Tutorial 5 - Manual, Semi-Automatic and Fully Automatic Segmentation Using 3D Slicer

In this tutorial, we will learn how to segment out regions in three ways: manual, semi-automatic using thresholding, and fully automatic using an AI-based segmentation tool using 3D Slicer. The segmentation is demonstrated on brain MRI sample data.
3D Slicer Documentation on Segmentation: slicer.readthedocs.io/en/late...
TIME STAMPS
0:00 Intro
01:38 Identify regions to segment
2:21 Manual Segmentation
4:47 Semi-Automatic Segmentation
7:46 Segmentation Module
9:01 Automatic Segmentation
9:30 HD Brain Extraction Tool
10:52 Automatic brain extraction
16:01 Display Segmented Mask and Image
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[@adeoluwaoyin]

Thank you. This helped 😊

[@machine.mindscape]

Thank you! I'll upload more videos on different annotation tools soon

[@adeoluwaoyin]

@@machine.mindscape my msc dissertation is on segmenting the pituitary gland. Given its size and location, what would you advise?

[@nermin6554]

thanks a lot for sach a helpful tutorial. I was wondering that weather I can use these semi outomati method for cat brain MRI segmentation as well as human brain ? Since lots of extension which belong human do not work for animal brain.

[@machine.mindscape]

I think this is because of the size variation between human and animal brains. If you don't find an extension for this, you can use the semi-automatic method as a start to annotate a few scan, and train ML model and then generate more annotations using the trained model!