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Include Advanced settings support for TotalSegmentator tool in MITK
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Advanced setting flags like:

  • --fast: For faster runtime and less memory requirements use this option. It will run a lower resolution model (3mm instead of 1.5mm).
  • --preview: This will generate a 3D rendering of all classes, giving you a quick overview if the segmentation worked and where it failed (see preview.png in output directory).
  • --ml: This will save one nifti file containing all labels instead of one file for each class. Saves runtime during saving of nifti files.
  • --roi_subset: Takes a space separated list of class names (e.g. spleen colon brain) and only saves those classes. Saves runtime during saving of nifti files.
  • --statistics: This will generate a file statistics.json with volume (in mm³) and mean intensity of each class.
  • --radiomics: This will generate a file statistics_radiomics.json with radiomics features of each class. You have to install pyradiomics to use this (pip install pyradiomics).

exist for TotalSegmentator.
Some of these could be potentially also included in the MITK along with GPU selection options (like in the nnUNet tool) in the tool workflow after the basic segmentation workflow is working. (T29457)

Event Timeline

a178n triaged this task as Normal priority.Feb 15 2023, 12:25 PM
a178n created this task.

After discussion, it's decided that out of the abovementioned "advanced" flags, only --fast will be implemented along with GPU selection.
The --statistics flag seems to bring to some value & it's inclusion was separately discussed here: T29465

Hi Ralf,

I checked Slicer & TotalSegmentator in it.

  1. They have managed to include Subtask support, as well. See : .So, we should also make this is MITK, I suppose.
  2. Slicer doesn't allow user managed python environments. They setup the TotalSegmentator backend, no choice. So, they download a commit hash to avoid version conflicts in the future. We can see the it here:

Deleted branch from rMITK MITK: feature/T29458-totalsegmentator-advanced.