I have created an AI model for organ segmentation. The models input and output are a 2D CT slice and a 2D mask array. These 2D arrays are then joined into a 3D array for the whole CT series.
I used 3D Slicer to generate the annotations which were used for training (seg.nrrd).
Now I would like to view my inferences on 3D slicer along with the original input (the CT series) so I can eventually edit them.
I have managed to rudimentary replicate the seg.nrrd header and create nrrds that work well with slicer for most series. Some of them however will not register perfectly. The way I managed to fix this so far was oppening the series in 3D slicer, creating a mock seg.nrrd and then copying the important header information (space origin and others) and this fixes my problem.
My question is, is there any way to automatically replicate what the 3dslicer software does to create the seg.nrrd file?
I have been searching through simpleitk and slicer.io but have not found the answer for this yet.
I did try getting some information from simpleitk GetOrigin and get GetSpacing functions (calling it on the loaded complete series) but outputs were different from the 3DSlicer software header.
Thank you very much