Biology subjects

Chiew, M.

Publications and source records attributed to Chiew, M..

22 records · Page 2Linked to original sources

bioRxiv2020

Methods for quantitative susceptibility and R2* mapping in whole post-mortem brains at 7T

Susceptibility weighted magnetic resonance imaging (MRI) is sensitive to the local concentration of iron and myelin. Here, we describe a robust image processing pipeline for quantitative susceptibility mapping (QSM) and R2* mapping of fixed post-mortem, whole-brain data. Using this pipeline, we compare the resulting quantitative maps in brains from patients with amyotrophic lateral sclerosis (ALS) and controls, with validation against iron and myelin histology. Twelve post-mortem brains were scanned with a multi-echo gradient echo sequence at 7T, from which susceptibility and R2* maps were generated. Semi-quantitative histological analysis for ferritin (the principal iron storage protein) and myelin proteolipid protein was performed in the primary motor, anterior cingulate and visual cortices. Magnetic susceptibility and R2* values in primary motor cortex were higher in ALS compared to control brains. Magnetic susceptibility and R2* showed positive correlations with both myelin and ferritin estimates from histology. Four out of nine ALS brains exhibited clearly visible hyperintense susceptibility and R2* values in the primary motor cortex. Our results demonstrate the potential for MRI-histology studies in whole, fixed post-mortem brains to investigate the biophysical source of susceptibility weighted MRI signals in neurodegenerative diseases like ALS.

neuroscience↗

bioRxiv2019

Highly Accelerated Vessel-Selective Arterial Spin Labelling Angiography using Sparsity and Smoothness Constraints

PurposeTo demonstrate that vessel-selectivity in arterial spin labeling angiography can be achieved without any scan time penalty or noticeable loss of image quality compared to conventional arterial spin labeling angiography.\n\nMethodsSimulations on a numerical phantom were used to assess whether the increased sparsity of vessel-encoded angiograms compared to non-vessel-encoded angiograms alone can improve reconstruction results in a compressed sensing framework. Further simulations were performed to study whether the difference in relative sparsity between non-selective and vessel-selective dynamic angiograms were sufficient to achieve similar image quality at matched scan times in the presence of noise. Finally, data were acquired from 5 healthy volunteers to validate the technique in vivo. All data, both simulated and in vivo, were sampled in 2D using a golden angle radial trajectory and reconstructed by enforcing both image domain sparsity and temporal smoothness on the angiograms in a parallel imaging and compressed sensing framework.\n\nResultsRelative sparsity was established as a primary factor governing the reconstruction fidelity. Using the proposed reconstruction scheme, differences between vessel-selective and non-selective angiography were negligible compared to the dominant factor of total scan time in both simulations and in vivo experiments at acceleration factors up to R = 34. The reconstruction quality was not heavily dependent on hand-tuning the parameters of the reconstruction.\n\nConclusionThe increase in relative sparsity of vessel-selective angiograms compared to non-selective angiograms can be leveraged to achieve higher acceleration without loss of image quality, resulting in the acquisition of vessel-selective information at no scan time cost.

neuroscience↗

bioRxiv2019

Improved Statistical Efficiency of Simultaneous Multi-Slice fMRI by Reconstruction with Spatially Adaptive Temporal Smoothing

We introduce an approach to reconstruction of simultaneous multi-slice (SMS)-fMRI data that improves statistical efficiency. The method incorporates regularization to adjust temporal smoothness in a spatially varying, encoding-dependent manner, reducing the g-factor noise amplification per temporal degree of freedom. This results in a net improvement in tSNR and GLM efficiency, where the efficiency gain can be derived analytically as a function of the encoding and reconstruction parameters. Residual slice leakage and aliasing is limited when fMRI signal energy is dominated by low frequencies. Analytical predictions, simulated and experimental results demonstrate a marked improvement in statistical efficiency in the temporally regularized reconstructions compared to conventional slice-GRAPPA reconstructions, particularly in central brain regions. Furthermore, experimental results confirm that residual slice leakage and aliasing errors are not noticeably increased compared to slice-GRAPPA reconstruction. This approach to temporally regularized image reconstruction in SMS-fMRI improves statistical power, and allows for explicit choice of reconstruction parameters by directly assessing their impact on noise variance per degree of freedom.

neuroscience↗

bioRxiv2019

Density-Weighted Concentric Ring Trajectory using simultaneous multi-band acceleration: 3D Metabolite-cycled Magnetic Resonance Spectroscopy Imaging at 3 T

Simultaneous multi-slice or multi-band parallel imaging is frequently used in fMRI to accelerate acquisition. In this study, we propose a new a non-water-suppressed multi-band MRSI using a density weighted concentric ring trajectory (DW-CRT) acquisition. The properties of multi-band acquisition scheme were compared against single-band acquisition in phantoms and in-vivo experiments. High-quality spectra were acquired for all simultaneously acquired three slices from a limited volume of interest with an in-plane resolution of 5 x 5 mm2 in 19.2 min. The achieved in vivo spectral quality of the multi-band method allowed the reliable metabolic mapping of four major metabolites with Cramer-Rao lower bounds below 50%, using a LCModel analysis. Metabolite maps and LCModel quality metrics were compared between multi-band and single-band acquisition schemes for both phantom and in-vivo measurements. Structural similarity (SSIM) index and conventional coefficient of variance analysis of both phantom and in-vivo measurements revealed a SSIM index higher than 0.83, corresponding to a coefficient of variance of less than 30%. These findings demonstrate that our multi-band DW-CRT MRSI demonstrate a multi-band acceleration, simultaneously acquired 3 slices, with no apparently loss in spectral quality, reducing scan time by a factor of 3 without any significant penalty.

neuroscience↗