Convert DICOM RT structure set (RS) to NIFTI

Support
1

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?

2

After you install SlicerRT extension, you can load RT structure sets from DICOM and export the segmentation to NIFTI files.

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.

3

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!!!

4

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