Thank you Douglas for the suggestion, I will try this method!
Alexarae
On Thu, Jul 10, 2014 at 11:43 AM, Douglas N Greve <gr...@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
> gr...@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.
>
>
_______________________________________________
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.
