Document Type
Article
Publication Date
6-27-2020
Abstract
Brain extraction, or skull-stripping, is an essential pre-processing step in neuro-imaging that has a direct impact on the quality of all subsequent processing and analyses steps. It is also a key requirement in multi-institutional collaborations to comply with privacy-preserving regulations. Existing automated methods, including Deep Learning (DL) based methods that have obtained state-of-the-art results in recent years, have primarily targeted brain extraction without considering pathologically-affected brains. Accordingly, they perform sub-optimally when applied on magnetic resonance imaging (MRI) brain scans with apparent pathologies such as brain tumors. Furthermore, existing methods focus on using only T1-weighted MRI scans, even though multi-parametric MRI (mpMRI) scans are routinely acquired for patients with suspected brain tumors. In this study, we present a comprehensive performance evaluation of recent deep learning architectures for brain extraction, training models on mpMRI scans of pathologically-affected brains, with a particular focus on seeking a practically-applicable, low computational footprint approach, generalizable across multiple institutions, further facilitating collaborations. We identified a large retrospective multi-institutional dataset of n=3340 mpMRI brain tumor scans, with manually-inspected and approved gold-standard segmentations, acquired during standard clinical practice under varying acquisition protocols, both from private institutional data and public (TCIA) collections. To facilitate optimal utilization of rich mpMRI data, we further introduce and evaluate a novel ‘‘modality-agnostic training’’ technique that can be applied using any available modality, without need for model retraining. Our results indicate that the modality-agnostic approach1 obtains accurate results, providing a generic and practical tool for brain extraction on scans with brain tumors.
Recommended Citation
Thakur, Siddhesh; Doshi, Jimit; Pati, Sarthak; Rathore, Saima; Sako, Chiharu; Bilello, Michel; Ha, Sung Min; Shukla, Gaurav; Flanders, Adam; Kotrotsou, Aikaterini; Milchenko, Mikhail; Liem, BS, Spencer; Alexander, Gregory S; Lombardo, Joseph; Palmer, Joshua D; LaMontagne, Pamela; Nazeri, Arash; Talbar, Sanjay; Kulkarni, Uday; Marcus, Daniel; Colen, Rivka; Davatzikos, Christos; Erus, Guray; and Bakas, Spyridon, "Brain extraction on MRI scans in presence of diffuse glioma: Multi-institutional performance evaluation of deep learning methods and robust modality-agnostic training" (2020). Department of Radiation Oncology Faculty Papers. Paper 136.
https://jdc.jefferson.edu/radoncfp/136
Creative Commons License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License.
PubMed ID
32603860
Language
English
Comments
This article is the author’s final published version in NeuroImage, Volume 220, June 2020, Article number 117081.
The published version is available at https://doi.org/10.1016/j.neuroimage.2020.117081. Copyright © Thakur et al.