arXiv:2511.12899v1 Announce Type: new Abstract: Due to the diversity of brain anatomy and the scarcity of annotated data, supervised anomaly detection for brain MRI remains challenging, driving the development of unsupervised anomaly detection (UAD) approaches. Current UAD methods typically utilize artificially generated noise perturbations on healthy MRIs to train generative models for normal anatomy reconstruction, enabling anomaly detection via residual mapping. However, such simulated anomalies lack the biophysical fidelity and morphological complexity characteristic of true clinical lesions. To advance UAD in brain MRI, we conduct the first systematic frequency-domain analysis of pathological signatures, revealing two key properties: (1) anomalies exhibit unique frequency patterns distinguishable from normal anatomy, and (2) low-frequency signals maintain consistent representations across healthy scans. These insights motivate our Frequency-Decomposition Preprocessing (FDP) framework, the first UAD method to leverage frequency-domain reconstruction for simultaneous pathology suppression and anatomical preservation. FDP can integrate seamlessly with existing anomaly simulation techniques, consistently enhancing detection performance across diverse architectures while maintaining diagnostic fidelity. Experimental results demonstrate that FDP consistently improves anomaly detection performance when integrated with existing methods. Notably, FDP achieves a 17.63% increase in DICE score with LDM while maintaining robust improvements across multiple baselines. The code is available at https://github.com/ls1rius/MRI_FDP.