The Brain Tumor Segmentation (BraTS) Challenge: Local Synthesis of Healthy Brain Tissue via Inpainting

Florian Kofler, Felix Meissen, Felix Steinbauer, Robert Graf, Stefan K Ehrlich +101 more

5/15/2023

eess.IVcs.CVcs.LG

No official code found. Best implementation: BraTS-inpainting/2023_challenge (22 stars, MIT, last commit 2024-07-15). 1 more below.

Abstract

A myriad of algorithms for the automatic analysis of brain MR images is available to support clinicians in their decision-making. For brain tumor patients, the image acquisition time series typically starts with an already pathological scan. This poses problems, as many algorithms are designed to analyze healthy brains and provide no guarantee for images featuring lesions. Examples include, but are not limited to, algorithms for brain anatomy parcellation, tissue segmentation, and brain extraction. To solve this dilemma, we introduce the BraTS inpainting challenge. Here, the participants explore inpainting techniques to synthesize healthy brain scans from lesioned ones. The following manuscript contains the task formulation, dataset, and submission procedure. Later, it will be updated to summarize the findings of the challenge. The challenge is organized as part of the ASNR-BraTS MICCAI challenge.

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Code Implementations(2)

BraTS-inpainting/2023_challengeCommunity100%

MIT

BraTS 2023 Inpainting Challenge (Local Synthesis) Repository for Participants. Includes baseline model and infill mask generation script.

221Python, Jupyter NotebookApr 28, 20232 years agoMIT

braininfillinpaintingmri

BraTS-inpainting/inpaintingCommunity57%

AGPL-3.0

Official package to compute metrics for the BraTS inpainting challenge https://arxiv.org/abs/2305.08992

60PythonSep 14, 20231 years agoAGPL-3.0

imageinpaintingsynthesis

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Cite this paper

@article{kofler2023brain,
  title  = {The Brain Tumor Segmentation (BraTS) Challenge: Local Synthesis of Healthy Brain Tissue via Inpainting},
  author = {Florian Kofler and Felix Meissen and Felix Steinbauer and Robert Graf and Stefan K Ehrlich and Annika Reinke and Eva Oswald and Diana Waldmannstetter and Florian Hoelzl and Izabela Horvath and Oezguen Turgut and Suprosanna Shit and Christina Bukas and Kaiyuan Yang and Johannes C. Paetzold and Ezequiel de da Rosa and Isra Mekki and Shankeeth Vinayahalingam and Hasan Kassem and Juexin Zhang and Ke Chen and Ying Weng and Alicia Durrer and Philippe C. Cattin and Julia Wolleb and M. S. Sadique and M. M. Rahman and W. Farzana and A. Temtam and K. M. Iftekharuddin and Maruf Adewole and Syed Muhammad Anwar and Ujjwal Baid and Anastasia Janas and Anahita Fathi Kazerooni and Dominic LaBella and Hongwei Bran Li and Ahmed W Moawad and Gian-Marco Conte and Keyvan Farahani and James Eddy and Micah Sheller and Sarthak Pati and Alexandros Karagyris and Alejandro Aristizabal and Timothy Bergquist and Verena Chung and Russell Takeshi Shinohara and Farouk Dako and Walter Wiggins and Zachary Reitman and Chunhao Wang and Xinyang Liu and Zhifan Jiang and Elaine Johanson and Zeke Meier and Ariana Familiar and Christos Davatzikos and John Freymann and Justin Kirby and Michel Bilello and Hassan M Fathallah-Shaykh and Roland Wiest and Jan Kirschke and Rivka R Colen and Aikaterini Kotrotsou and Pamela Lamontagne and Daniel Marcus and Mikhail Milchenko and Arash Nazeri and Marc-André Weber and Abhishek Mahajan and Suyash Mohan and John Mongan and Christopher Hess and Soonmee Cha and Javier Villanueva-Meyer and Errol Colak and Priscila Crivellaro and Andras Jakab and Abiodun Fatade and Olubukola Omidiji and Rachel Akinola Lagos and O O Olatunji and Goldey Khanna and John Kirkpatrick and Michelle Alonso-Basanta and Arif Rashid and Miriam Bornhorst and Ali Nabavizadeh and Natasha Lepore and Joshua Palmer and Antonio Porras and Jake Albrecht and Udunna Anazodo and Mariam Aboian and Evan Calabrese and Jeffrey David Rudie and Marius George Linguraru and Juan Eugenio Iglesias and Koen Van Leemput and Spyridon Bakas and Benedikt Wiestler and Ivan Ezhov and Marie Piraud and Bjoern H Menze},
  year   = {2023},
  eprint = {2305.08992},
  archivePrefix = {arXiv},
  url    = {http://arxiv.org/abs/2305.08992v3}
}

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