I have been working with the new MONAI Auto3DSeg and have a few questions if someone could help me out:
1- Where can I find the source for the models used? For example, “Madiastinal anatomy TS2” is not in MONAI’s model zoo and it’s also not an available subtask or roi_subset in Total Segmentator.
2- Were some of these models trained by Slicer community contributors?
3- Is there a way to run Auto3DSeg’s inference from cmd line without launching Slicer and switching modules?
Most models that you can find online in various model zoos are not optimized for real-world usage. We created these models with @diazandr3s specifically to make them practically, clinically useful.
You can download these models and run them without Slicer GUI, from the command-line or via network requests within Slicer’s Python environment; or even completely independently from Slicer. To make it really easy to use without Slicer, we have separated the inference script into a standalone Python file.