not sure if it can be done in fv, but you can create a mask of just the cerebellum cortex and wm with mri_binarize (use --match A B, where A and B are the segids for the two ROIs), then use mri_mask to mask everything else out of your segmentation

On 03/03/2014 06:01 PM, charles laidi wrote:

Dear Freesurfers,

I have just performed cerebellar segmentation with freesurfer. I checked the segmentation was correct using freeview : freeview -v t1_xxx/mri/aseg.mgz:colormap=lut:opacity=0.2

I would like to create a figure for my article. However, I'm not able to find a way to highlight only cerebellar cortex / white matter with freeview, instead of having every label of other subcortical structures in different colors. I would like to have only the cerebellum colored. Could this be done with freeview ?

Thanks a lot,

Charles

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