# Display a segmented data in Slicer 3D view

**URL:** <https://discourse.slicer.org/t/display-a-segmented-data-in-slicer-3d-view/7889>\
**Category:** Support\
**Created:** [August 6, 2019, 6:39am UTC](https://discourse.slicer.org/t/display-a-segmented-data-in-slicer-3d-view/7889 "2019-08-06T06:39:55Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![mikecsu](https://avatars.discourse-cdn.com/v4/letter/m/3da27b/32.png) [@mikecsu](https://discourse.slicer.org/u/mikecsu)\
**Post date:** [August 6, 2019, 6:39am UTC](https://discourse.slicer.org/t/display-a-segmented-data-in-slicer-3d-view/7889/1 "2019-08-06T06:39:55Z")

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Operating system:win 10  
Slicer version:4.10  
Expected behavior:  
Actual behavior:

Hi，everyone.

I would like to know" Is it possible to display a segmented data with " nrrd " format in slicer 3D view ?“.  
Here " segmented data” means , it is not segmented by slicer (i didn’t use the " Segment Editor " module to do this work.) The below pic shows how my " segmented data" looks like( i open it with ITK-SNAP):

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/3/d/3d3e131be6910e6e403a6ac81669510138453b44.png)

Black pixel value 0  
Grey pixel value 1  
White pixel value 2

There are 3 parts basically.

I noticed some differences when i do the segmentation work with slicer(using "Segment editor ") as well as without slicer (using my own method to obtain segmented results).

With slicer , i can oabtain results with the following pic， we can see the segmented result is the “Segmentation.seg.nrrd” file and " iDose (1) Processed-SimpleITK.nrrd" is the voulme data.

![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/7/6/7693441faba750d69dde25eefa2089e7259c1bae.png)

Without slicer, i have the following files, " idose(1)-wxy.nrrd" is the volume data , “Segment\_1.nrrd” is my " segmented data".  
 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/1/c/1c9be4b60689fcd31c2bf3e87f1a2323ab260bcc.png)

Then ,here is my question, how am i able to convert “Segment\_1.nrrd” to “Segment\_1.Seg.nrrd”( i guess the data should be in “.Seg.nrrd” format for all the segmented data to correctly display in slicer views ），so i can display my " segmented data" correctly in slicer view.

Is there anything i can do to achieve this goal ?

Any help would be appreciated.

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**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:** [August 7, 2019, 3:14am UTC](https://discourse.slicer.org/t/display-a-segmented-data-in-slicer-3d-view/7889/2 "2019-08-07T03:14:23Z")

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You can load ITKSnap segmentation as labelmap then convert it to segmentation:

- Use “Add data” dialog, click on “Show options”, check “labelmap” checkbox, click OK
- Go to “Data” module, right-click on the labelmap volume, and choose “Convert labelmap to segmentation node”

Segmentation is saved as a 4D nrrd file. If your segments don’t overlap each other then you can export them as a single 3D merged labelmap and save that:

- Go to “Data” module, right-click on the segmentation node, and choose “Export visible segments to binary labelmap”
- Use “Save data” to save the exported labelmap to .nrrd file

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**Author:** ![mikecsu](https://avatars.discourse-cdn.com/v4/letter/m/3da27b/32.png) [@mikecsu](https://discourse.slicer.org/u/mikecsu)\
**Post date:** [August 8, 2019, 3:20am UTC](https://discourse.slicer.org/t/display-a-segmented-data-in-slicer-3d-view/7889/3 "2019-08-08T03:20:02Z")

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Thank you so much @lassoan.