PCA denoising and Wiener deconvolution of 31P 3D CSI data to enhance effective SNR and improve point spread function

Purpose: This study evaluates the performance of 2 processing methods, that is, principal component analysis-based denoising and Wiener deconvolution, to enhance the quality of phosphorus 3D chemical shift imaging data. Methods: Principal component analysis-based denoising increases the SNR while maintaining spectral information. Wiener deconvolution reduces the FWHM of the voxel point spread function, which is increased by Hamming filtering or Hamming-weighted acquisition. The proposed methods are evaluated using simulated and in vivo 3D phosphorus chemical shift imaging data by 1) visual inspection of the spatial signal distribution; 2) SNR calculation of the PCr peak; and 3) fitting of metabolite basis functions. Results: With the optimal order of processing steps, we show that the effective SNR of in vivo phosphorus 3D chemical shift imaging data can be increased. In simulations, we show we can preserve phosphorus-containing metabolite peaks that had an SNR < 1 before denoising. Furthermore, using Wiener deconvolution, we were able to reduce the FWHM of the voxel point spread function with only partially reintroducing Gibb-ringing artifacts while maintaining the SNR. After data processing, fitting of the phosphorus-containing metabolite signals improved. Conclusion: In this study, we have shown that principal component analysis-based denoising in combination with regularized Wiener deconvolution allows increasing the effective spectral SNR of in vivo phosphorus 3D chemical shift imaging data, with reduction of the FWHM of the voxel point spread function. Processing increased the effective SNR by at least threefold compared to Hamming weighted acquired data and minimized voxel bleeding. With these methods, fitting of metabolite amplitudes became more robust with decreased fitting residuals

Identifying the source of spurious signals caused by B 0 inhomogeneities in single-voxel 1H MRS

PURPOSE: Single-voxel MRS (SV MRS) requires robust volume localization as well as optimized crusher and phase-cycling schemes to reduce artifacts arising from signal outside the volume of interest. However, due to local magnetic field gradients (B 0 inhomogeneities), signal that was dephased by the crusher gradients during acquisition might rephase, leading to artifacts in the spectrum. Here, we analyzed this mechanism, aiming to identify the source of signals arising from unwanted coherence pathways (spurious signals) in SV MRS from a B 0 map. METHODS: We investigated all possible coherence pathways associated with imperfect localization in a semi-localized by adiabatic selective refocusing (semi-LASER) sequence for potential rephasing of signals arising from unwanted coherence pathways by a local magnetic field gradient. We searched for locations in the B 0 map where the signal dephasing due to external (crusher) and internal (B 0 ) field gradients canceled out. To confirm the mechanism, SV-MR spectra (TE = 31 ms) and 3D-CSI data with the same volume localization as the SV experiments were acquired from a phantom and 2 healthy volunteers. RESULTS: Our analysis revealed that potential sources of spurious signals were scattered over multiple locations throughout the brain. This was confirmed by 3D-CSI data. Moreover, we showed that the number of potential locations where spurious signals could originate from monotonically decreases with crusher strength. CONCLUSION: We proposed a method to identify the source of spurious signals in SV 1 H MRS using a B 0 map. This can facilitate MRS sequence design to be less sensitive to experimental artifacts

Metabolic profiling of colorectal cancer organoids: A comparison between high-resolution magic angle spinning magnetic resonance spectroscopy and solution nuclear magnetic resonance spectroscopy of polar extracts

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Towards 1H-MRSI of the human brain at 7T with slice-selective adiabatic refocusing pulses

Contains fulltext : 70576.pdf (publisher's version ) (Closed access)OBJECTIVE: To explore the possibilities of proton spectroscopic imaging (1H-MRSI) of the human brain at 7 Tesla with adiabatic refocusing pulses. MATERIALS AND METHODS: A combination of conventional slice selective excitation and two pairs of slice selective adiabatic refocusing pulses (semi-LASER) results in the formation of an echo from a localized volume. Depending on the used radio frequency (rf) coil efficiency and available rf power, the duration of the adiabatic full passage pulses (AFPs) is adapted to enable echo times down to 50 ms (head coil) or 30 ms (local surface coil). RESULTS: An AFP duration of 5 ms with a corresponding bandwidth of 5.1 kHz resulted in a chemical shift displacement error of 23% over 3.8 ppm at 7T. Using a local surface coil and an echo time down to 30 ms, we detected not only the three main metabolites (NAA, Cr and Cho), but also coupled signals from myo-inositol and glutamate/glutamine in spectra from 0.14 cc voxels with linewidths down to 10 Hz in 10 min measurement time. CONCLUSIONS: The semi-LASER pulse sequence enables 1H-MRSI of the human brain at 7T for larger parts of the brain as well as small localized areas with both a high spectral and spatial resolution

Deuterium body array for the simultaneous measurement of hepatic and renal glucose metabolism and gastric emptying with dynamic 3D deuterium metabolic imaging at 7T

Deuterium metabolic imaging (DMI) is a novel noninvasive method to assess tissue metabolism and organ (patho)physiology in vivo using deuterated substrates, such as [6,6'- 2 H 2 ]-glucose. The liver and kidneys play a central role in whole-body glucose homeostasis, and in type 2 diabetes, both hepatic and renal glucose metabolism are dysregulated. Diabetes is also associated with gastric emptying abnormalities. In this study, we developed a four-channel 2 H transmit/receive body array coil for DMI in the human abdomen at 7 T and assessed its performance. In addition, the feasibility of simultaneously measuring gastric emptying, and hepatic and renal glucose uptake and metabolism with dynamic 3D DMI upon administration of deuterated glucose, was investigated. Simulated and measured B 1 + patterns were in good agreement. The intrasession variability of the natural abundance deuterated water signal in the liver and right kidney, measured in nine healthy volunteers, was 5.6% ± 0.9% and 4.9% ± 0.7%, respectively. Dynamic 3D DMI scans with oral administration of [6,6'- 2 H 2 ]-glucose showed similar kinetics of deuterated glucose appearance and disappearance in the liver and kidney. The measured gastric emptying half time was 80 ± 10 min, which is in good agreement with scintigraphy measurements. In conclusion, DMI with oral administration of [6,6'- 2 H 2 ]-glucose enables simultaneous assessment of gastric emptying and liver and kidney glucose uptake and metabolism. When applied in patients with diabetes, this approach may advance our understanding of the interplay between disturbances in liver and kidney glucose uptake and metabolism and gastric emptying, at a detail that cannot be achieved by any other method

Simulation-based evaluation of SAR and flip angle homogeneity for five transmit head arrays at 14 T

INTRODUCTION: Various research sites are pursuing 14 T MRI systems. However, both local SAR and RF transmit field inhomogeneity will increase. The aim of this simulation study is to investigate the trade-offs between peak local SAR and flip angle uniformity for five transmit coil array designs at 14 T in comparison to 7 T. METHODS: Investigated coil array designs are: 8 dipole antennas (8D), 16 dipole antennas (16D), 8 loop coils (8D), 16 loop coils (16L), 8 dipoles/8 loop coils (8D8L) and for reference 8 dipoles at 7 T. Both RF shimming and k T-points were investigated by plotting L-curves of peak SAR levels vs flip angle homogeneity. RESULTS: For RF shimming, the 16L array performs best. For k T-points, superior flip angle homogeneity is achieved at the expense of more power deposition, and the dipole arrays outperform the loop coil arrays. DISCUSSION AND CONCLUSION: For most arrays and regular imaging, the constraint on head SAR is reached before constraints on peak local SAR are violated. Furthermore, the different drive vectors in k T-points alleviate strong peaks in local SAR. Flip angle inhomogeneity can be alleviated by k T-points at the expense of larger power deposition. For k T-points, the dipole arrays seem to outperform loop coil arrays

Proton metabolic mapping of the brain at 7 T using a two-dimensional free induction decay-echo-planar spectroscopic imaging readout with lipid suppression

The increased signal-to-noise ratio (SNR) and chemical shift dispersion at high magnetic fields (≥7 T) have enabled neuro-metabolic imaging at high spatial resolutions. To avoid very long acquisition times with conventional magnetic resonance spectroscopic imaging (MRSI) phase-encoding schemes, solutions such as pulse-acquire or free induction decay (FID) sequences with short repetition time and inner volume selection methods with acceleration (echo-planar spectroscopic imaging [EPSI]), have been proposed. With the inner volume selection methods, limited spatial coverage of the brain and long echo times may still impede clinical implementation. FID-MRSI sequences benefit from a short echo time and have a high SNR per time unit; however, contamination from strong extra-cranial lipid signals remains a problem that can hinder correct metabolite quantification. L2-regularization can be applied to remove lipid signals in cases with high spatial resolution and accurate prior knowledge. In this work, we developed an accelerated two-dimensional (2D) FID-MRSI sequence using an echo-planar readout and investigated the performance of lipid suppression by L2-regularization, an external crusher coil, and the combination of these two methods to compare the resulting spectral quality in three subjects. The reduction factor of lipid suppression using the crusher coil alone varies from 2 to 7 in the lipid region of the brain boundary. For the combination of the two methods, the average lipid area inside the brain was reduced by 2% to 38% compared with that of unsuppressed lipids, depending on the subject's region of interest. 2D FID-EPSI with external lipid crushing and L2-regularization provides high in-plane coverage and is suitable for investigating brain metabolite distributions at high fields

Fast and silent MRI using nonlinear gradient fields at the ultrasonic gradient switching frequency of 20 kHz with a Point Spread Function framework reconstruction

PURPOSE: To demonstrate the feasibility of using a nonlinear gradient field for spatial encoding at the ultrasonic switching frequency of 20 kHz and present a framework to reconstruct data acquired in this way. METHODS: Nonlinear encoding at 20 kHz was realized by using a single-axis silent gradient insert for imaging in the periphery, that, is the nonlinear region, of the gradient field. The gradient insert induces a rapidly oscillating gradient field in the phase-encode direction, which enables nonlinear encoding when combined with a Cartesian readout from the linear whole-body gradients. Data from a 2D gradient echo sequence were reconstructed using a point spread function (PSF) framework. Accelerated scans were also simulated via retrospective undersampling (R = 1 to R = 8) to determine the effectiveness of the PSF-framework for accelerated imaging. RESULTS: Using a nonlinear gradient field switched at 20 kHz and the PSF-framework resulted in images of comparable quality to images from conventional Cartesian linear encoding. At increased acceleration factors (R ≤ 8), the PSF-framework outperformed linear SENSE reconstructions by improved controlling of aliasing artifacts. CONCLUSION: Using the PSF-framework, images of comparable quality to conventional SENSE reconstructions are possible via combining traditional linear and ultrasonic oscillating nonlinear encoding fields. Using nonlinear gradient fields relaxes the demand for strictly linear gradient fields, enabling much higher slew rates with a reduced risk of peripheral nerve stimulation or cardiac stimulation, which could aid in extension to ultrasonic whole-body MRI. The lack of aliasing artifacts also highlights the potential of accelerated imaging using the PSF-framework

Deuterium echo-planar spectroscopic imaging (EPSI) in the human liver in vivo at 7 T

PURPOSE: To demonstrate the feasibility of deuterium echo-planar spectroscopic imaging (EPSI) to accelerate 3D deuterium metabolic imaging in the human liver at 7 T. METHODS: A deuterium EPSI sequence, featuring a Hamming-weighted k-space acquisition pattern for the phase-encoding directions, was implemented. Three-dimensional deuterium EPSI and conventional MRSI were performed on a water/acetone phantom and in vivo in the human liver at natural abundance. Moreover, in vivo deuterium EPSI measurements were acquired after oral administration of deuterated glucose. The effect of acquisition time on SNR was evaluated by retrospectively reducing the number of averages. RESULTS: The SNR of natural abundance deuterated water signal in deuterium EPSI was 6.5% and 5.9% lower than that of MRSI in the phantom and in vivo experiments, respectively. In return, the acquisition time of in vivo EPSI data could be reduced retrospectively to 2 min, beyond the minimal acquisition time of conventional MRSI (of 20 min in this case), while still leaving sufficient SNR. Three-dimensional deuterium EPSI, after administration of deuterated glucose, enabled monitoring of hepatic glucose dynamics with full liver coverage, a spatial resolution of 20 mm isotropic, and a temporal resolution of 9 min 50 s, which could retrospectively be shortened to 2 min. CONCLUSION: In this work, we demonstrate the feasibility of accelerated 3D deuterium metabolic imaging of the human liver using deuterium EPSI. The acceleration obtained with EPSI can be used to increase temporal and/or spatial resolution, which will be valuable to study tissue metabolism of deuterated compounds over time

Pushing functional MRI spatial and temporal resolution further: High-density receive arrays combined with shot-selective 2D CAIPIRINHA for 3D echo-planar imaging at 7 T

To be able to examine dynamic and detailed brain functions, the spatial and temporal resolution of 7 T MRI needs to improve. In this study, it was investigated whether submillimeter multishot 3D EPI fMRI scans, acquired with high-density receive arrays, can benefit from a 2D CAIPIRINHA sampling pattern, in terms of noise amplification (g-factor), temporal SNR and fMRI sensitivity. High-density receive arrays were combined with a shot-selective 2D CAIPIRINHA implementation for multishot 3D EPI sequences at 7 T. In this implementation, in contrast to conventional inclusion of extra kz gradient blips, specific EPI shots are left out to create a CAIPIRINHA shift and reduction of scan time. First, the implementation of the CAIPIRINHA sequence was evaluated with a standard receive setup by acquiring submillimeter whole brain T2 *-weighted anatomy images. Second, the CAIPIRINHA sequence was combined with high-density receive arrays to push the temporal resolution of submillimeter 3D EPI fMRI scans of the visual cortex. Results show that the shot-selective 2D CAIPIRINHA sequence enables a reduction in scan time for 0.5 mm isotropic 3D EPI T2 *-weighted anatomy scans by a factor of 4 compared with earlier reports. The use of the 2D CAIPIRINHA implementation in combination with high-density receive arrays, enhances the image quality of submillimeter 3D EPI scans of the visual cortex at high acceleration as compared to conventional SENSE. Both the g-factor and temporal SNR improved, resulting in a method that is more sensitive to the fMRI signal. Using this method, it is possible to acquire submillimeter single volume 3D EPI scans of the visual cortex in a subsecond timeframe. Overall, high-density receive arrays in combination with shot-selective 2D CAIPIRINHA for 3D EPI scans prove to be valuable for reducing the scan time of submillimeter MRI acquisitions