# PEPSI: Pathology-Enhanced Pulse-Sequence-Invariant Representations for Brain MRI Source: [PEPSI: Pathology-Enhanced Pulse-Sequence-Invariant Representations for Brain MRI]() Collection index: [llms.txt]() Data updated: 2026-01-04T04:43:02.615Z Authors: Peirong Liu, Oula Puonti, Annabel Sorby-Adams, William T. Kimberly, Juan E. Iglesias Published: 2024-03-10T14:33:55.000Z ## Abstract Remarkable progress has been made by data-driven machine-learning methods in the analysis of MRI scans. However, most existing MRI analysis approaches are crafted for specific MR pulse sequences (MR contrasts) and usually require nearly isotropic acquisitions. This limits their applicability to diverse real-world clinical data, where scans commonly exhibit variations in appearances due to being obtained with varying sequence parameters, resolutions, and orientations -- especially in the presence of pathology. In this paper, we propose PEPSI, the first pathology-enhanced, and pulse-sequence-invariant feature representation learning model for brain MRI. PEPSI is trained entirely on synthetic images with a novel pathology encoding strategy, and enables co-training across datasets with diverse pathologies and missing modalities. Despite variations in pathology appearances across different MR pulse sequences or the quality of acquired images (e.g., resolution, orientation, artifacts, etc), PEPSI produces a high-resolution image of reference contrast (MP-RAGE) that captures anatomy, along with an image specifically highlighting the pathology. Our experiments demonstrate PEPSI's remarkable capability for image synthesis compared with the state-of-the-art, contrast-agnostic synthesis models, as it accurately reconstructs anatomical structures while differentiating between pathology and normal tissue. We further illustrate the efficiency and effectiveness of PEPSI features for downstream pathology segmentations on five public datasets covering white matter hyperintensities and stroke lesions. Code is available at https://github.com/peirong26/PEPSI. ## Recorded benchmark results A research result applies to its stated dataset, split, metric and evaluation configuration. Compare like-for-like settings, preserve the metric's unit and direction, and distinguish paper-reported results from independent reproduction. The best result recorded here is not a claim of exhaustive, current global coverage. - [Anatomy and Pathology Image Synthesis on ISLES (test)](): Anatomy and Pathology Image Synthesis; ISLES (test); L1 Loss: 0.016. - [Anatomy and Pathology Image Synthesis on ADNI3 (test)](): Anatomy and Pathology Image Synthesis; ADNI3 (test); L1 Loss: 0.023. - [Anatomy and Pathology Image Synthesis on ATLAS (test)](): Anatomy and Pathology Image Synthesis; ATLAS (test); L1 Loss: 0.038. - [Healthy Anatomy Reconstruction on ADNI T1w MRI 3](): Healthy Anatomy Reconstruction; ADNI T1w MRI 3; L1 Loss: 0.02. - [Healthy Anatomy Reconstruction on ATLAS Stroke T1w MRI](): Healthy Anatomy Reconstruction; ATLAS Stroke T1w MRI; L1 Loss: 0.025. - [Healthy Anatomy Reconstruction on HCP T1w MRI (808/87)](): Healthy Anatomy Reconstruction; HCP T1w MRI (808/87); L1 Error: 0.023. - [Healthy Anatomy Reconstruction on ADHD200 T1w MRI](): Healthy Anatomy Reconstruction; ADHD200 T1w MRI; L1 Loss: 0.015. - [Healthy Anatomy Reconstruction on AIBL T1w MRI (601/67)](): Healthy Anatomy Reconstruction; AIBL T1w MRI (601/67); L1 Loss: 0.012. - [Healthy Anatomy Reconstruction on HCP T2w MRI](): Healthy Anatomy Reconstruction; HCP T2w MRI; L1 Error: 0.018. - [Healthy Anatomy Reconstruction on AIBL T2w MRI](): Healthy Anatomy Reconstruction; AIBL T2w MRI; L1 Loss: 2.4. - [Healthy Anatomy Reconstruction on ADNI FLAIR MRI 3 (298/33)](): Healthy Anatomy Reconstruction; ADNI FLAIR MRI 3 (298/33); L1 Loss: 0.023. - [Healthy Anatomy Reconstruction on AIBL FLAIR MRI](): Healthy Anatomy Reconstruction; AIBL FLAIR MRI; L1 Loss: 0.021. - [Healthy Anatomy Reconstruction on OASIS3 CT](): Healthy Anatomy Reconstruction; OASIS3 CT; L1 Error: 0.027. - [Healthy anatomy reconstruction on T1w MRI Simulated Pathology (test)](): Healthy Anatomy Reconstruction; T1w MRI Simulated Pathology (test); L1 Loss (F): 0.0257. - [Healthy anatomy reconstruction on T2w MRI Simulated Pathology (test)](): Healthy Anatomy Reconstruction; T2w MRI Simulated Pathology (test); L1 Error (F): 0.0295. - [Healthy anatomy reconstruction on FLAIR MRI Simulated Pathology (test)](): Healthy Anatomy Reconstruction; FLAIR MRI Simulated Pathology (test); L1 Loss (F): 0.0301. - [Healthy anatomy reconstruction on CT Simulated Pathology 1,000 samples (test)](): Healthy Anatomy Reconstruction; CT Simulated Pathology 1,000 samples (test); L1 Error (F): 0.0473. - [Healthy Anatomy Reconstruction on ADNI T1w MRI](): Healthy Anatomy Reconstruction; ADNI T1w MRI; L1 Loss: 0.014. ## Original sources and implementation [Original paper]() [PDF]() [Implementation]()