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Hi, If you have T1-weighted images and have them registered to your diffusion images, then using FIRST would be our recommended way of creating subcortical ROIs. All the best, Mark On 13 May 2014, at 16:06, Paul Geha <[log in to unmask]> wrote: > Dear FSL expert, > > I am running tractography and would like to use striatal sub-divisions as targets. What is the best way to define and extract sub-cortical targets from each subject. Do you recommend using FAST ? Does FIRST have any use in this case. > Thank you for the advice! > Best, > Paul