Hi Stephan,

Some different methods of creating ROI masks are covered in the FSL course practicals. Look in the Creating an example mask section here:

http://fsl.fmrib.ox.ac.uk/fslcourse/graduate/lectures/practicals/registration/index.html

and the Create a mask to probe statistics section here:

http://fsl.fmrib.ox.ac.uk/fslcourse/graduate/lectures/practicals/feat1/

Paul

On Tue, 30 Jun 2020 at 17:11, stephan Wunderlich <[log in to unmask]> wrote:
Dear all,

How can I create a mask which only contains the grey matter and basal ganglia of the MNI template?

Best,
Stephan

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