# How to get the 3D map with PET and MR in Slicer

**URL:** <https://discourse.slicer.org/t/how-to-get-the-3d-map-with-pet-and-mr-in-slicer/24591>\
**Category:** Community\
**Tags:** pet\
**Created:** [August 1, 2022, 1:35pm UTC](https://discourse.slicer.org/t/how-to-get-the-3d-map-with-pet-and-mr-in-slicer/24591 "2022-08-01T13:35:58Z")\
**Posts on this page:** 7\
**Page:** 1

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**Author:** ![slicer365](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/slicer365/32/67549_2.png) [@slicer365](https://discourse.slicer.org/u/slicer365)\
**Post date:** [August 1, 2022, 1:35pm UTC](https://discourse.slicer.org/t/how-to-get-the-3d-map-with-pet-and-mr-in-slicer/24591/1 "2022-08-01T13:35:59Z")

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![微信图片_20220731214903](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/f/6/f6eba7d04d37ab1039b087a56ba51fb3ea289f61.jpeg)

How to use slicer get the result like the above picture,it used PET-CT.

 ![1659275425770](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/1/9/195b6e8c7d292bfe57d0881a8c76022d0db4bf94.png)

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**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [August 1, 2022, 5:14pm UTC](https://discourse.slicer.org/t/how-to-get-the-3d-map-with-pet-and-mr-in-slicer/24591/2 "2022-08-01T17:14:15Z")

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This module should do what you are asking for:

[https://slicer.readthedocs.io/en/latest/user\_guide/modules/probevolumewithmodel.html](https://slicer.readthedocs.io/en/latest/user_guide/modules/probevolumewithmodel.html)

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**Author:** ![slicer365](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/slicer365/32/67549_2.png) [@slicer365](https://discourse.slicer.org/u/slicer365)\
**Post date:** [August 1, 2022, 10:11pm UTC](https://discourse.slicer.org/t/how-to-get-the-3d-map-with-pet-and-mr-in-slicer/24591/3 "2022-08-01T22:11:35Z")

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Thank you very much for your answer, yes, I know about this module, but this model just adjusts the surface of the brain, when I use Easy Clip to crop the brain, the inside of it doesn’t change very well.

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**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [August 2, 2022, 3:22pm UTC](https://discourse.slicer.org/t/how-to-get-the-3d-map-with-pet-and-mr-in-slicer/24591/4 "2022-08-02T15:22:17Z")

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you probably need to re-run after clipping to sample the volume at the new coordinates. The clipped surface may have few vertices though so it may not work well, is that what you mean? maybe a picture would help explain.

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**Author:** ![slicer365](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/slicer365/32/67549_2.png) [@slicer365](https://discourse.slicer.org/u/slicer365)\
**Post date:** [August 3, 2022, 5:36am UTC](https://discourse.slicer.org/t/how-to-get-the-3d-map-with-pet-and-mr-in-slicer/24591/5 "2022-08-03T05:36:34Z")

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Thank you ! As you see,this picture

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/5/2/520cbf424a203c9ce0b9657cff362a3e74acb889.jpeg)

This color is not very smooth!  
Difficulty identifying abnormal metabolic structures

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<div class="post-metadata">

**Author:** ![slicer365](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/slicer365/32/67549_2.png) [@slicer365](https://discourse.slicer.org/u/slicer365)\
**Post date:** [August 3, 2022, 5:37am UTC](https://discourse.slicer.org/t/how-to-get-the-3d-map-with-pet-and-mr-in-slicer/24591/6 "2022-08-03T05:37:24Z")

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Is it because my model is not standard enough?

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<div class="post-metadata">

**Author:** ![pieper](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/pieper/32/8_2.png) [@pieper](https://discourse.slicer.org/u/pieper)\
**Post date:** [August 3, 2022, 1:39pm UTC](https://discourse.slicer.org/t/how-to-get-the-3d-map-with-pet-and-mr-in-slicer/24591/7 "2022-08-03T13:39:02Z")

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I see - yes, if you go to the Models module Display section you can turn on display of the edges and you’ll see those are large polygons in the cut part so the volume is not sampled well.

There may be other options, but one approach could be to import the clipped model into a segmentation (right click on model in data module), then re-export it as a model (right click on segmentation or use the Segmentations module) and the re-run the Probe module. Converting the segmentation back to a model should have more vertices on the cut plane, but they may get optimized out so you might have to adjust the advanced parameters.