Hi Eugenio,

Thanks, I'll give that a try. Just a quick question, the correct ROI id's for each subfield are in the LUT ? Is there a different LUT in the DEV version for the hippo and Amy subdivisions individually and also the anterior /posterior divisions and are there different numbers for each hemisphere? If I use the MRI_segment_Label can I make a mask for the whole structure volumes for the hippo and Amy just by listing all the ID's i.e.

mri_segment lh.hippoAmygLabels-T1.v2x.FSvoxelSpace.mgz 7001 7003 7005 7006 7007 7008 7009 7010 7015 LeftAmygdala.nii

Thanks again Eugenio really appreciate the help

Cheers

Erik

External Email - Use Caution

Hi Erik,

The subfield module gives you a segmentation in the same space as brain.mgz and the rest of volumes in the recon-all stream:

[lr]h.hippoAmygLabels-T1.v2x.FSvoxelSpace.mgz

You can use mri_extract_label to create binary masks.

Cheers,

/Eugenio

Juan Eugenio Iglesias

ERC Senior Research Fellow

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

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

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Erik O'Hanlon <erikohanlon@rcsi.ie>

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

Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022

RCSI LEADING THE WORLD TO BETTER HEALTH

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

External Email - Use Caution

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

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

Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022

RCSI LEADING THE WORLD TO BETTER HEALTH