Reduce, Then Encode: Multiscale Volumetric Reduction for 2D Foundation Models in Brain MRI

Abstract

Pretrained 2D foundation models offer a practical alternative to dedicated 3D pretraining for brain structural magnetic resonance imaging (sMRI), but their use on volumetric data requires bridging the mismatch between a 2D encoder and a 3D volume input. Existing methods typically encode slices independently and integrate their features afterwards. We introduce Multiscale Volumetric Reduction (MVR), a reduce-then-encode approach that compresses each anatomical view from (D) slices into (M << D) complementary 2D components before foundation-model encoding. MVR combines an uncentered-PCA base component derived from the original through-plane intensities with residual detail components constructed from multiscale spatial descriptors. The reduction is estimated from the training volumes without diagnostic labels or gradient-based optimization and remains fixed thereafter. The resulting components are independently processed by a shared frozen 2D foundation model and concatenated for linear probing. Under this frozen-encoder setting, MVR achieves strong overall performance across ADNI, OASIS, and ABIDE relative to the evaluated 2D-to-3D adaptation methods and simple input-reduction baselines, while also generalizing strongly from ADNI to AIBL.