arXiv subjects

Amirmohammad Shamaei

Publications and source records attributed to Amirmohammad Shamaei.

5 recordsLinked to original sources

arXiv2026

HyperFitS -- Hypernetwork Fitting Spectra for metabolic quantification of ${}^1$H MR spectroscopic imaging

Purpose: Proton magnetic resonance spectroscopic imaging ($^1$H MRSI) enables the mapping of whole-brain metabolites concentrations in-vivo. However, a long-standing problem for its clinical applicability is the metabolic quantification, which can require extensive time for spectral fitting. Recently, deep learning methods have been able to provide whole-brain metabolic quantification in only a few seconds. However, neural network implementations often lack configurability and require retraining to change predefined parameter settings. Methods: We introduce HyperFitS, a hypernetwork for spectral fitting for metabolite quantification in whole-brain $^1$H MRSI that flexibly adapts to a broad range of baseline corrections and water suppression factors. Metabolite maps of human subjects acquired at 3T and 7T with isotropic resolutions of 10 mm, 3.4 mm and 2 mm by water-suppressed and water-unsuppressed MRSI were quantified with HyperFitS and compared to conventional LCModel fitting. Results: Metabolic maps show a substantial agreement between the new and gold-standard methods, with significantly faster fitting times by HyperFitS. Quantitative results further highlight the impact of baseline parametrization on metabolic quantification, which can alter results by up to 30%. Conclusion: HyperFitS shows strong agreement with state-of-the-art conventional methods, while reducing processing times from hours to a few seconds. Compared to prior deep learning based spectral fitting methods, HyperFitS enables a wide range of configurability and can adapt to data quality acquired with multiple protocols and field strengths without retraining.

cs.LG↗

arXiv2026

Synthetic Data in MR Spectroscopy: Current Practices, Applications, and Considerations

The use of synthetic data has emerged as an essential tool in Magnetic Resonance Spectroscopy (MRS) research and applications, providing advantages for optimization of acquisition, software validation, deep learning applications, and enhanced reproducibility. Importantly, synthetic data addresses challenges of limited training data availability, particularly for clinical populations, and offers controlled solutions for investigating uncertainties and unexplained variance with in vivo data. This work provides a review and evaluation of current practices in the use and generation of synthetic data within the MRS field. Conducted by the MRS Synthetic Data Working Group under the Code & Data Sharing Committee of the MRS Study Group of the International Society for Magnetic Resonance in Medicine (ISMRM), this manuscript encompasses existing literature, supplemented by collective experience and in-house methodologies.

physics.med-ph↗

arXiv2025

Deep learning water-unsuppressed MRSI at ultra-high field for simultaneous quantitative metabolic, susceptibility and myelin water imaging

Purpose: Magnetic Resonance Spectroscopic Imaging (MRSI) maps endogenous brain metabolism while suppressing the overwhelming water signal. Water-unsuppressed MRSI (wu-MRSI) allows simultaneous imaging of water and metabolites, but large water sidebands cause challenges for metabolic fitting. We developed an end-to-end deep-learning pipeline to overcome these challenges at ultra-high field. Methods:Fast high-resolution wu-MRSI was acquired at 7T with non-cartesian ECCENTRIC sampling and ultra-short echo time. A water and lipid removal network (WALINET+) was developed to remove lipids, water signal, and sidebands. MRSI reconstruction was performed by DeepER and a physics-informed network for metabolite fitting. Water signal was used for absolute metabolite quantification, quantitative susceptibility mapping (QSM), and myelin water fraction imaging (MWF). Results: WALINET+ provided the lowest NRMSE (< 2%) in simulations and in vivo the smallest bias (< 20%) and limits-of-agreement (+-63%) between wu-MRSI and ws-MRSI scans. Several metabolites such as creatine and glutamate showed higher SNR in wu-MRSI. QSM and MWF obtained from wu-MRSI and GRE showed good agreement with 0 ppm/5.5% bias and +-0.05 ppm/ +- 12.75% limits-of-agreement. Conclusion: High-quality metabolic, QSM, and MWF mapping of the human brain can be obtained simultaneously by ECCENTRIC wu-MRSI at 7T with 2 mm isotropic resolution in 12 min. WALINET+ robustly removes water sidebands while preserving metabolite signal, eliminating the need for water suppression and separate water acquisitions.

eess.IV↗

arXiv2025

Enhancing and Accelerating Brain MRI through Deep Learning Reconstruction Using Prior Subject-Specific Imaging

Magnetic resonance imaging (MRI) is a crucial medical imaging modality. However, long acquisition times remain a significant challenge, leading to increased costs, and reduced patient comfort. Recent studies have shown the potential of using deep learning models that incorporate information from prior subject-specific MRI scans to improve reconstruction quality of present scans. Integrating this prior information requires registration of the previous scan to the current image reconstruction, which can be time-consuming. We propose a novel deep-learning-based MRI reconstruction framework which consists of an initial reconstruction network, a deep registration model, and a transformer-based enhancement network. We validated our method on a longitudinal dataset of T1-weighted MRI scans with 2,808 images from 18 subjects at four acceleration factors (R5, R10, R15, R20). Quantitative metrics confirmed our approach's superiority over existing methods (p < 0.05, Wilcoxon signed-rank test). Furthermore, we analyzed the impact of our MRI reconstruction method on the downstream task of brain segmentation and observed improved accuracy and volumetric agreement with reference segmentations. Our approach also achieved a substantial reduction in total reconstruction time compared to methods that use traditional registration algorithms, making it more suitable for real-time clinical applications. The code associated with this work is publicly available at https://github.com/amirshamaei/longitudinal-mri-deep-recon.

cs.CV↗

arXiv2023

Spectro-ViT: A Vision Transformer Model for GABA-edited MRS Reconstruction Using Spectrograms

Purpose: To investigate the use of a Vision Transformer (ViT) to reconstruct/denoise GABA-edited magnetic resonance spectroscopy (MRS) from a quarter of the typically acquired number of transients using spectrograms. Theory and Methods: A quarter of the typically acquired number of transients collected in GABA-edited MRS scans are pre-processed and converted to a spectrogram image representation using the Short-Time Fourier Transform (STFT). The image representation of the data allows the adaptation of a pre-trained ViT for reconstructing GABA-edited MRS spectra (Spectro-ViT). The Spectro-ViT is fine-tuned and then tested using \textit{in vivo} GABA-edited MRS data. The Spectro-ViT performance is compared against other models in the literature using spectral quality metrics and estimated metabolite concentration values. Results: The Spectro-ViT model significantly outperformed all other models in four out of five quantitative metrics (mean squared error, shape score, GABA+/water fit error, and full width at half maximum). The metabolite concentrations estimated (GABA+/water, GABA+/Cr, and Glx/water) were consistent with the metabolite concentrations estimated using typical GABA-edited MRS scans reconstructed with the full amount of typically collected transients. Conclusion: The proposed Spectro-ViT model achieved state-of-the-art results in reconstructing GABA-edited MRS, and the results indicate these scans could be up to four times faster.

eess.IV↗