Brainstem segmentation

Software Support
1

HI, everyone.

I used the fastersurfer for the brain segmentation. And I found that the brainstem segmentation of (mid-brain) part is not completely segmented. So, can you give me an advice for other deep learning model or software the better brain_stem segmentation?

Thank you!

2

Hi @curtis_sohn,

I do not know what fastersurfer is, but have you tried FreeSurfer’s recon-allwith the -brainstem-structures flag? And if so, were you on the most recent FreeSurfer version?

Best,
Steven

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3

Thanks for the reply. I used the GitHub - Deep-MI/FastSurfer: PyTorch implementation of FastSurferCNN. Is there a specific command line for segment only brainstem using Freesurfer (I’m using 7.1)??

4

You can refer to the Usage section (section 3) on the documentation:

https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures

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