Hi,
Is there any extension in 3D-Slicer which offers automated brain segmentation for parts such as - Amygdala, Hippocampus, Insula etc.? Which extension has the best accuracy?
I was able to find SlicerNeuroSegmentation, but it seems to have a dependency on FreeSurfer and I was wondering if a more stand-alone module exists in 3d-Slicer.
Thanks!
I think FreeSurfer with SlicerFreeSurfer is your best bet, especially the new SuperSynth tool to handle pretty much any brain scan. It’s not integrated directly with Slicer but it’s easy to install and use on it’s own.
Here’s an example applying SuperSynth to the MRHead SampleData that includes a color table to use if loading the nifti file directly.
The results look good to me, especially considering this is a scan from over 20 years ago.
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Hi @pieper, thanks for the quick reply. I will use this extension and get back to you.
It seems a standalone extension in 3D-Slicer doesn’t exist as of now for brain parcellation?