# Convert DICOM RT structure set (RS) to NIFTI

**URL:** <https://discourse.slicer.org/t/convert-dicom-rt-structure-set-rs-to-nifti/29354>\
**Category:** Support\
**Tags:** dicom\
**Created:** [May 8, 2023, 2:04pm UTC](https://discourse.slicer.org/t/convert-dicom-rt-structure-set-rs-to-nifti/29354 "2023-05-08T14:04:46Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![Luana\_CONTE](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/luana_conte/32/65924_2.png) [@Luana\_CONTE](https://discourse.slicer.org/u/Luana_CONTE)\
**Post date:** [May 8, 2023, 2:04pm UTC](https://discourse.slicer.org/t/convert-dicom-rt-structure-set-rs-to-nifti/29354/1 "2023-05-08T14:04:46Z")

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Operating system: Windows 11 Pro  
Slicer version: 5.2.2  
Expected behavior:  
Actual behavior:

Hello everybody,  
I have got some DICOM series with their RS structures and I need to convert them in NIFTI format in a batch. Is there any solution?

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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:** [May 10, 2023, 4:33am UTC](https://discourse.slicer.org/t/convert-dicom-rt-structure-set-rs-to-nifti/29354/2 "2023-05-10T04:33:05Z")

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After you install SlicerRT extension, you [can load RT structure sets from DICOM](https://slicer.readthedocs.io/en/latest/user_guide/modules/dicom.html#read-dicom-files-into-the-scene) and [export the segmentation to NIFTI files](https://slicer.readthedocs.io/en/latest/user_guide/modules/segmentations.html#export-segmentation-to-labelmap-volume-file).

In general, I would recommend not to use NIFTI files, as they have many issues and limitations. For example, they cannot store overlapping labels; they just store label values (but not what each label value means - segment name, standard terminology codes, color, etc.), cannot store segmentations acquired with tilted gantry, etc. Segmentation NRRD files (.seg.nrrd) do not have these limitations.

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**Author:** ![Luana\_CONTE](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/luana_conte/32/65924_2.png) [@Luana\_CONTE](https://discourse.slicer.org/u/Luana_CONTE)\
**Post date:** [May 11, 2023, 7:39am UTC](https://discourse.slicer.org/t/convert-dicom-rt-structure-set-rs-to-nifti/29354/3 "2023-05-11T07:39:32Z")

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Many thanks for your reply.

I have followed the procedure you suggested. When I have tried to save the RT struct in NIFTI, there was not the extensions. The only possible extensions in the drop-menu were nnrd and nhdr only.  
In addition, after converting in seg.nrrd format, I checked the file in an external envoronment (I have used matlab) but I could not see any value. It seems that there wasn’t any conversion at all.  
Can you please help me?

I was also wondering if there is an option to convert in NIFTI the images (not only RT struct), as well?

Many thanks!!!

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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:** [May 11, 2023, 10:44pm UTC](https://discourse.slicer.org/t/convert-dicom-rt-structure-set-rs-to-nifti/29354/4 "2023-05-11T22:44:45Z")

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> [@Luana\_CONTE](#):
>
> The only possible extensions in the drop-menu were nnrd and nhdr only

Make sure you use the export function in Segmentations module and that you use the current Slicer version (5.2.2).