# 3D coordinate of input 3D matrix

**URL:** <https://discourse.slicer.org/t/3d-coordinate-of-input-3d-matrix/34937>\
**Category:** Support\
**Tags:** segmentation, coordinates\
**Created:** [March 17, 2024, 8:47pm UTC](https://discourse.slicer.org/t/3d-coordinate-of-input-3d-matrix/34937 "2024-03-17T20:47:20Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![Cathy123](https://avatars.discourse-cdn.com/v4/letter/c/e8c25b/32.png) [@Cathy123](https://discourse.slicer.org/u/Cathy123)\
**Post date:** [March 17, 2024, 8:47pm UTC](https://discourse.slicer.org/t/3d-coordinate-of-input-3d-matrix/34937/1 "2024-03-17T20:47:20Z")

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Hi, I have some problems of 3D coordinates and segmentation.

1. what’s the coordinate relationship between 3D slicer and my volume coordinate? When I load my 3D matrix( 512_512_512 object) in the software, how can i set the coordinate with my volume coordinate?
2. for the 3D volume(512_512_512), it is a binary volume. The values on the object that can be seen are 1, and i want to ask how to do segment? can it be segment automatically or semi-automatically? after segmentation, how can i set the coordinate at the center of intersection betweent to the two segment parts?  
 ![volume](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/d/1/d174c4dffce9809abb5db4f017f9ebfd90adf372.jpeg)

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**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [March 17, 2024, 9:17pm UTC](https://discourse.slicer.org/t/3d-coordinate-of-input-3d-matrix/34937/2 "2024-03-17T21:17:48Z")

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Please read  
[https://slicer.readthedocs.io/en/latest/user\_guide/coordinate\_systems.html](https://slicer.readthedocs.io/en/latest/user_guide/coordinate_systems.html)

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<div class="post-metadata">

**Author:** ![Cathy123](https://avatars.discourse-cdn.com/v4/letter/c/e8c25b/32.png) [@Cathy123](https://discourse.slicer.org/u/Cathy123)\
**Post date:** [March 18, 2024, 2:13pm UTC](https://discourse.slicer.org/t/3d-coordinate-of-input-3d-matrix/34937/3 "2024-03-18T14:13:20Z")

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> [@Cathy123](#):
>
> for the 3D volume(512_512_512), it is a binary volume. The values on the object that can be seen are 1, and i want to ask how to do segment? can it be segment automatically or semi-automatically?

Thank you so much. What about the second question?" for the 3D volume(512_512_ 512), it is a binary volume. The values on the object that can be seen are 1, and i want to ask how to do segment? can it be segment automatically or semi-automatically?"

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**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [March 18, 2024, 3:35pm UTC](https://discourse.slicer.org/t/3d-coordinate-of-input-3d-matrix/34937/4 "2024-03-18T15:35:38Z")

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In short, you can segment a binary image if you like with the segment editor.

Segmentation is to define specific regions in intensity images with continuous grayscale as binary images. I am not sure what you want to do by segmenting it (because the screenshot above already shows something segmented).

You will find most tools not working very well for an image that consists only 0 and 1. But if your goal is to use something like scissors, or some morphological operations, you can do those.

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<div class="post-metadata">

**Author:** ![Cathy123](https://avatars.discourse-cdn.com/v4/letter/c/e8c25b/32.png) [@Cathy123](https://discourse.slicer.org/u/Cathy123)\
**Post date:** [March 18, 2024, 6:56pm UTC](https://discourse.slicer.org/t/3d-coordinate-of-input-3d-matrix/34937/5 "2024-03-18T18:56:27Z")

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Thank you so much. It is a segmented image shown above. I want to go on conducting with aneurysm segmentation, so I need to segmented based on it.

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**Author:** ![muratmaga](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/muratmaga/32/3622_2.png) [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Post date:** [March 18, 2024, 7:09pm UTC](https://discourse.slicer.org/t/3d-coordinate-of-input-3d-matrix/34937/6 "2024-03-18T19:09:09Z")

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If you want to split that whole thing into two segments as shown in schematic, you can easily achieve that using the scissors tool.