Juan E. Iglesias

Peirong Liu, Oula Puonti, Xiaoling Hu et al.

Recent learning-based approaches have made astonishing advances in calibrated medical imaging like computerized tomography (CT), yet they struggle to generalize in uncalibrated modalities -- notably magnetic resonance (MR) imaging, where performance is highly sensitive to the differences in MR contrast, resolution, and orientation. This prevents broad applicability to diverse real-world clinical protocols. We introduce Brain-ID, an anatomical representation learning model for brain imaging. With the proposed "mild-to-severe" intra-subject generation, Brain-ID is robust to the subject-specific brain anatomy regardless of the appearance of acquired images (e.g., contrast, deformation, resolution, artifacts). Trained entirely on synthetic data, Brain-ID readily adapts to various downstream tasks through only one layer. We present new metrics to validate the intra- and inter-subject robustness of Brain-ID features, and evaluate their performance on four downstream applications, covering contrast-independent (anatomy reconstruction/contrast synthesis, brain segmentation), and contrast-dependent (super-resolution, bias field estimation) tasks. Extensive experiments on six public datasets demonstrate that Brain-ID achieves state-of-the-art performance in all tasks on different MRI modalities and CT, and more importantly, preserves its performance on low-resolution and small datasets. Code is available at https://github.com/peirong26/Brain-ID.

Peirong Liu, Oula Puonti, Annabel Sorby-Adams et al.

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.

Peirong Liu, Ana Lawry Aguila, Juan E. Iglesias

Data-driven machine learning has made significant strides in medical image analysis. However, most existing methods are tailored to specific modalities and assume a particular resolution (often isotropic). This limits their generalizability in clinical settings, where variations in scan appearance arise from differences in sequence parameters, resolution, and orientation. Furthermore, most general-purpose models are designed for healthy subjects and suffer from performance degradation when pathology is present. We introduce UNA (Unraveling Normal Anatomy), the first modality-agnostic learning approach for normal brain anatomy reconstruction that can handle both healthy scans and cases with pathology. We propose a fluid-driven anomaly randomization method that generates an unlimited number of realistic pathology profiles on-the-fly. UNA is trained on a combination of synthetic and real data, and can be applied directly to real images with potential pathology without the need for fine-tuning. We demonstrate UNA's effectiveness in reconstructing healthy brain anatomy and showcase its direct application to anomaly detection, using both simulated and real images from 3D healthy and stroke datasets, including CT and MRI scans. By bridging the gap between healthy and diseased images, UNA enables the use of general-purpose models on diseased images, opening up new opportunities for large-scale analysis of uncurated clinical images in the presence of pathology. Code is available at https://github.com/peirong26/UNA.

Peirong Liu, Oula Puonti, Xiaoling Hu et al.

Recent learning-based approaches have made astonishing advances in calibrated medical imaging like computerized tomography (CT), yet they struggle to generalize in uncalibrated modalities -- notably magnetic resonance (MR) imaging, where performance is highly sensitive to the differences in MR contrast, resolution, and orientation. This prevents broad applicability to diverse real-world clinical protocols. Here we introduce BrainFM, a modality-agnostic, multi-task vision foundation model for human brain imaging. With the proposed "mild-to-severe" intra-subject generation and "real-synth" mix-up training strategy, BrainFM is resilient to the appearance of acquired images (e.g., modality, contrast, deformation, resolution, artifacts), and can be directly applied to five fundamental brain imaging tasks, including image synthesis for CT and T1w/T2w/FLAIR MRI, anatomy segmentation, scalp-to-cortical distance, bias field estimation, and registration. We evaluate the efficacy of BrainFM on eleven public datasets, and demonstrate its robustness and effectiveness across all tasks and input modalities. Code is available at https://github.com/jhuldr/BrainFM.