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Sikerdebaard / dcmrtstruct2nii

DICOM RT-Struct to mask
MIT License
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Segmentation masks for multiple organs are placed in the same NII .gz file #45

Closed LReion closed 1 year ago

LReion commented 1 year ago

I have an RT file and a DICOM folder, and I want to put the specified several organs in the same segmentation.nii .gz file, and then add labels to each organ to facilitate the production of the dataset.

Sikerdebaard commented 1 year ago

Hi @LReion unfortunately this is currently unsupported by dcmrtstruct2nii. The reason for this is that structures can overlap and there is currently no strategy implemented to resolve overlaps.

Perhaps fslutils has a tool to do what you want. For example you could merge the NIfTI file outputs from dcmrtstruct2nii with fslmerge or perhaps fslroi.

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Fslutils