Brain-IT-VQA: From Brain Signals to Answers

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.

Brain tumor diagnosis is largely dependent on Magnetic Resonance Imaging (MRI) evaluation, which requires radiologists to synthesize thousands of images across multiple 3D sequences and longitudinal studies. This process requires advanced neuro-radiology training, poses substantial cognitive load, and is highly time-consuming. Despite increasing demands in radiology, this expertise is difficult to scale, straining the current health systems. Vision-Language Models (VLMs) provide an opportunity to reduce this burden through a semi-automated, interactive interpretation of complex brain MRIs. However, they are currently underutilized in neuro-oncology due to a lack of specialized benchmarks for evaluating them. We introduce a clinically relevant visual question answering (VQA) benchmark -- the UCSF-PDGM-VQA dataset -- consisting of 2,387 QA pairs from 473 glioma-related MRI studies in the public UCSF-PDGM dataset. We further establish a performance baseline for six state-of-the-art vision-language models (VLMs) and one large language model on this dataset. We find that current models are incapable of effectively processing multi-sequence, 3-dimensional MRI scans, thus resulting in a suppression of visual features and over-reliance on language priors, causing modality collapse. These findings underscore a critical deficiency in current model reliability and safety within clinical settings, necessitating the development of robust, domain-specific VLMs.

Vision-language models (VLMs) achieve strong visual question answering (VQA) performance, but processing large cluttered images is computationally expensive when only a small region is relevant. Electroencephalography (EEG) signals, which capture human neural responses to visual stimuli, can provide a human-derived semantic cue about the region of interest (ROI). However, EEG-guided visual category decoding remains imperfect, making direct ROI routing unreliable. In this work, we propose BrainFocus, a reliable EEG-guided efficient VLM framework for VQA. An EEG classifier predicts a target category, and a YOLO detector localizes the matching ROI. The VLM receives the cropped ROI only when both predictions pass confidence thresholds; otherwise, it processes the full image. For evaluation, we build on EEG-ImageNet to construct a 40-class benchmark comprising generated cluttered images and real object-centric images, with target-ROI annotations and 600 English visual question-answer pairs. Across Qwen3.5-VL 2B, 4B, and 9B models, BrainFocus improves VQA accuracy by 4.14-9.87 percentage points (pp) on cluttered scenes while reducing input tokens and total tokens by 23.2%-39.4% and 23.2%-39.3%, and end-to-end floating-point operations (FLOPs) by 23.2%-39.5%. These results demonstrate that EEG can guide efficient VLM inference even when its semantic decoding is imperfect.