OpenBrain: An Auditable Generated-Label Release for Whole-Brain MRI Parcellation

We present NeuroQA, a large-scale benchmark for visual question answering in 3D brain magnetic resonance imaging (MRI), with 56,953 QA pairs from 12,977 subjects across 12 datasets. It spans ages 5-104 and five clinical domains: Alzheimer's, Parkinson's, tumors, white matter disease, and neurodevelopment. Unlike prior medical Visual Question Answering (VQA) efforts that operate on 2D slices or rely on narrow diagnostic labels, NeuroQA pairs every item with a full 3D volume. It evaluates 11 clinically grounded reasoning skills across Yes/No, multiple-choice, and open-ended formats. Of the 203 templates, 131 are image-grounded (answerable from a 3-plane viewer) and 72 are image-informed (ground truth from quantitative volumetry or clinical instruments). To remove text-only shortcuts, we apply answer-distribution refinement, reducing closed-format text-only accuracy from $>$80% to 44.6%; image necessity is assessed separately through an image-grounding protocol released with the benchmark. A 38-rule deterministic pipeline and two rounds of expert review verify every QA pair against FreeSurfer measurements, metadata, or radiology report fields, with zero same-subject contradictions across templates. We conduct a clinician evaluation in which two clinicians independently assess 100 frozen test items on a three-plane viewer. On closed-format (Yes/No + multiple-choice) test-public items, the best zero-shot vision-language model and a supervised 3D CNN baseline reach 47.5% and 43.7% accuracy respectively, both below the 49.4% text-only majority-template floor. NeuroQA adopts a two-tier release with public QA pairs for open-access datasets and reproducible generation scripts for datasets restricted by data use agreements (DUAs), plus subject-level splits, a held-out private test set, and an online leaderboard.

Radiology report generation has matured almost entirely on 2D chest radiographs, where the default route to better reports is a larger backbone or a pre-training one on medical data. We revisit that assumption on 3D multi-sequence brain MRI, a volumetric multi-disease regime, and find that the model is not the lever. Zero-shot medical and radiology vision-language models transfer poorly to brain MRI, with chest radiograph specialists failing most conspicuously, and five backbones fine-tuned identically across three model families and an order of magnitude in scale differ only marginally. What determines the quality of the report is the information injected into the prompt. We delegate perception to upstream 3D segmentation and classification, serialize their outputs into a structured fact sentence, and prompt a LoRA-adapted vision-language model with it; we call this PerFact. In a controlled study that fixes the backbone, data split, target reports, and adaptation while varying only the injected grounding, perception-derived facts outperform retrieved prior reports, retrieval becomes redundant once facts are present, and end-to-end predicted facts remain effective without any ground-truth annotation at inference. The residual gap between predicted and oracle facts is explained by the granularity of the facts rather than by the generator. Closed-ended visual question answering comes at no measurable cost to report quality, though the grounding source has little effect on it. On 3D brain MRI, grounding information, not model choice, is the dominant controllable factor in report quality.

Medical vision-language models typically generate diagnoses through single-pass inference without indicating which image regions support their conclusions. This lack of spatial grounding limits clinical utility: outputs cannot be audited, and models may hallucinate findings on normal scans. We present BrReMark (Brain Rethink via ROI Marking), a framework that introduces explicit region marking into brain MRI diagnosis. The model first generates hypotheses about potential abnormalities and grounds them through explicit bounding box marking, then verifies conclusions by re-examining the marked evidence. Training combines supervised fine-tuning on structured reasoning trajectories with reinforcement learning using a composite reward over localization accuracy and diagnostic reasoning. Furthermore, we integrate a domain randomization-based pathology synthesis augmentation strategy to improve the model's generalizability to out-of-distribution (OOD) data. On internal benchmark, BrReMark improves mAP50 from 0.74% to 37.54% compared to the base model, while achieving 21.57% Clinical F1 and 45.26% diagnostic accuracy. On NOVA OOD benchmark, it also achieves competitive overall performance with a 45.7% reduction in false positives compared to the state-of-the-art, indicating reduced hallucination on rare pathologies. These findings suggest that explicit hypothesis-verification grounding is a practical path toward trustworthy open-ended brain MRI diagnosis across both in-distribution and OOD settings.