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
>
>

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> Freesurfer@nmr.mgh.harvard.edu
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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Fax: 617-726-7422

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