Yes the LUT evolves but remains backwards compatible.
And yes, the command looks OK to me!
Cheers,
/E
--
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>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, 29 May 2018 at 13:00
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] hippo subfields and amygdala
External Email - Use Caution
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
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.uk>
Sent: 29 May 2018 11:44:41
To: Freesurfer support list
Subject: Re: [Freesurfer] hippo subfields and amygdala
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
