Automatic Segmentation of GPi/GPe

Hi there,

Is there any possibility to automatically segment the globus pallidus internus and externus like what we do in recon all of freesurfer? However, the latter would segment for you the whole globus pallidus volume as in Desikan-Killiany atlas without differentiating it into gpi and gpe!


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Hi @bassam.alfatly, I am also hoping to find a tool that can do this. I did a little searching and found FSL MIST (Multimodal Image Segmentation Tool, 2016), but it sounds like it also ultimately combines GPe and GPi into a single ROI for each subject. MIST/UserGuide - FslWiki Automatic segmentation of the striatum and globus pallidus using MIST: Multimodal Image Segmentation Tool - ScienceDirect

Hopefully there is a better alternative. Please let me know if you have found anything.


There are at least two human brain atlases that include this division of the globus pallidus - the Pauli and the Keuken atlases. You might use these as your definitions for the regions by nonlinear alignment to a template. If you want something more precise, then you could use these as starting points.

Both these atlases divide the pallidum up into the two parts of Globus Pallidus internal and external parts. The ventral pallidum is also available in the Pauli atlas. The Pauli atlas uses the MNI 2009c nonlinear asymmetric template as its reference template space. The Keuken atlas uses “MNI04 space”, a 0.4mm resolution version of an MNI template space.

The Keuken sub-cortical atlas paper and a version I put together for AFNI users

Keuken GPi, GPe from Elderly MPM atlas.

Pauli GPi, GPe (index values 5,6)