# How to Work on a DICOM file with Burned In Segmentation 

**URL:** <https://discourse.slicer.org/t/how-to-work-on-a-dicom-file-with-burned-in-segmentation/24740>\
**Category:** Support\
**Tags:** segmentation, dicom, python, 3d-model\
**Created:** [August 13, 2022, 4:55pm UTC](https://discourse.slicer.org/t/how-to-work-on-a-dicom-file-with-burned-in-segmentation/24740 "2022-08-13T16:55:51Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![PrinceAla93](https://avatars.discourse-cdn.com/v4/letter/p/7ab992/32.png) [@PrinceAla93](https://discourse.slicer.org/u/PrinceAla93)\
**Post date:** [August 13, 2022, 4:55pm UTC](https://discourse.slicer.org/t/how-to-work-on-a-dicom-file-with-burned-in-segmentation/24740/1 "2022-08-13T16:55:51Z")

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Hello All,  
I have obtained a dicom image set with the segmented objects of interest burnt in (ie: for red nucleus, the image just shows up as white around that area). I am wondering if 3D slicer can take that Burnt in data of the object, extract it, and recompile the object without the burn in. Further, could i write a python script that could extract that data?

I used brainlab to segment the dicom but brainlab has no way of exporting those object segmentations

I hope this makes sense

Thanks

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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 13, 2022, 9:07pm UTC](https://discourse.slicer.org/t/how-to-work-on-a-dicom-file-with-burned-in-segmentation/24740/2 "2022-08-13T21:07:18Z")

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> [@PrinceAla93](#):
>
> brainlab has no way of exporting those object segmentations

BrainLab can save segmentation as DICOM segmentation object. Slicer can load this segmentation if the [Quantitative Reporting extension](https://qiicr.gitbooks.io/quantitativereporting-guide). This workflow has been tested and works well.

You may also consider using Slicer for segmentation. There are lots of manual, semi-automatic, and fully automatic segmentation tools for all kinds of structures.

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**Author:** ![PrinceAla93](https://avatars.discourse-cdn.com/v4/letter/p/7ab992/32.png) [@PrinceAla93](https://discourse.slicer.org/u/PrinceAla93)\
**Post date:** [August 13, 2022, 9:15pm UTC](https://discourse.slicer.org/t/how-to-work-on-a-dicom-file-with-burned-in-segmentation/24740/3 "2022-08-13T21:15:55Z")

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Thank you for your response!

how strange, then why are the brainlab reps telling me that the only way they will allow for exporting the object segmentations is if they are burnt in.

Do you have a link or a resource to the workflow mentioned?

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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 13, 2022, 9:21pm UTC](https://discourse.slicer.org/t/how-to-work-on-a-dicom-file-with-burned-in-segmentation/24740/4 "2022-08-13T21:21:19Z")

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These capabilities are described in the DICOM conformance statement of the software application: [DICOM - Brainlab](https://www.brainlab.com/dicom)

See test results of DICOM segmentation object export from Brainlab and import into 3D Slicer here: [Brainlab - DICOM4QI](https://dicom4qi.readthedocs.io/en/latest/results/seg/brainlab/)

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<div class="post-metadata">

**Author:** ![PrinceAla93](https://avatars.discourse-cdn.com/v4/letter/p/7ab992/32.png) [@PrinceAla93](https://discourse.slicer.org/u/PrinceAla93)\
**Post date:** [August 13, 2022, 9:23pm UTC](https://discourse.slicer.org/t/how-to-work-on-a-dicom-file-with-burned-in-segmentation/24740/5 "2022-08-13T21:23:34Z")

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Thank you so much!!  
You may have just saved this med students research!!