gloria
(Gloria)
1
Hi
I want to know if for the segmentation of gray and white matter of a rat mri I need an atlas or not???
lassoan
(Andras Lasso)
2
Considering there was not response, most likely Slicer users don’t segment rat MRI using an atlas.
You can probably get good segmentation by using a few modules:
- Make the image more uniform using bias correction by “N4ITK MRI Bias Correction” module
- Apply anisotropic smoothing to reduce noise by “Curvature anisotropic diffusion” or “Gradient anisotropic diffusion” module
- Use SwissSkullStripper extension to extract the brain (choose a similar existing rat MRI image and corresponding brain mask as inputs)
- Segment white and gray matter using Segment Editor (Thresholding effect, followed by Smoothing effect, using Joint smoothing method)