@@ -20,6 +22,24 @@ The Torso Processing ToolBox (TPTBox) is a multi-functional package to handle any sort of bids-conform dataset (CT, MRI, ...) +## Publication + +This is the official repository of "TPTBox: Extensive torso processing toolbox for simple and automatic analysis of CT and MR imaging" + +If you use this toolbox, please cite our publication: https://doi.org/10.1016/j.softx.2026.103055 +``` +@article{MollerGraf2026TPTBox, + title = {TPTBox: Extensive torso processing toolbox for simple and automatic analysis of CT and MR imaging}, + journal = {SoftwareX}, + pages = {103055}, + year = {2026}, + issn = {2352-7110}, + doi = {https://doi.org/10.1016/j.softx.2026.103055}, + url = {https://www.sciencedirect.com/science/article/pii/S2352711026005467}, + author = {Hendrik Möller and Robert Graf and Tanja Lerchl and Daniel Rueckert and Jan S. Kirschke}, +} +``` + ## Features - **Dataset Handling**: Loop over datasets, search query, and find images and their corresponding derivatives @@ -114,69 +134,3 @@ Each sub-package has its own README with API tables and examples. Click on the n | [`mesh3D`](https://tptbox.readthedocs.io/en/latest/modules/mesh3d/) | 3D surface mesh generation and rendering from segmentation volumes | | [`stitching`](https://tptbox.readthedocs.io/en/latest/modules/stitching/) | Multi-station NIfTI stitching for whole-body or long-spine acquisitions | | [`logger`](https://tptbox.readthedocs.io/en/latest/modules/logger/) | Structured, consistent logging for medical image processing pipelines | - - - -# Publications - -An incomplete list of publications that actively used TPTBox: - -1. **Denoising diffusion-based MRI to CT image translation enables automated spinal segmentation**; Graf, Robert; -Schmitt, Joachim; Schlaeger, Sarah; Möller, Hendrik Kristian; Sideri-Lampretsa, Vasiliki; Sekuboyina, Anjany; Krieg, Sandro Manuel; -Wiestler, Benedikt; Menze, Bjoern; Rueckert, Daniel; Kirschke, Jan; **European Radiology Experimental, 2023** - -2. **Modeling the acquisition shift between axial and sagittal MRI for di usion super-resolution to enable axial spine segmentation**; Graf, Robert; Möller, Hendrik; McGinnis, Julian; Rühling, Sebastian; Weihrauch, Maren; Atad, Matan; Shit, -Suprosanna; Menze, Bjoern; Mühlau, Mark; Paetzold, Johannes C.; Rueckert, Daniel; Kirschke, Jan S.; **Proceedings of Machine Learning Research, 2024** - -3. **Detecting unforeseen data properties with diffusion autoencoder embeddings using spine MRI data**; Graf, Robert; Hunecke, Florian; Pohl, Soeren; Atad, Matan; Möller, Hendrik; Starck, Sophie; Kröncke, Thomas; Bette, Stefanie; Bamberg, -Fabian; Pischon, Tobias; Niendorf, Thoralf; Schmidt, Carsten; Paetzold, Johannes C.; Rueckert, Daniel; Kirschke, Jan S.; **International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2024** - -4. **SPINEPS—automatic whole spine segmentation of T2-weighted MR images using a two-phase approach to multi-class semantic and instance segmentation**; Möller, Hendrik; Graf, Robert; Schmitt, Joachim; Keinert-Weth, Benjamin; -Schön, Hanna; Atad, Matan; Sekuboyina, Anjany; Streckenbach, Felix; Kofler, Florian; -Kroencke, Thomas; Bette, Stefanie; Willich, Stefan N.; Keil, Thomas; Niendorf, Thoralf; -Pischon, Tobias; Endemann, Beate; Menze, Bjoern; Rueckert, Daniel; Kirschke, Jan S.; -**European Radiology, 2025** - -5. **VIBESegmentator: full body MRI segmentation for the NAKO and UK Biobank**; -Graf, Robert; Platzek, Paul; Riedel, Evamaria Olga; Ramschütz, Constanze; Starck, Sophie; Möller, Hendrik K.; Atad, Matan; Völzke, -Henry; Bülow, Robin; Schmidt, Carsten Oliver; Rüdebusch, Julia; Jung, Matthias; Reisert, Marco; Weiss, Jakob; Lö ler, Maximilian T.; -Bamberg, Fabian; Wiestler, Benedikt; Paetzold, Johannes C.; Rueckert, Daniel; Kirschke, Jan S.; **European Radiology, 2025** - -6. **Generating synthetic high-resolution spinal STIR and T1w images from T2w FSE and low-resolution axial Dixon**; Graf, Robert; Platzek, Paul-Sören; Riedel, Evamaria Olga; Kim, Su Hwan; Lenhart, Nicolas; Ramschütz, Constanze; Paprottka, -Karolin Johanna; Kertels, Olivia Ruriko; Möller, Hendrik Kristian; Atad, Matan; Bülow, Robin; Werner, Nicole; Völzke, Henry; Schmidt, -Carsten Oliver; Wiestler, Benedikt; Paetzold, Johannes C.; Rueckert, Daniel; Kirschke, Jan S.; **European Radiology, 2025** - -7. **MAGO-SP: detection and correction of water-fat swaps in magnitude-only VIBE MRI**; -Graf, Robert; Möller, Hendrik; Starck, Sophie; Atad, Matan; Braun, Philipp; Stelter, Jonathan; Peters, Annette; Krist, Lilian; Willich, -Stefan N.; Völzke, Henry; Bülow, Robin; Pischon, Tobias; Niendorf, Thoralf; Paetzold, Johannes C.; Karampinos, Dimitrios; Rueckert, -Daniel; Kirschke, Jan S.; **International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI), 2025** - -8. **Automated Thoracolumbar Stump Rib Detection and Analysis in a Large CT Cohort**; -Möller, Hendrik; Dima, Alina; Keinert-Weth, Benjamin; Graf, Robert; Atad, Matan; Paetzold, -Johannes; Jungmann, Friederike; Braren, Rickmer; Kofler, Florian; Menze, Bjoern; Rueckert, -Daniel; Kirschke, Jan S.; Schön, Hanna; **MDPI AI, 2026** - -9. **PARASIDE: An automatic paranasal sinus segmentation and structure analysis tool for magnetic resonance imaging**; Möller, Hendrik; -Krautschick, Lukas; Graf, Robert; Atad, Matan; Busch, Chia-Jung; Beule, Achim Georg; -Scharf, Christian; Kaderali, Lars; Menze, Bjoern; Rueckert, Daniel; Kirschke, Jan S.; -Paperlein, Fabian; **Computers in Biology and Medicine, 2026** - -10. **One Sequence to Segment Them All: Efficient Data Augmentation for CT and MRI Cross-Domain 3D Spine Segmentation;** Molinier, -Nathan*; Möller, Hendrik*; Dagonneau, Thomas; Curto-Vilalta, Anna; Graf, Robert; Atad, -Matan; Rueckert, Daniel; Kirschke, Jan S.; Cohen-Adad, Julien; **International Conference on -Medical Image Computing and Computer-Assisted Intervention (MICCAI) , 2026** - -11. **VERIDAH: Solving Enumeration Anomaly Aware Vertebra -Labeling across Imaging Sequences;** Möller, Hendrik; Schön, Hanna; Graf, Robert; -Atad, Matan; Molinier, Nathan; Sekuboyina, Anjany; Budai, Bettina; Bamberg, Fabian; -Ringhof, Steffen; Schlett, Christopher; Pischon, Tobias; Niendorf, Thoralf; Decker, Josua; -Weber, Marc-André; Menze, Bjoern; Rueckert, Daniel; Kirschke, Jan S.; **European -Radiology (under review), 2026** - -12. **Rule-based key-point extraction for MR-guided biomechanical digital twins of the spine**; Graf, Robert; Lerchl, -Tanja; Nispel, Kati; Möller, Hendrik; Atad, Matan; McGinnis, Julian; Watrinet, Julius Maria; Paetzold, Johannes C.; Rueckert, Daniel; -Kirschke, Jan S.; **International Workshop on Digital Twin for Healthcare (DT4H), 2025** - -13. **VERPEX: Anatomical Landmark Extraction on 3D Vertebrae exploiting Segmentation Masks**; Möller, Hendrik; Wang, Alissa Yuxuan; Graf, Robert; -Nispel, Kati; Atad, Matan; Menze, Bjoern; Rueckert, Daniel; Kirschke, Jan S.; Lerchl, Tanja; -**International Workshop on Digital Twin for Healthcare (DT4H), 2026**