Hi Stefano

you can use either mri_binarize --match or mri_extract_label with labels 10 and 49 (which I got from FreeSurferColorLUT.txt)

cheers Bruce On Tue, 29 Apr 2014, stdp82@virgilio.it wrote:

Hi list, I'd like obtain FS thalami mask (nii.gz) to import in FSL and use it as seed mask in probtrackx.

Thanks,

Stefano