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?
I do not know what
fastersurfer is, but have you tried FreeSurfer’s
-brainstem-structures flag? And if so, were you on the most recent FreeSurfer version?
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)??
You can refer to the Usage section (section 3) on the documentation: