Thank you Douglas for the suggestion, I will try this method!

Alexarae

On Thu, Jul 10, 2014 at 11:43 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu

wrote:

If you have matlab, it would be pretty easy to do it there, something like

aseg = MRIread('aseg.mgz'); seg = MRIread('seg_edited.mgz');

% Your first seg inside cerebellum indseg1 = find(seg.vol == 1 & (aseg.vol == 8 | aseg.vol == 47)); % cerebellum cortex = 8 and 47, see $FREESURFER_HOME/FreeSurferColorLUT.txt

aseg.vol(indseg1) = X1; % X1 = whatever index you want for your first segmentation, make it unique

MRIwrite(aseg,'newaseg.mgz')

On 07/09/2014 01:26 PM, N/A N/A wrote:

...

Hi Freesurfer forum,

I have never used the forum before but I am a long time user of Freesurfer and I am currently working on making a new atlas for the cerebellum. However I am having a problem loading my /seg_edited.mgz/ files into the /rebuild_gca_atlas.csh/ script. So I renamed my /aseg.mgz/ file to /seg_edited/ and that worked but my resulting image is not great.

I think it did not work with my original /seg_edited/ file because the atlas needed cortex data to complete the process and my original /seg_edited/ file did not have and my /aseg/ does.

I would like to try and combine my /aseg/ file and my original /seg_edited/ files together but I realized that no one has apparently asked about doing that before on your forums. Is there anyway to combine those files?

I would appreciate any advise on the matter!

Thank you, Alexarae Bryon

FIU student

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.