Slicer Liver Export

Code for my blog post.

Export the segmentation files in Totalsegmentor

Export the nii.gz segmentation files in Totalsegmentor into 3D models (STL, OBJ, PLY)

1. Download the Totalsegmentor CT dataset from here and extract the dataset to your preferred location.
2. Open the export_from_Slicer.py script and modify the following variables:
   • TotalSegmentor_path: The path to the Totalsegmentor dataset
   • export_path: The path to the export directory
   • selected_segment: The selected segment to export
   • export_type: The type of export {obj, stl, ply}
   • skip_image_id: The list of image ids to skip due to some error files that 3DSlicer can't load
3. Open the 3DSlicer and navigate to python console: View > Python console
4. Run the script by pressing Ctrl + g (or Cmd + g on macOS) and select the export_from_Slicer.py script
5. The 3D models will be saved to the export directory