arXiv subjects

Hyeong-Geol Shin

Publications and source records attributed to Hyeong-Geol Shin.

8 recordsLinked to original sources

arXiv2026

MWF-MIMOSA for efficient simultaneous relaxometry and myelin water fraction mapping

Quantitative magnetic resonance imaging (qMRI) provides improved sensitivity and specificity to tissue composition and pathological alterations compared with conventional contrast-weighted imaging. Among various qMRI biomarkers, myelin water imaging is of particular interest because myelin plays a central role in brain function and its alteration is closely associated with many neurological diseases. However, conventional myelin water fraction (MWF) mapping techniques are often limited by long scan times, low spatial resolution, reduced signal-to-noise ratio (SNR), and high specific absorption rate (SAR). Here, we propose MWF-MIMOSA for efficient simultaneous T1, T2, T2* mapping, magnetic susceptibility source separation, and MWF estimation. To achieve this, multi-contrast and multi-slice zero-shot self-supervised learning (MZS-SSL) was used to jointly reconstruct whole-brain complex-valued images. To improve computational efficiency of the parameter estimation step, a multilayer perceptron (MLP) was trained within the GACELLE GPU-accelerated parameter estimation framework to circumvent the computationally intensive Bloch simulation process, resulting in a >100-fold computational speed-up in MWF estimation. Numerical simulations were performed to evaluate the accuracy and precision of MWF-MIMOSA, and in-vivo results further demonstrated its robustness. Comparison with existing myelin water imaging methods showed that MWF-MIMOSA is highly correlated with established approaches, while providing complementary quantitative parameter maps at higher spatial resolution and with shorter scan times. Notably, simultaneous multi-parametric mapping was achieved in 5 min at 1 mm isotropic resolution, and in 10 min at 0.7 mm isotropic resolution. These results demonstrate the potential of MWF-MIMOSA for fast, high-resolution simultaneous relaxometry and myelin water imaging.

physics.med-ph↗

arXiv2025

Self-supervised training of deep denoisers in multi-coil MRI considering noise correlations

Deep learning-based denoising methods have shown powerful results for improving the signal-to-noise ratio of magnetic resonance (MR) images, mostly by leveraging supervised learning with clean ground truth. However, acquiring clean ground truth images is often expensive and time-consuming. Self supervised methods have been widely investigated to mitigate the dependency on clean images, but mostly rely on the suboptimal splitting of K-space measurements of an image to yield input and target images for ensuring statistical independence. In this study, we investigate an alternative self-supervised training method for deep denoisers in multi-coil MRI, dubbed Coil2Coil (C2C), that naturally split and combine the multi-coil data among phased array coils, generating two noise-corrupted images for training. This novel approach allows exploiting multi-coil redundancy, but the images are statistically correlated and may not have the same clean image. To mitigate these issues, we propose the methods to pproximately decorrelate the statistical dependence of these images and match the underlying clean images, thus enabling them to be used as the training pairs. For synthetic denoising experiments, C2C yielded the best performance against prior self-supervised methods, reporting outcome comparable even to supervised methods. For real-world denoising cases, C2C yielded consistent performance as synthetic cases, removing only noise structures.

eess.IV↗

arXiv2024

χ-sepnet: Deep neural network for magnetic susceptibility source separation

Magnetic susceptibility source separation ($χ$-separation), an advanced quantitative susceptibility mapping (QSM) method, enables the separate estimation of para- and diamagnetic susceptibility source distributions in the brain. The method utilizes reversible transverse relaxation (R2'=R2*-R2) to complement frequency shift information for estimating susceptibility source concentrations, requiring time-consuming data acquisition for R2 in addition R2*. To address this challenge, we develop a new deep learning network, $χ$-sepnet, and propose two deep learning-based susceptibility source separation pipelines, $χ$-sepnet-R2' for inputs with multi-echo GRE and multi-echo spin-echo, and $χ$-sepnet-R2* for input with multi-echo GRE only. $χ$-sepnet is trained using multiple head orientation data that provide streaking artifact-free labels, generating high-quality $χ$-separation maps. The evaluation of the pipelines encompasses both qualitative and quantitative assessments in healthy subjects, and visual inspection of lesion characteristics in multiple sclerosis patients. The susceptibility source-separated maps of the proposed pipelines delineate detailed brain structures with substantially reduced artifacts compared to those from conventional regularization-based reconstruction methods. In quantitative analysis, $χ$-sepnet-R2' achieves the best outcomes followed by $χ$-sepnet-R2*, outperforming the conventional methods. When the lesions of multiple sclerosis patients are assessed, both pipelines report identical lesion characteristics in most lesions ($χ$para: 99.6% and $χ$dia: 98.4% out of 250 lesions). The $χ$-sepnet-R2* pipeline, which only requires multi-echo GRE data, has demonstrated its potential to offer broad clinical and scientific applications, although further evaluations for various diseases and pathological conditions are necessary.

eess.IV↗

arXiv2024

In-vivo high-resolution χ-separation at 7T

A recently introduced quantitative susceptibility mapping (QSM) technique, $χ$-separation, offers the capability to separate paramagnetic ($χ_{\text{para}}$) and diamagnetic ($χ_{\text{dia}}$) susceptibility distribution within the brain. In-vivo high-resolution mapping of iron and myelin distribution, estimated by $χ$-separation, could provide a deeper understanding of brain substructures, assisting the investigation of their functions and alterations. This can be achieved using 7T MRI, which benefits from a high signal-to-noise ratio and susceptibility effects. However, applying $χ$-separation at 7T presents difficulties due to the requirement of an $R_2$ map, coupled with issues such as high specific absorption rate (SAR), large $B_1$ transmit field inhomogeneities, and prolonged scan time. To address these challenges, we developed a novel deep neural network, R2PRIMEnet7T, designed to convert a 7T $R_2^*$ map into a 3T $R_2'$ map. Building on this development, we present a new pipeline for $χ$-separation at 7T, enabling us to generate high-resolution $χ$-separation maps from multi-echo gradient-echo data. The proposed method is compared with alternative pipelines, such as an end-to-end network and linearly-scaled $R_2'$, and is validated against $χ$-separation maps at 3T, demonstrating its accuracy. The 7T $χ$-separation maps generated by the proposed method exhibit similar contrasts to those from 3T, while 7T high-resolution maps offer enhanced clarity and detail. Quantitative analysis confirms that the proposed method surpasses the alternative pipelines. The proposed method results well delineate the detailed brain structures associated with iron and myelin. This new pipeline holds promise for analyzing iron and myelin concentration changes in various neurodegenerative diseases through precise structural examination.

q-bio.QM↗

arXiv2024

A human brain atlas of chi-separation for normative iron and myelin distributions

Iron and myelin are primary susceptibility sources in the human brain. These substances are essential for healthy brain, and their abnormalities are often related to various neurological disorders. Recently, an advanced susceptibility mapping technique, which is referred to as chi-separation, has been proposed, successfully disentangling paramagnetic iron from diamagnetic myelin. This method opened a potential for generating high resolution iron and myelin maps in the brain. Utilizing this technique, this study constructs a normative chi-separation atlas from 106 healthy human brains. The resulting atlas provides detailed anatomical structures associated with the distributions of iron and myelin, clearly delineating subcortical nuclei, thalamic nuclei, and white matter fiber bundles. Additionally, susceptibility values in a number of regions of interest are reported along with age-dependent changes. This atlas may have direct applications such as localization of subcortical structures for deep brain stimulation or high-intensity focused ultrasound and also serve as a valuable resource for future research.

eess.IV↗

arXiv2021

BUDA-SAGE with self-supervised denoising enables fast, distortion-free, high-resolution T2, T2*, para- and dia-magnetic susceptibility mapping

To rapidly obtain high resolution T2, T2* and quantitative susceptibility mapping (QSM) source separation maps with whole-brain coverage and high geometric fidelity. We propose Blip Up-Down Acquisition for Spin And Gradient Echo imaging (BUDA-SAGE), an efficient echo-planar imaging (EPI) sequence for quantitative mapping. The acquisition includes multiple T2*-, T2'- and T2-weighted contrasts. We alternate the phase-encoding polarities across the interleaved shots in this multi-shot navigator-free acquisition. A field map estimated from interim reconstructions was incorporated into the joint multi-shot EPI reconstruction with a structured low rank constraint to eliminate geometric distortion. A self-supervised MR-Self2Self (MR-S2S) neural network (NN) was utilized to perform denoising after BUDA reconstruction to boost SNR. Employing Slider encoding allowed us to reach 1 mm isotropic resolution by performing super-resolution reconstruction on BUDA-SAGE volumes acquired with 2 mm slice thickness. Quantitative T2 and T2* maps were obtained using Bloch dictionary matching on the reconstructed echoes. QSM was estimated using nonlinear dipole inversion (NDI) on the gradient echoes. Starting from the estimated R2 and R2* maps, R2' information was derived and used in source separation QSM reconstruction, which provided additional para- and dia-magnetic susceptibility maps. In vivo results demonstrate the ability of BUDA-SAGE to provide whole-brain, distortion-free, high-resolution multi-contrast images and quantitative T2 and T2* maps, as well as yielding para- and dia-magnetic susceptibility maps. Derived quantitative maps showed comparable values to conventional mapping methods in phantom and in vivo measurements. BUDA-SAGE acquisition with self-supervised denoising and Slider encoding enabled rapid, distortion-free, whole-brain T2, T2* mapping at 1 mm3 isotropic resolution in 90 seconds.

physics.med-ph↗

arXiv2020

DeepResp: Deep learning solution for respiration-induced B0 fluctuation artifacts in multi-slice GRE

Respiration-induced B$_0$ fluctuation corrupts MRI images by inducing phase errors in k-space. A few approaches such as navigator have been proposed to correct for the artifacts at the expense of sequence modification. In this study, a new deep learning method, which is referred to as DeepResp, is proposed for reducing the respiration-artifacts in multi-slice gradient echo (GRE) images. DeepResp is designed to extract the respiration-induced phase errors from a complex image using deep neural networks. Then, the network-generated phase errors are applied to the k-space data, creating an artifact-corrected image. For network training, the computer-simulated images were generated using artifact-free images and respiration data. When evaluated, both simulated images and in-vivo images of two different breathing conditions (deep breathing and natural breathing) show improvements (simulation: normalized root-mean-square error (NRMSE) from 7.8% to 1.3%; structural similarity (SSIM) from 0.88 to 0.99; ghost-to-signal-ratio (GSR) from 7.9% to 0.6%; deep breathing: NRMSE from 13.9% to 5.8%; SSIM from 0.86 to 0.95; GSR 20.2% to 5.7%; natural breathing: NRMSE from 5.2% to 4.0%; SSIM from 0.94 to 0.97; GSR 5.7% to 2.8%). Our approach does not require any modification of the sequence or additional hardware, and may therefore find useful applications. Furthermore, the deep neural networks extract respiration-induced phase errors, which is more interpretable and reliable than results of end-to-end trained networks.

eess.IV↗

arXiv2019

Artificial neural network for myelin water imaging

Purpose: To demonstrate the application of artificial-neural-network (ANN) for real-time processing of myelin water imaging (MWI). Methods: Three neural networks, ANN-IMWF, ANN-IGMT2, and ANN-II, were developed to generate MWI. ANN-IMWF and ANN-IGMT2 were designed to output myelin water fraction (MWF) and geometric mean T2 (GMT2,IEW), respectively whereas ANN-II generates a T2 distribution. For the networks, gradient and spin echo data from 18 healthy controls (HC) and 26 multiple sclerosis patients (MS) were utilized. Among them, 10 HC and 12 MS had the same scan parameters and were used for training (6 HC and 6 MS), validation (1 HC and 1 MS), and test sets (3 HC and 5 HC). The remaining data had different scan parameters and were applied to exam the effects of the scan parameters. The network results were compared with those of conventional MWI in the white matter mask and regions of interest (ROI). Results: The networks produced highly accurate results, showing averaged normalized root-mean-squared error under 3% for MWF and 0.4% for GMT2,IEW in the white matter mask of the test set. In the ROI analysis, the differences between ANNs and conventional MWI were less than 0.1% in MWF and 0.1 ms in GMT2,IEW (no statistical difference and R2 > 0.97). Datasets with different scan parameters showed increased errors. The average processing time was 0.68 sec in ANNs, gaining 11,702 times acceleration in the computational speed (conventional MWI: 7,958 sec). Conclusion: The proposed neural networks demonstrate the feasibility of real-time processing for MWI with high accuracy.

eess.IV↗