TotalSegmentator for MRI dataset

Is there an full body (or lower limb) muscle segmentation model from MRI images? As I understand totalsegmentator is specifically for CT.

There are a couple of pre-trained MRI segmentation models for MONAI Auto3DSeg (brain, prostate, etc) and you can probably find some spine segmentation models, but I don’t remember seeing any for lower lung muscles. However, it is almost sure your can train Auto3DSeg or nnUNet model for this quite easily, by manually segment cases (perhaps a few dozen is enough to get started)

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We have a project underway to try training an MR segmenter based on TotalSegmentator using the SynthSeg approach (not muscles yet though). The preprint paper actually just went up on arxiv:

Would be great to generalize to other segmentation tasks.


This looks interesting @pieper. Is the trained model available publicly?

Not currently, but I’ll check.

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Andras, @DeepaKrishnaswamy and @Cosmin_Ciausu are working on this. We absolutely will make everything publicly available, but there are some experiments and refinements that we want to do first. It’s great to see the interest. This most definitely adds a lot to the motivation to continue this work!

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