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Thanks a mill Eugenio,
Best regards
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 13:02:07 To: Freesurfer support list Subject: Re: [Freesurfer] hippo subfields and amygdala
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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
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Erik O'Hanlon erikohanlon@rcsi.ie
Erik O'Hanlon Postdoctoral researcher
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RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.comhttp://www.rcsi.com/
Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022http://www.rcsi.ie/strategy2018
RCSI LEADING THE WORLD TO BETTER HEALTH
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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
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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
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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
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Erik O'Hanlon erikohanlon@rcsi.ie
Erik O'Hanlon Postdoctoral researcher
[cid:image001.png@01D3F74D.423505F0]
RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.comhttp://www.rcsi.com/
Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022http://www.rcsi.ie/strategy2018
RCSI LEADING THE WORLD TO BETTER HEALTH
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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
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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
[cid:image003.png@01D3F74D.423505F0]
RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohanlon@rcsi.ie W: www.rcsi.comhttp://www.rcsi.com/
Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022http://www.rcsi.ie/strategy2018
RCSI LEADING THE WORLD TO BETTER HEALTH
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