NeCS-Flow: Necrosis-Guided Contrast-Enhanced MRI Synthesis with Rectified-Flow Refinement
Abstract
Background: Gadolinium-based contrast agents raise concerns about tissue deposition, adverse reactions, and increased costs. Purpose: To develop and validate a deep learning pipeline for gadolinium-free post-contrast T1w brain MRI synthesis incorporating necrotic scaling and Posterior-Mean Rectified Flow (PMRF) refinement, and to evaluate diagnostic utility through a blinded multi-reader study. Study Type: Retrospective. Population: 454 patients with adult-type gliomas (grade 2-4) from four publicly available datasets. Training used 374 patients; internal testing used 60 held-out patients; external validation used 20 patients. Field Strength/Sequence: 1.5-3.0 T; pre-contrast T1w, T2w, and FLAIR as inputs; post-contrast T1w as synthesis target. Assessment: A three-stage pipeline comprising nnU-Net Necrotic core segmentation, necrotic-scaling-guided U-Net Contrast Synthesis, and PMRF perceptual refinement (NeCS-Flow) was evaluated using whole-brain and tumor-region similarity metrics, enhancing tumor Dice scores, perceptual quality metrics, and a blinded three-reader study assessing diagnostic accuracy, enhancement detection, image quality, and real-versus-synthetic discriminability. Statistical Tests: Paired t-tests and two one-sided tests for model comparison; Fisher's exact test and two-sample t-tests for reader study comparisons, with p < 0.05 considered significant. Results: Necrotic scaling consistently improved real versus synthetic enhancing tumor Dice internally (HGG: 0.793 to 0.816) and externally (HGG: 0.465 to 0.612). NeCS-Flow outperformed two benchmark architectures on all quantitative metrics in internal and external testing, although absolute enhancing tumor accuracy declined for all models on the external cohort. PMRF refinement improved perceptual realism across both tumor types, reducing both FID and KID. Readers distinguished synthetic from real images only modestly above chance (overall accuracy 61.7%), and no significant differences between real and synthetic images were found for any clinical metric. Data Conclusion: NeCS-Flow synthesizes perceptually realistic and diagnostically equivalent post-contrast T1w brain MRI, with necrotic scaling improving enhancing tumor delineation and PMRF refinement improving perceptual realism across gliomas. Performance on an external cohort was preserved relative to benchmark methods, though reduced in absolute terms.
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BibTeX
@misc{goni2026necsflow,
title = {{NeCS-Flow: Necrosis-Guided Contrast-Enhanced MRI Synthesis with Rectified-Flow Refinement}},
author = {Eunate Alzaga Goñi and Walter Zhao and Rhea Adams and Shahrzad Moinian and Yanfei Xiong and Tianhe Wu and Kewei Yan and Katie Shpanskaya and Anil Vasireddi and Jessica Houk and Evan Calabrese and Dan Ma},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.21.760821},
url = {https://www.biorxiv.org/content/10.64898/2026.10.21.760821v1},
note = {CC BY-NC},
}
RIS
TY - UNPB
TI - NeCS-Flow: Necrosis-Guided Contrast-Enhanced MRI Synthesis with Rectified-Flow Refinement
AU - Eunate Alzaga Goñi
AU - Walter Zhao
AU - Rhea Adams
AU - Shahrzad Moinian
AU - Yanfei Xiong
AU - Tianhe Wu
AU - Kewei Yan
AU - Katie Shpanskaya
AU - Anil Vasireddi
AU - Jessica Houk
AU - Evan Calabrese
AU - Dan Ma
PY - 2026
DA - 2026/10/21
PB - bioRxiv
DO - 10.64898/2026.10.21.760821
UR - https://www.biorxiv.org/content/10.64898/2026.10.21.760821v1
AB - Background: Gadolinium-based contrast agents raise concerns about tissue deposition, adverse reactions, and increased costs. Purpose: To develop and validate a deep learning pipeline for gadolinium-free post-contrast T1w brain MRI synthesis incorporating necrotic scaling and Posterior-Mean Rectified Flow (PMRF) refinement, and to evaluate diagnostic utility through a blinded multi-reader study. Study Type: Retrospective. Population: 454 patients with adult-type gliomas (grade 2-4) from four publicly available datasets. Training used 374 patients; internal testing used 60 held-out patients; external validation used 20 patients. Field Strength/Sequence: 1.5-3.0 T; pre-contrast T1w, T2w, and FLAIR as inputs; post-contrast T1w as synthesis target. Assessment: A three-stage pipeline comprising nnU-Net Necrotic core segmentation, necrotic-scaling-guided U-Net Contrast Synthesis, and PMRF perceptual refinement (NeCS-Flow) was evaluated using whole-brain and tumor-region similarity metrics, enhancing tumor Dice scores, perceptual quality metrics, and a blinded three-reader study assessing diagnostic accuracy, enhancement detection, image quality, and real-versus-synthetic discriminability. Statistical Tests: Paired t-tests and two one-sided tests for model comparison; Fisher's exact test and two-sample t-tests for reader study comparisons, with p < 0.05 considered significant. Results: Necrotic scaling consistently improved real versus synthetic enhancing tumor Dice internally (HGG: 0.793 to 0.816) and externally (HGG: 0.465 to 0.612). NeCS-Flow outperformed two benchmark architectures on all quantitative metrics in internal and external testing, although absolute enhancing tumor accuracy declined for all models on the external cohort. PMRF refinement improved perceptual realism across both tumor types, reducing both FID and KID. Readers distinguished synthetic from real images only modestly above chance (overall accuracy 61.7%), and no significant differences between real and synthetic images were found for any clinical metric. Data Conclusion: NeCS-Flow synthesizes perceptually realistic and diagnostically equivalent post-contrast T1w brain MRI, with necrotic scaling improving enhancing tumor delineation and PMRF refinement improving perceptual realism across gliomas. Performance on an external cohort was preserved relative to benchmark methods, though reduced in absolute terms.
SN - 2692-8205
ER -