External Email - Use Caution 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-boun...@nmr.mgh.harvard.edu> on behalf of Erik O'Hanlon <erikohan...@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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, Eugenio <e.igles...@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-boun...@nmr.mgh.harvard.edu> on behalf of Erik O'Hanlon <erikohan...@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: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> RCSI LEADING THE WORLD TO BETTER HEALTH [cid:image002.png@01D3F74D.423505F0] 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 [cid:image003.png@01D3F74D.423505F0] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/> Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018> RCSI LEADING THE WORLD TO BETTER HEALTH [cid:image004.png@01D3F74D.423505F0]
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