James J. Lah

Shuai Huang, James J. Lah, Jason W. Allen et al.

Purpose: For quantitative susceptibility mapping (QSM), the lack of ground-truth in clinical settings makes it challenging to determine suitable parameters for the dipole inversion. We propose a probabilistic Bayesian approach for QSM with built-in parameter estimation, and incorporate the nonlinear formulation of the dipole inversion to achieve a robust recovery of the susceptibility maps. Theory: From a Bayesian perspective, the image wavelet coefficients are approximately sparse and modelled by the Laplace distribution. The measurement noise is modelled by a Gaussian-mixture distribution with two components, where the second component is used to model the noise outliers. Through probabilistic inference, the susceptibility map and distribution parameters can be jointly recovered using approximate message passing (AMP). Methods: We compare our proposed AMP with built-in parameter estimation (AMP-PE) to the state-of-the-art L1-QSM, FANSI and MEDI approaches on the simulated and in vivo datasets, and perform experiments to explore the optimal settings of AMP-PE. Reproducible code is available at https://github.com/EmoryCN2L/QSM_AMP_PE Results: On the simulated Sim2Snr1 dataset, AMP-PE achieved the lowest NRMSE, DFCM and the highest SSIM, while MEDI achieved the lowest HFEN. On the in vivo datasets, AMP-PE is robust and successfully recovers the susceptibility maps using the estimated parameters, whereas L1-QSM, FANSI and MEDI typically require additional visual fine-tuning to select or double-check working parameters. Conclusion: AMP-PE provides automatic and adaptive parameter estimation for QSM and avoids the subjectivity from the visual fine-tuning step, making it an excellent choice for the clinical setting.

Shuai Huang, Xuan Kan, James J. Lah et al.

Current atlas-based approaches to brain network analysis rely heavily on standardized anatomical or connectivity-driven brain atlases. However, these fixed atlases often introduce significant limitations, such as spatial misalignment across individuals, functional heterogeneity within predefined regions, and atlas-selection biases, collectively undermining the reliability and interpretability of the derived brain networks. To address these challenges, we propose a novel atlas-free brain network transformer (atlas-free BNT) that leverages individualized brain parcellations derived directly from subject-specific resting-state fMRI data. Our approach computes ROI-to-voxel connectivity features in a standardized voxel-based feature space, which are subsequently processed using the BNT architecture to produce comparable subject-level embeddings. Experimental evaluations on sex classification and brain-connectome age prediction tasks demonstrate that our atlas-free BNT consistently outperforms state-of-the-art atlas-based methods, including elastic net, BrainGNN, Graphormer and the original BNT. Our atlas-free approach significantly improves the precision, robustness, and generalizability of brain network analyses. This advancement holds great potential to enhance neuroimaging biomarkers and clinical diagnostic tools for personalized precision medicine.

Shuai Huang, James J. Lah, Jason W. Allen et al.

Magnetic resonance (MR)-$T_2^*$ mapping is widely used to study hemorrhage, calcification and iron deposition in various clinical applications, it provides a direct and precise mapping of desired contrast in the tissue. However, the long acquisition time required by conventional 3D high-resolution $T_2^*$ mapping method causes discomfort to patients and introduces motion artifacts to reconstructed images, which limits its wider applicability. In this paper we address this issue by performing $T_2^*$ mapping from undersampled data using compressive sensing (CS). We formulate the reconstruction as a nonconvex problem that can be decomposed into two subproblems. They can be solved either separately via the standard approach or jointly via the alternating direction method of multipliers (ADMM). Compared to previous CS-based approaches that only apply sparse regularization on the spin density $\boldsymbol X_0$ and the relaxation rate $\boldsymbol R_2^*$, our formulation enforces additional sparse priors on the $T_2^*$-weighted images at multiple echoes to improve the reconstruction performance. We performed convergence analysis of the proposed algorithm, evaluated its performance on in vivo data, and studied the effects of different sampling schemes. Experimental results showed that the proposed joint-recovery approach generally outperforms the state-of-the-art method, especially in the low-sampling rate regime, making it a preferred choice to perform fast 3D $T_2^*$ mapping in practice. The framework adopted in this work can be easily extended to other problems arising from MR or other imaging modalities with non-linearly coupled variables.