NeuroQA: A Large-Scale Image-Grounded Benchmark for 3D Brain MRI Understanding

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.

Generating Novel Brain Morphology by Deforming Learned Templates

Designing generative models for 3D structural brain MRI that synthesize morphologically-plausible and attribute-specific (e.g., age, sex, disease state) samples is an active area of research. Existing approaches based on frameworks like GANs or diffusion models synthesize the image directly, which may limit their ability to capture intricate morphological details. In this work, we propose a 3D brain MRI generation method based on state-of-the-art latent diffusion models (LDMs), called MorphLDM, that generates novel images by applying synthesized deformation fields to a learned template. Instead of using a reconstruction-based autoencoder (as in a typical LDM), our encoder outputs a latent embedding derived from both an image and a learned template that is itself the output of a template decoder; this latent is passed to a deformation field decoder, whose output is applied to the learned template. A registration loss is minimized between the original image and the deformed template with respect to the encoder and both decoders. Empirically, our approach outperforms generative baselines on metrics spanning image diversity, adherence with respect to input conditions, and voxel-based morphometry. Our code is available at https://github.com/alanqrwang/morphldm.