Segmentation MRI rat


I want to know if for the segmentation of gray and white matter of a rat mri I need an atlas or not???

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)