labels >7000, you shouldn’t see a rendering of the subfields – but they will indeed remain visible in the orthogonal views. If you want to get rid of them, you can use mri_threshold:
mri_threshold lh.hippoAmygLabels-T1-HippoAMYT1andT2FLAIR.v20.FS60.FSvoxelSpace.mgz 6999 onlyAmyg.mgz
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
ERC Senior Research Fellow
Centre for Medical Image Computing (CMIC)
University College London, and
Research Affiliate
Computer Science and Artificial Intelligence Laboratory (CSAIL)
Massachusetts Institute of Technology
http://www.jeiglesias.com
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: Friday, 16 November 2018 at 08:15
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] loading and rendering the Amygdala nuclei only in Freeview
External Email - Use Caution
Hi FS Experts,
I'm trying to make some images of my amygdala nuclei in freeview and selected my T1 as background and then loaded up lh.hippoAmygLabels-T1-HippoAMYT1andT2FLAIR.v20.FS60.FSvoxelSpace.mgz image which loads up perfectly.
I selected the "show existing labels " and the freesurfer colour LUT but when I select the range for 7001-7015 for amygdala only, the hippocampal subfields are still there. Is there a way to only load the amygdala nuclei. I'm sure it's something simple I'm
just not doing, but I can't seem to get it to work.
Any pointers gladly accepted
Thanks
Erik
Erik O'Hanlon
Postdoctoral researcher
RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont D9 Ireland
T: 8093740
E: erikohanlon@rcsi.ie W: www.rcsi.com
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