Problems with segmentation of bone, muscle and fat

Support
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1

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.

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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.

2

Can you share the file that you’re working with?

3

Sorry, I thought the JPEG version would be usable. It seems that I can’t upload .nii files. I hope this link will work, but unfortunately, it will expire on August 27.

Gems06.nii

4

I’m not an expert but it seems like you have a small number of layers, I only distinguish one where you can clearly see the two muscles. If you’re planning to use Grow from Seeds I think you need multiple layers where you can see the tissue. However, I just use the threshold as a mask and the paint the two segments. I also use grow from seeds but didn’t notice any visible change in the segmentation.

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