The first step in many MRI analysis sequences is the removal of extra-meningeal tissues from the MRI of the entire head. The Brain Surface Extractor (BSE) works by using a Marr-Hildreth edge detector to find a boundary between the brain and the skull. Since the space of the CSF and the skull are dark in a T1 scan, the borders between the brain and the scalp are relatively well defined. However, these strong edges are often interrupted due to the finite resolution of MRI acquisition and actual anatomical connections between the brain and the rest of the body, Optic nerves, brainstem, etc. Thus, BSE uses mathematical morphological operators (erosion, dilation, etc.) to further improve the edge detection result and provide better tissue separation. Additionally, the edge detection result is improved by the application of an anisotropic diffusion filter prior to performing edge detection.
To perform the skull removal task in BrainSuite, use the BSE tool, which can be accessed from the Cortex → Skull Stripping (BSE) item.
The BSE dialog allows you to traverse each part of the skull removal process and adjust the parameters according to the intermediate results.
Steps :
1. Anisotropic diffusion filter
2. Edge detection
3. Finding a brain
4. Extract the brain
5. Adjusting the BSE parameters
