TotalSegmentator: robust segmentation of 104 anatomical structures in CT images

Abstract: In this work we focus on automatic segmentation of multiple anatomical structures in (whole body) CT images. Many segmentation algorithms exist for this task. However, in most cases they suffer from 3 problems: 1. They are difficult to use (the code and data is not publicly available or difficult to use). 2. They do not generalize (often the training dataset was curated to only contain very clean images which do not reflect the image distribution found during clinical routine), 3. The algorithm can only segment one anatomical structure. For more structures several algorithms have to be used which increases the effort required to set up the system. In this work we publish a new dataset and segmentation toolkit which solves all three of these problems: In 1204 CT images we segmented 104 anatomical structures (27 organs, 59 bones, 10 muscles, 8 vessels) covering a majority of relevant classes for most use cases. We show an improved workflow for the creation of ground truth segmentations which speeds up the process by over 10x. The CT images were randomly sampled from clinical routine, thus representing a real world dataset which generalizes to clinical application. The dataset contains a wide range of different pathologies, scanners, sequences and sites. Finally, we train a segmentation algorithm on this new dataset. We call this algorithm TotalSegmentator and make it easily available as a pretrained python pip package (pip install totalsegmentator). Usage is as simple as TotalSegmentator -i ct.nii.gz -o seg and it works well for most CT images. The code is available at https://github.com/wasserth/TotalSegmentator and the dataset at https://doi.org/10.5281/zenodo.6802613.