Subcortical visualization software


I was hoping to gather some recommendations for subcortical visualization. Particularly, visualization of unparcellated data (just the beta maps without region assignment). I’ve encountered brainpainter but this seems more suited to clinical applications. Generally, it seems that subcortical visualization software is sparse (the cortex is greedy for attention :slight_smile: ).

Thanks in advance for your thoughts,


If your subcortical regions are mesh based, or converted from voxels to mesh (e.g. Surfice Advanced/ConvertVoxelwiseToMesh menu item), you might want to use Surfice. The images below are made selecting the Scripting/Python/subcortical menu item

Another option is MRIcroGL. The image below is from the MRIcroGL Scripting/Templates/basic menu item. You can use the “overlayDepth” slider to improve visibility of deep structures like subcortical activations.


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Thanks for the quick reply! I’ll look into these.