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