Problems with segmentation of bone, muscle and fat

Hello everyone,

I’m new to using 3D Slicer and could really use your help. My aim is to segment the muscle, fat, and bone on MRI slices of a rat. here is the data in question: Gems06.

As for my steps, I’ve uploaded the data in NIFTI format (.nii) into 3D Slicer and followed these steps:

  1. Uploaded the slices and used the Crop Volume module to define a Region of Interest (ROI) volume.
    2.In the Segment Editor module, I created two different segments, each representing a different muscle, using the paint tool.
    3.I then utilized the Grow from Seeds tool to generate a volume.

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However, I’m encountering issues with the segmentation results. They’re not matching what I saw in the tutorials, and the quality is poor.


I’ve considered a couple of possible reasons for this:

1.The threshold the the slices. The threshold goes from 0 to 0.642 which is different from what I have worked with

  1. I only work with one view and the other samples I worked with had the 3 views.

Could you please provide some guidance and input to help me achieve better segmentation results?

Thank you all in advance for your assistance.