RT structures not converted as expected

[Paul Wright]

Hi

I have some newbie questions from my first time converting RT structures to nifti. I have it working in general but there are a few things I do not understand:

General format:

plastimatch convert --modality MR -interpolation nn --input /folder/with/RTstruct.dcm --referenced-ct /folder/with/baseMRnn.dcm --output-img mymask.nii

All my RT structure files contain a single structure. I want my output to be a 3D nifti that is a binary mask showing the structure.

--output-img does not save an image, even though it says it can output nifti.

--output-prefix saves the mask as MHA regardless of whether I specify nifti either in --output-prefix or --output-img

--output-ss-img saves a 4D nifti with two volumes; the second is all zeroes; I hoped adding --prune-empty would fix this but it does not

--output-labelmap saves a 3D image with just ones and zeros as expected, but is always in UINT32, even when I specify --output-type uchar (the ss-img is in UINT8).

I can live with these outputs, and convert the image to what I want in "post", but I would like to understand this new tool I'm using, so any information would be appreciated.

Many thanks

Paul Wright