# Help with Segmentation of MRI

**URL:** <https://discourse.slicer.org/t/help-with-segmentation-of-mri/14485>\
**Category:** Support\
**Created:** [November 8, 2020, 5:11am UTC](https://discourse.slicer.org/t/help-with-segmentation-of-mri/14485 "2020-11-08T05:11:05Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![ssk](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ssk/32/8777_2.png) [@ssk](https://discourse.slicer.org/u/ssk)\
**Post date:** [November 8, 2020, 5:11am UTC](https://discourse.slicer.org/t/help-with-segmentation-of-mri/14485/1 "2020-11-08T05:11:05Z")

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I am new to segmenting MRI’s and learning to do so for a project. How do I quantify volumes/areas, etc from an MRI image?

Tissue in question is extraorbital muscles (as circled in image). I wish to isolate it on multiple slices to measure the volume or quantify it somehow. When I try to segment it using paint, the edges are bumpy.

Please give me some beginner’s advice an point me towards learner level resources to MRI quantification of images.

Thank you!

 ![Screenshot 2020-11-08 at 01.08.11](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/3/a/3afaba8d5cc8fe6d7c1229b04de170cebafba8f2.jpeg) ![Screenshot 2020-11-08 at 01.09.15](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/2/a/2ae233de59c6332d284dc0e74546f535d14b6bef.jpeg) ![Screenshot 2020-11-08 at 01.03.44](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/b/6/b6824f0af92e9443ce6c040b33beed2987cff585.jpeg)

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**Author:** ![manjula](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/manjula/32/80981_2.png) [@manjula](https://discourse.slicer.org/u/manjula)\
**Post date:** [November 8, 2020, 11:05am UTC](https://discourse.slicer.org/t/help-with-segmentation-of-mri/14485/2 "2020-11-08T11:05:48Z")

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There are many tools available. The way you have mentioned, you first need to segment the extraocular muscles.

There are resources at [https://www.slicer.org/wiki/Documentation/4.10/Training#Segmentation](https://www.slicer.org/wiki/Documentation/4.10/Training#Segmentation)

Also if you google you will find a few more.

Once you have properly segment them you can use segmentation statistics to get the volume and many more parameters if you require so.

[![](https://img.youtube.com/vi/fM_rxfDTRi0/maxresdefault.jpg "Segment statistics - new module in 3D Slicer") ](https://www.youtube.com/watch?v=fM_rxfDTRi0)