Hi Martina you can use mri_binarize --match 17 --match 18... to do this.

cheers Bruce

On Thu, 24 May 2012, Martina Papmeyer wrote:

Hello everyone,

I guess that this might be a simple question but I couldn't find an answer to my problem yet.

I would like to extract and visualize four labels from my aseg.mgz file for illustration purposes. I tried the following:

mri_extract_label aseg.mgz 17 18 53 54 filename.mgz

(the values correspond to left/right amygdala and left/right hippocampus as specified in FreeSurferColorLUT.txt file)

This command unfortunately combines all the four selected labels together so that I can't differentiate amygdala and hippocampus anymore when I load the filename.mgz file together with my FreeSurferColorLUT.txt file in tkmedit.

Is there any other FS tool I can use?

Any form of help would be highly appreciated!

Many thanks and all best wishes, Martina