# create color mask in dicom volumen and save this change.

**URL:** <https://discourse.slicer.org/t/create-color-mask-in-dicom-volumen-and-save-this-change/10567>\
**Category:** Support\
**Created:** [March 5, 2020, 8:11pm UTC](https://discourse.slicer.org/t/create-color-mask-in-dicom-volumen-and-save-this-change/10567 "2020-03-05T20:11:49Z")\
**Posts on this page:** 14\
**Page:** 1

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**Author:** ![Carlos\_Ferro](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/carlos_ferro/32/6209_2.png) [@Carlos\_Ferro](https://discourse.slicer.org/u/Carlos_Ferro)\
**Post date:** [March 5, 2020, 8:11pm UTC](https://discourse.slicer.org/t/create-color-mask-in-dicom-volumen-and-save-this-change/10567/1 "2020-03-05T20:11:49Z")

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it´s posible to create color mask and add this color mask in dicom volume, without that this mask to see in binary.  
or is possible create color mask of fiducial an save this mask in dicom volume .

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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:** [March 5, 2020, 8:15pm UTC](https://discourse.slicer.org/t/create-color-mask-in-dicom-volumen-and-save-this-change/10567/3 "2020-03-05T20:15:08Z")

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Yes, you can define colored masks in Segment Editor module and export it to DICOM (RT structure set or as segmentation object). You need to install SlicerRT (for RT structure set) and Quantitative Reporting (for segmentation object) extensions before initiating DICOM export.

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**Author:** ![Carlos\_Ferro](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/carlos_ferro/32/6209_2.png) [@Carlos\_Ferro](https://discourse.slicer.org/u/Carlos_Ferro)\
**Post date:** [March 5, 2020, 8:22pm UTC](https://discourse.slicer.org/t/create-color-mask-in-dicom-volumen-and-save-this-change/10567/4 "2020-03-05T20:22:38Z")

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How do I export it without the masks becoming binary?

I do not get it.  
Could you give me a step by step.

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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:** [March 5, 2020, 8:39pm UTC](https://discourse.slicer.org/t/create-color-mask-in-dicom-volumen-and-save-this-change/10567/5 "2020-03-05T20:39:50Z")

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You can add any number of segments and you can assign a color to each segment. See tutorials [here](https://www.slicer.org/wiki/Documentation/Nightly/Training#Segmentation).

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**Author:** ![Carlos\_Ferro](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/carlos_ferro/32/6209_2.png) [@Carlos\_Ferro](https://discourse.slicer.org/u/Carlos_Ferro)\
**Post date:** [March 5, 2020, 8:53pm UTC](https://discourse.slicer.org/t/create-color-mask-in-dicom-volumen-and-save-this-change/10567/6 "2020-03-05T20:53:21Z")

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If I understand the segmentation.  
What I don’t understand is how to export these rgb segmentations in the dicom volume without looking binary.

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**Author:** ![Carlos\_Ferro](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/carlos_ferro/32/6209_2.png) [@Carlos\_Ferro](https://discourse.slicer.org/u/Carlos_Ferro)\
**Post date:** [March 5, 2020, 10:46pm UTC](https://discourse.slicer.org/t/create-color-mask-in-dicom-volumen-and-save-this-change/10567/7 "2020-03-05T22:46:57Z")

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in mask volume i can save the mask in binary, but how i can save this mask in color?

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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:** [March 5, 2020, 11:03pm UTC](https://discourse.slicer.org/t/create-color-mask-in-dicom-volumen-and-save-this-change/10567/8 "2020-03-05T23:03:29Z")

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Segment colors are saved in both RT structure sets and DICOM segmentation objects.

What would you like to do with the created DICOM data objects? What software will use them and for what purpose?

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**Author:** ![Carlos\_Ferro](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/carlos_ferro/32/6209_2.png) [@Carlos\_Ferro](https://discourse.slicer.org/u/Carlos_Ferro)\
**Post date:** [March 5, 2020, 11:22pm UTC](https://discourse.slicer.org/t/create-color-mask-in-dicom-volumen-and-save-this-change/10567/9 "2020-03-05T23:22:36Z")

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I need to make one volumen whit this color segmentation and fiducials points to generate navigate imagen.

This is posible?

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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:** [March 6, 2020, 12:06am UTC](https://discourse.slicer.org/t/create-color-mask-in-dicom-volumen-and-save-this-change/10567/10 "2020-03-06T00:06:19Z")

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Would you like to use it for surgical navigation? What software/system would you like to import the data into? Medtronic, BrainLab, some radiation therapy treatment planning system, …?

FYI, you can do surgical planning and navigation in Slicer. You can also run Medtronic StealthStation/BrainLab in parallel with Slicer, get registration and real-time navigation information from the commercial navigation system and deploy experimental features in Slicer. See more information at [www.slicerigt.org](http://www.slicerigt.org).

Example of parallel navigation in Slicer and StealthStation:

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<div class="post-metadata">

**Author:** ![Carlos\_Ferro](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/carlos_ferro/32/6209_2.png) [@Carlos\_Ferro](https://discourse.slicer.org/u/Carlos_Ferro)\
**Post date:** [March 6, 2020, 1:32pm UTC](https://discourse.slicer.org/t/create-color-mask-in-dicom-volumen-and-save-this-change/10567/11 "2020-03-06T13:32:13Z")

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hello, thank’s for the information.  
i have other question.

I would like to mount this image with the color masks in the fiagon system, or the brainlab one.  
What I want is to generate the dicom image already in color and that it be put into the system to perform the procedure.

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<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:** [March 6, 2020, 2:05pm UTC](https://discourse.slicer.org/t/create-color-mask-in-dicom-volumen-and-save-this-change/10567/12 "2020-03-06T14:05:45Z")

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I don’t think either these systems can load color image volumes. BrainLab can load segmentations exported from Slicer.

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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:** [March 6, 2020, 2:18pm UTC](https://discourse.slicer.org/t/create-color-mask-in-dicom-volumen-and-save-this-change/10567/13 "2020-03-06T14:18:10Z")

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> [@lassoan](#):
>
> BrainLab can load segmentations exported from Slicer.

Yes, that’s true, and also diffusion tractography results in dicom format. But only their most recent systems support this.

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<div class="post-metadata">

**Author:** ![Carlos\_Ferro](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/carlos_ferro/32/6209_2.png) [@Carlos\_Ferro](https://discourse.slicer.org/u/Carlos_Ferro)\
**Post date:** [March 6, 2020, 2:35pm UTC](https://discourse.slicer.org/t/create-color-mask-in-dicom-volumen-and-save-this-change/10567/14 "2020-03-06T14:35:02Z")

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Hello, how can I export the segmentation in dicom format, in addition to the fiducials that I put in the mask also in dicom.

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<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:** [March 6, 2020, 3:23pm UTC](https://discourse.slicer.org/t/create-color-mask-in-dicom-volumen-and-save-this-change/10567/15 "2020-03-06T15:23:06Z")

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> [@Carlos\_Ferro](#):
>
> Hello, how can I export the segmentation in dicom format

See instructions here: [Documentation/Nightly/Modules/DICOM - Slicer Wiki](https://www.slicer.org/wiki/Documentation/Nightly/Modules/DICOM#DICOM_export)

> [@Carlos\_Ferro](#):
>
> fiducials that I put in the mask also in dicom

I am not aware of any commonly used DICOM data object that could store landmark points that commercial surgical navigation systems can import. You can draw small segments and mark them manually in the commercial system. 3D Slicer is essential for surgical planning and navigation research exactly because of such trivial limitations. The usual surgical navigation research/prototyping setup is that Slicer runs in parallel with commercial systems and you develop all new features in Slicer. Clinicians primarily rely on the commercial system, while they may look at additional information provided by the research system.