Does Tumor-Mask Guidance Improve Glioma Grade Classification from T2-Weighted MRI Alone? An Out-of-Fold Evaluation with nnU-Net and Ground-Truth Localization

Multi-sequence MRI is the standard for glioma assessment, but complete or contrast-enhanced protocols are not always available (withheld gadolinium, low-field MRI, incomplete archives). We asked whether tumor localization improves grade classification from T2-weighted MRI alone. In this retrospective study of the BraTS2020 training cohort (369 patients; legacy labels 293 high-grade [HGG], 76 low-grade [LGG]), 74 patients (15 LGG) were held out at the patient level for internal testing. A 2D U-Net trained in five development folds supplied out-of-fold whole-tumor masks for training 3D CNN classifiers; nnU-Net served as a segmentation benchmark. Classifiers received T2 alone or T2 plus a mask, which at test time came from the 2D U-Net, nnU-Net, the ground truth (oracle) or random noise. Analyses used five seeds, DeLong tests with Holm correction and development-set cross-validation. Whole-tumor Dice was 0.807 (95% CI 0.773–0.840) for the 2D U-Net and 0.877 (0.857–0.895) for nnU-Net. The T2-only CNN reached an ROC-AUC of 0.814 (95% CI 0.702–0.913). Mask-guided variants reached 0.677–0.742, none above T2-only (Holm-adjusted p = 1.00 for all four confirmatory comparisons of informative masks). Cross-validation reproduced this ranking (0.782 vs. 0.707). With LGG as the positive class, PR-AUC was 0.571 (no-skill 0.203). Tumor-mask guidance did not improve T2-only grading at any level of mask quality, including ground truth. The results concern a legacy grade label in one public cohort and require external testing.

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Publication Details

Journal
Journal of Imaging
Published
2026-10-26
DOI
https://doi.org/10.3390/jimaging12110533
Primary Topic
Brain Tumor Detection and Classification
Type
article
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article

Does Tumor-Mask Guidance Improve Glioma Grade Classification from T2-Weighted MRI Alone? An Out-of-Fold Evaluation with nnU-Net and Ground-Truth Localization

Atman Mukesh Desai, Laura Marie Prolo, Vivek Sanker, D Wang et al.
Journal of Imaging
Brain Tumor Detection and Classification
article

Does Tumor-Mask Guidance Improve Glioma Grade Classification from T2-Weighted MRI Alone? An Out-of-Fold Evaluation with nnU-Net and Ground-Truth Localization

Atman Mukesh Desai, Laura Marie Prolo, Vivek Sanker, D Wang, Philip Heesen, John Kevin Ratliff, Harminder Singh, María José Cavagnaro, Zhikai Li, Alexander Thaller, Dhanya Mahesh, Ravi Teja Medikonda, Linda Liverani, Michael Lim
article en

Abstract

Multi-sequence MRI is the standard for glioma assessment, but complete or contrast-enhanced protocols are not always available (withheld gadolinium, low-field MRI, incomplete archives). We asked whether tumor localization improves grade classification from T2-weighted MRI alone. In this retrospective study of the BraTS2020 training cohort (369 patients; legacy labels 293 high-grade [HGG], 76 low-grade [LGG]), 74 patients (15 LGG) were held out at the patient level for internal testing. A 2D U-Net trained in five development folds supplied out-of-fold whole-tumor masks for training 3D CNN classifiers; nnU-Net served as a segmentation benchmark. Classifiers received T2 alone or T2 plus a mask, which at test time came from the 2D U-Net, nnU-Net, the ground truth (oracle) or random noise. Analyses used five seeds, DeLong tests with Holm correction and development-set cross-validation. Whole-tumor Dice was 0.807 (95% CI 0.773–0.840) for the 2D U-Net and 0.877 (0.857–0.895) for nnU-Net. The T2-only CNN reached an ROC-AUC of 0.814 (95% CI 0.702–0.913). Mask-guided variants reached 0.677–0.742, none above T2-only (Holm-adjusted p = 1.00 for all four confirmatory comparisons of informative masks). Cross-validation reproduced this ranking (0.782 vs. 0.707). With LGG as the positive class, PR-AUC was 0.571 (no-skill 0.203). Tumor-mask guidance did not improve T2-only grading at any level of mask quality, including ground truth. The results concern a legacy grade label in one public cohort and require external testing.

Journal of ImagingVol. 12(11)
Dartmouth College (US), University of Oslo (NO), Medical University of Graz (AT), University of Zurich (CH), Santa Clara Valley Medical Center (US), Stanford Medicine (US), Addenbrooke's Hospital (GB), Stanford University (US)
Openalex Percentile: Top 17%
Brain Tumor Detection and Classification
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