Dear Roma,
this is not so easy, because for the surface atlases I use the Freesurfer annotation format. You could try to change the code in cat_surf_render.m that is used for displaying atlas ROIs. Around line 154 you can find the code for reading atlas information. You have to set all ROIs to "0" or "Nan" that you don't want to display:
[fsv,cdata,colortable] = cat_io_FreeSurfer('read_annotation',O.pcdata); %clear fsv;
[sentry,id] = sort(colortable.table(:,5));
M.cdata = cdata; nid=1;
for sentryi = 1:numel(sentry)
ROI = round(cdata)==sentry(sentryi);
if sum(ROI)>0 && ( (sentryi==numel(sentry)) || sentry(sentryi)~=sentry(sentryi+1) && ...
(sentryi==1 || sentry(sentryi)~=sentry(sentryi+1))),
M.cdata(round(cdata)==sentry(sentryi)) = nid;
labelmap(nid,:) = colortable.table(id(sentryi),1:3)/255;
labelnam(nid) = colortable.struct_names(id(sentryi));
nid=nid+1;
ROIv(nid) = sum(ROI);
end
end
Best,
Christian
On Tue, 21 May 2019 16:41:49 +0100, Roma Siugzdaite <[log in to unmask]> wrote:
>Dear expert,
>
>It is a question about visualization only. Let's say with some analysis
>outside the toolbox I found few brain areas form DK40 that are important
>for my group of participants and I would like to visualize them.
>Practically I need to make few areas in colors and trasparent the rest of
>the DK40 atlas. How can I do it? is any way in CAT12 to make (to visualize)
>only several areas of interest? Because now I can put the boundaries of the
>atlas, but nothing else.
>
>or any other toolbox that does it would be great!
>cheers,
>Roma
>
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