BRATS2021: Exploring Each Sequence in Multi-modal Input for Baseline U-net Performance

Polina Druzhinina, Ekaterina Kondrateva, Arseny Bozhenko, Vyacheslav Yarkin, Maxim Sharaev, Anvar Kurmukov

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

Since 2012 the BraTS competition has become a benchmark for brain MRI segmentation. The top-ranked solutions from the competition leaderboard of past years are primarily heavy and sophisticated ensembles of deep neural networks. The complexity of the proposed solutions can restrict their clinical use due to the long execution time and complicate the model transfer to the other datasets, especially with the lack of some MRI sequences in multimodal input. The current paper provides a baseline segmentation accuracy for each separate MRI modality and all four sequences (T1, T1c, T2, and FLAIR) on conventional 3D U-net architecture. We explore the predictive ability of each modality to segment enhancing core, tumor core, and whole tumor. We then compare the baseline performance with BraTS 2019–2020 state-of-the-art solutions. Finally, we share the code and trained weights to facilitate further research on model transfer to different domains and use in other applications.

Original languageEnglish
Title of host publicationBrainlesion
Subtitle of host publicationGlioma, Multiple Sclerosis, Stroke and Traumatic Brain Injuries - 7th International Workshop, BrainLes 2021, Held in Conjunction with MICCAI 2021, Revised Selected Papers
EditorsAlessandro Crimi, Spyridon Bakas
PublisherSpringer Science and Business Media Deutschland GmbH
Pages194-203
Number of pages10
ISBN (Print)9783031089985
DOIs
Publication statusPublished - 2022
Event7th International Brain Lesion Workshop, BrainLes 2021, held in conjunction with the Medical Image Computing and Computer Assisted Intervention, MICCAI 2021 - Virtual, Online
Duration: 27 Sep 202127 Sep 2021

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume12962 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference7th International Brain Lesion Workshop, BrainLes 2021, held in conjunction with the Medical Image Computing and Computer Assisted Intervention, MICCAI 2021
CityVirtual, Online
Period27/09/2127/09/21

Keywords

  • brain MRI
  • BRATS2021
  • Medical segmentation
  • U-Net

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