# Segmenting an image into homogenous compartments

**URL:** <https://discourse.slicer.org/t/segmenting-an-image-into-homogenous-compartments/28051>\
**Category:** Support\
**Tags:** segmentation\
**Created:** [February 26, 2023, 8:48am UTC](https://discourse.slicer.org/t/segmenting-an-image-into-homogenous-compartments/28051 "2023-02-26T08:48:03Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![Zinoviy\_Weinstein](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/zinoviy_weinstein/32/18379_2.png) [@Zinoviy\_Weinstein](https://discourse.slicer.org/u/Zinoviy_Weinstein)\
**Post date:** [February 26, 2023, 8:48am UTC](https://discourse.slicer.org/t/segmenting-an-image-into-homogenous-compartments/28051/1 "2023-02-26T08:48:03Z")

</div>

Operating system: Ubuntu 22.04  
Slicer version: 5.2.2  
Hello All.  
I have an MRI scan that I need to segment into N homogenous compartments for later reconstruction. The challenge here is that it’s not whatever organ, and the rest is background, but it has to be compartments.  
Is there a way to do that with slicer?  
UPDATE:  
Here is a link to the file via google drive: [https://drive.google.com/file/d/1zFCewDPTZrOlu\_-3JxJOX0wXDwuqYPos/view?usp=share\_link](https://drive.google.com/file/d/1zFCewDPTZrOlu_-3JxJOX0wXDwuqYPos/view?usp=share_link)

---

<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [February 27, 2023, 4:54pm UTC](https://discourse.slicer.org/t/segmenting-an-image-into-homogenous-compartments/28051/2 "2023-02-27T16:54:12Z")

</div>

This is a follow-up on discussion on [Segmenting an image into homogenous compartments - #4 by ZInoviy - Image Analysis - Image.sc Forum](https://forum.image.sc/t/segmenting-an-image-into-homogenous-compartments/77759/4)

---

<div class="post-metadata">

**Author:** ![lassoan](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/lassoan/32/13_2.png) [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Post date:** [February 27, 2023, 4:55pm UTC](https://discourse.slicer.org/t/segmenting-an-image-into-homogenous-compartments/28051/3 "2023-02-27T16:55:45Z")

</div>

@Zinoviy_Weinstein You have shared a single slice. Do you need to do 2D image segmentation? What is the clinical goal?

---

<div class="post-metadata">

**Author:** ![Zinoviy\_Weinstein](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/zinoviy_weinstein/32/18379_2.png) [@Zinoviy\_Weinstein](https://discourse.slicer.org/u/Zinoviy_Weinstein)\
**Post date:** [February 28, 2023, 7:31am UTC](https://discourse.slicer.org/t/segmenting-an-image-into-homogenous-compartments/28051/4 "2023-02-28T07:31:04Z")

</div>

Yes. This is a 2D 1H anatomical image that needs to be segmented to use in later image reconstruction of “crappier” images.