I have to extract canine brains from around 60 patients in T1w 3D MRI-images. I tried both options
- SwissSkullstripper doesn’t extract all brain, but only a small part of the brain (image 1)
- HD Brain Extraction Tool works better, but doesn’t extract all brain as well (image 2)
I tried the HD Brain Extraction Tool with a atlas volume and atlas mask, which I manually segmented beforehand.
image 1: green is the atlas mask segmentation, blue is the brain extraction by Swiss SkullStripping
image 2: white is brain extraction by HD Brain Extraction
I am thankful for any tipps on how to extract the brain properly or any additional settings that may help. Thanks in advance!
