Segmentation for swine brain MRI

Support
1

Operating system: Windows
Slicer version: 4.8.1

Hello,
I require a segmentation of part of a swine brain and I have an atlas to use; however the EMSegmenter with Atlas does not allow for the swine atlas to be selected as the “task”. I am very new to segmentation- is there another module I can use to segment a volume using my Atlas or is there some way to upload my atlas as the task?

2

If you have a single pair of grayscale image + segmentation as atlas, then you can use image registration to warp the atlas to the new case:

  • install Elastix extension
  • register grayscale volumes using “General registration (Elastix)” module (atlas grayscale volume is moving, new case grayscale volume is fixed volume; choose to save the computed transform)
  • apply the computed transform to the atlas segmentation to warp it to the new case
3

Thank you, I will try this out. However, I also have another question- what is the best method/a good tutorial for segmenting the atlas in the first place? I have been trying to use the paint tool in Segment Editor but what I am painting is not showing on the atlas or creating an output volume.

4

This is a good starting point for learning segmentation: https://www.slicer.org/wiki/Documentation/Nightly/Training#Slicer4_Image_Segmentation

1 Like