Converting Segmentation to Volume automatically w/ Python or Matlab

[lassoan (Andras Lasso)]

You can load the segmentation and export to volume file. If you want the segmentation to have a particular geometry (origin, spacing, axis directions, and extents) then specify the CT volume as reference volume when you export to volume file (when you call ExportSegmentsBinaryLabelmapRepresentationToFiles).

See complete example here:

Overlapping Segmentions Export to NIFTI

Great idea, working perfectly now. Thanks so much for your extensive help. In case anyone else wants to do something similar, here is my final code: # ***** THE FINAL SCRIPT ***** # Required to have 3 segments - "Mask", "Single", "Multi" # Save Image data as Image Data.nii.gz node = slicer.mrmlScene.GetFirstNodeByClass('vtkMRMLScalarVolumeNode') file_path = "/Users/pete/OneDrive/ImageData.nii.gz" properties = {'useCompression': 1}; #use compression slicer.util.saveNode(node, file_path, prope…