conversion of DICOM Segmentation object to nifti file

[deepakri201]

Hi,

I'm interested in using highdicom to convert a DICOM Segmentation object to a nifti file (one per segment). I know that there are other converters available (dcmqi segimage2itkimage, pydicom-seg), but wanted to know if this was also an option using highdicom.

I've tried this from the documentation:

,but this does not return numpy arrays of the same dimensions as the underlying image data. It seems like I would have to extract any orientation information for each slice of the segmentation and create the volume myself in order for it to align with the image data.

Thanks!

Deepa

[CPBridge]

Hi @deepakri201, highdicom cannot convert directly to nifti but you should be able to do this via numpy and then nibabel/sitk.

You are using an old API for getting segments out of the segmentation dataset. Please refer to this similar issue for some hints on how to do this now: #202

[CPBridge]

See the new docs in #219 for more information on this