neuroimaging analysis teams

Abstract: Neuroimaging seeks brain regions whose imaging features correlate with variables of interest (e.g., diagnosis, age), usually via the General Linear Model (GLM). Region-Based Analysis dilutes or splits any effect that does not fill exactly one atlas region. Voxel-Based Analysis, with Cluster Extent Thresholding and Threshold-Free Cluster Enhancement built on it, fits a GLM per voxel and groups adjacent significant voxels. But neighboring voxels can share a statistic without sharing a GLM, which a per-voxel statistic cannot detect. GLOW (General Linear Models Optimized with Ward's method) instead builds a hierarchy of nested regions by greedily minimizing GLM error (provably a special case of Ward's clustering). Maximum-statistic (Westfall-Young) permutation controls family-wise error over all regions. Significance spreads to an effect's nested fragments and the regions containing it; a final pruning step seeks whole, pure effect extents. We plant synthetic effects of known extent and varying strength in Human Connectome Project (HCP) diffusion images and in white noise. Pruning delivers wholeness: GLOW returns a spatially consistent effect as one region on 57% of HCP trials, the best baseline on 35%; baselines recover comparable volume, but in many pure pieces. The cost is positive predictive value (PPV): GLOW is more sensitive (by up to 0.29), but its regions overrun the effect, mostly because no hierarchy region isolates it, not because of pruning. On HCP, GLOW's mean Dice gains 0.059 over the best baseline at weaker effects and gives back 0.005 at stronger ones. On white noise, GLOW trails by up to 0.61 Dice: its hierarchy holds the effect, but its permutation test does not certify it. Runtime grows roughly linearly with voxel count, about 4.5 times the voxel-wise methods' on the full HCP volume. The PPV loss may trace to the assumption of spatially independent residuals.

Abstract: Recent fMRI foundation models differ substantially in the spatial scale at which they represent brain activity. ROI- and connectivity-based models are efficient but coarse, whereas voxel-level models preserve fine-grained spatial structure but require specialized 3D/4D architectures and costly fMRI-specific pretraining. We ask how effectively an image-pretrained encoder can reuse the spatial organization of cortical activity. Motivated by evidence that macroscale brain activity is strongly constrained by brain geometry, we introduce FlatClip, a frozen-encoder surface-level baseline that renders cortical activity as geometry-aware flatmap sequences and reuses a frozen SigLIP2 image encoder with only a lightweight downstream probe. Across resting-state benchmarks, FlatClip serves as a competitive middle-ground representation, outperforming ROI-level baselines on HCP and ADNI tasks while remaining weaker on PPMI and below the strongest voxel-level models overall. On visual-fMRI decoding, restricting the input to visual or NSD-provided task-active cortex improves performance, highlighting the value of task-relevant cortical coverage. Spatial perturbation controls reduce the predictive performance of flatmap features under both retrained and fixed readouts, and anatomy-linked arrangements consistently outperform vertex permutations across three colormaps. Together, these results position surface-level flatmap sequences as a practical middle-ground baseline between ROI and voxel models, and support the utility of anatomy-linked spatial organization for reusing image-pretrained features. Code is available at https://github.com/OneMore1/FlatClip.

Abstract: Brain-age prediction models are commonly evaluated by predictive accuracy, yet accurate predictions alone do not establish that a model relies on reproducible or neurobiologically supported mechanisms. Post-hoc explanation methods can expose these mechanisms, but existing workflows typically stop at diagnosis or require correction targets to be specified before model analysis. We propose XAI-Refine, an automated explanation-knowledge loop for brain-age prediction from resting-state functional connectivity. At each iteration, XAI-Refine consolidates complementary post-hoc analyses across repeated training runs into reliable, structured model explanations. It converts each reliable explanation into a neutral neurobiological question, retrieves and verifies relevant literature, and compiles the verified evidence into an admissible set in the same typed explanation space. The target for refinement is defined as the minimal projection of the current model explanation onto the admissible set induced by applicable verified knowledge. This revised explanation is then translated into a differentiable constraint while preserving the originating model variable, measurement operator, and applicable scope. Candidate updates are promoted only when multi-seed validation confirms target-directed explanatory movement, predictive performance remains within a prespecified guardrail, and non-target explanatory drift remains bounded. Experiments on functional-connectivity-based brain-age prediction evaluate predictive performance, explanation reliability, literature alignment, and target-specific model revision, illustrating a structured route from post-hoc analysis to evidence-guided model refinement.