Operating system: Windows
Slicer version:5.6.2
Expected behavior: I have been trying to get a good brain segmentation for quite a while and have attempted the skull stripping without much success. I have watched several other videos as well, but still can’t get it to look complete or without the face/dura/etc. Any tips for this? Thank you!
Actual behavior:
@BDhoth Have you tried HDBET? I’ve had success with the 3D Slicer extension on MRI
https://extensions.slicer.org/view/HDBrainExtraction/32919/win
I have not tried that. I installed it. I really wish there were better instructions of how to use these extensions.
HDBET is pretty easy. It asks for input volume that you want to skull strip, and you can set two outputs for the new stripped volume and the new
brain mask segmentation. Set both of these outputs to “Create New…” and hit ‘Apply’.
Weird, that was what I did the first time and it came up with a weird “torch” error and failed. It worked this second time; however, how do I handle it in segment editor to have just the brain and no skull/face?
Thank you so much for your help!
It looks like you correctly created a brain mask segmentation in white, and a new skull-stripped volume. The green segment looks like it is from a different segmentation node created from threshold of the image before skull stripping.
If you go back to the data view, you can turn off the node named ‘Segmentation’ with the green head label to see only the brain mask label in white.
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