sure, we segment putamen, pallidum and caudate as part of the aseg.mgz 
(and nucleus accumbens, although that is less well-defined)
On Thu, 11 Feb 
2016, Syeda Wajiha Maryam wrote:

> Fear Freesurfer Experts,
> 
> I have a feeling this question has been asked already but I'm still confused
> about it. Is there a way to extract the basal ganglia structure using
> freesurfer?
> 
> Thanks in advance for your help!
> 
> Regards,
> Maryam
> 
>
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