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Published Paper Changes #156

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62 changes: 62 additions & 0 deletions CITATION.cff
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Original file line number Diff line number Diff line change
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cff-version: 1.2.0
title: "TPTBox: Torso Processing ToolBox"
message: "If you use this software, please cite both the software and the accompanying paper (see preferred-citation)."
type: software
authors:
- family-names: "Möller"
given-names: "Hendrik"
email: "hendrik.moeller@tum.de"
affiliation: "Technical University of Munich"
- family-names: "Graf"
given-names: "Robert"
email: "robert.graf@tum.de"
affiliation: "Technical University of Munich"
- family-names: "Lerchl"
given-names: "Tanja"
affiliation: "Technical University of Munich"
- family-names: "Rueckert"
given-names: "Daniel"
affiliation: "Technical University of Munich"
- family-names: "Kirschke"
given-names: "Jan S."
affiliation: "Technical University of Munich"
repository-code: "https://github.com/Hendrik-code/TPTBox"
url: "https://tptbox.readthedocs.io"
abstract: >-
The Torso Processing ToolBox (TPTBox) is a Python package for processing
BIDS-compliant medical imaging datasets (CT, MRI), with a focus on torso and
spine analysis. It provides NIfTI I/O, reorientation and resampling, Points of
Interest computation for vertebrae, 2D and 3D snapshots, registration,
stitching, and segmentation integrations.
keywords:
- medical imaging
- BIDS
- NIfTI
- spine
- segmentation
- registration
- computed tomography
- magnetic resonance imaging
license: Apache-2.0
version: 1.0.0
date-released: "2026-09-07"
preferred-citation:
type: article
title: "TPTBox: Extensive torso processing toolbox for simple and automatic analysis of CT and MR imaging"
authors:
- family-names: "Möller"
given-names: "Hendrik"
- family-names: "Graf"
given-names: "Robert"
- family-names: "Lerchl"
given-names: "Tanja"
- family-names: "Rueckert"
given-names: "Daniel"
- family-names: "Kirschke"
given-names: "Jan S."
journal: "SoftwareX"
year: 2026
start: 103055
issn: "2352-7110"
doi: "10.1016/j.softx.2026.103055"
url: "https://www.sciencedirect.com/science/article/pii/S2352711026005467"
90 changes: 22 additions & 68 deletions README.md
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</h1><br>


[![PyPI version tptbox](https://badge.fury.io/py/tptbox.svg)](https://pypi.python.org/pypi/tptbox/)
[![Python Versions](https://img.shields.io/pypi/pyversions/tptbox)](https://pypi.org/project/tptbox/)
[![DOI](https://img.shields.io/badge/DOI-10.1016%2Fj.softx.2026.103055-B31B1B)](https://doi.org/10.1016/j.softx.2026.103055)
[![Stable Version](https://img.shields.io/pypi/v/tptbox?label=stable)](https://pypi.python.org/pypi/tptbox/)
[![Python Versions](https://img.shields.io/pypi/pyversions/tptbox)](https://pypi.org/project/tptbox/)
[![Downloads](https://img.shields.io/pepy/dt/tptbox?label=downloads)](https://pepy.tech/project/tptbox)
[![tests](https://github.com/Hendrik-code/TPTBox/actions/workflows/tests.yml/badge.svg)](https://github.com/Hendrik-code/TPTBox/actions/workflows/tests.yml)
[![codecov](https://codecov.io/gh/Hendrik-code/TPTBox/graph/badge.svg?token=A7FWUKO9Y4)](https://codecov.io/gh/Hendrik-code/TPTBox)
[![Documentation](https://readthedocs.org/projects/tptbox/badge/?version=latest)](https://tptbox.readthedocs.io/en/latest/)
[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
[![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)

<p align="center">
Expand All @@ -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
Expand Down Expand Up @@ -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**
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