# Problems with segmentation of bone, muscle and fat 

**URL:** <https://discourse.slicer.org/t/problems-with-segmentation-of-bone-muscle-and-fat/36196>\
**Category:** Support\
**Tags:** segmentation, segmentations, segment-editor\
**Created:** [May 16, 2024, 5:29am UTC](https://discourse.slicer.org/t/problems-with-segmentation-of-bone-muscle-and-fat/36196 "2024-05-16T05:29:07Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![concker99](https://avatars.discourse-cdn.com/v4/letter/c/ccd318/32.png) [@concker99](https://discourse.slicer.org/u/concker99)\
**Post date:** [May 16, 2024, 5:29am UTC](https://discourse.slicer.org/t/problems-with-segmentation-of-bone-muscle-and-fat/36196/1 "2024-05-16T05:29:07Z")

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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](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/c/1/c13017f01b9fe909b510dfcdda6c41e0ba8765c7.jpeg).

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.

![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/9/9/99a41ef4c362ba9f75b221732871dbf8fdb18f60.png) ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/f/5/f573e284eb1abb4e2a8267466cbfd41ecba543e4.jpeg)

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

![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/1/d/1de94b79f9b556cd87655e8e62d2125f5e98d6a8.jpeg)  
 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/3/4/3445867a9f62c052e5d77ba87dcf05395f0f0cfe.jpeg)

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.

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**Author:** ![LeidyMoraV](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/leidymorav/32/70144_2.png) [@LeidyMoraV](https://discourse.slicer.org/u/LeidyMoraV)\
**Post date:** [May 29, 2024, 2:28pm UTC](https://discourse.slicer.org/t/problems-with-segmentation-of-bone-muscle-and-fat/36196/2 "2024-05-29T14:28:34Z")

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

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**Author:** ![concker99](https://avatars.discourse-cdn.com/v4/letter/c/ccd318/32.png) [@concker99](https://discourse.slicer.org/u/concker99)\
**Post date:** [May 29, 2024, 3:45pm UTC](https://discourse.slicer.org/t/problems-with-segmentation-of-bone-muscle-and-fat/36196/3 "2024-05-29T15:45:39Z")

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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](https://usherbrooke-my.sharepoint.com/:u:/g/personal/cota2317_usherbrooke_ca/EesDxJg23fxBgTs-1P36u0IB8NgNqvfNJIkyDo_lpDofug?e=ZmFzOQ)

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<div class="post-metadata">

**Author:** ![LeidyMoraV](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/leidymorav/32/70144_2.png) [@LeidyMoraV](https://discourse.slicer.org/u/LeidyMoraV)\
**Post date:** [May 29, 2024, 9:40pm UTC](https://discourse.slicer.org/t/problems-with-segmentation-of-bone-muscle-and-fat/36196/4 "2024-05-29T21:40:02Z")

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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.

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/2/7/27dea19a49c348401ba73dd7cb752c75d7203496.jpeg)