I would like to create a white matter mask in the original MRI space (without having to register it to a standard brain). To do this, I ran FAST but the white matter mask in FAST did not exclude subcortical regions. To exclude subcortical regions, I could run FIRST but FIRST is completed in MNI152 space, is that correct? If this is correct, then how should I create a white matter mask that excludes subcortical regions in FSL?
Thank you for you help.