NNFit: A Self-Supervised Deep Learning Method for Accelerated Quantification of High- Resolution Short Echo Time MR Spectroscopy Datasets.

Purpose To develop and evaluate the performance of NNFit, a self-supervised deep-learning method for quantification of high-resolution short echo-time (TE) echo-planar spectroscopic imaging (EPSI) datasets, with the goal of addressing the computational bottleneck of conventional spectral quantification methods in the clinical workflow. Materials and Methods This retrospective study included 89 short-TE whole-brain EPSI/GRAPPA scans from clinical trials for glioblastoma (Trial 1, May 2014-October 2018) and major-depressive-disorder (Trial 2, 2022- 2023). The training dataset included 685k spectra from 20 participants (60 scans) in Trial 1.

Influence of running on femoroacetabular joint bone-to-bone distances.

There is limited data quantifying the influence of running on hip cartilage mechanics. The goal of this investigation was to quantify changes in hip joint bone-to-bone distance in response to a 3-mile treadmill run. We acquired magnetic resonance (MR) images of the dominant hip of eight young, asymptomatic runners (five males, three females) before and immediately after they ran 3 miles at a self-selected pace on a level treadmill.

Vespa: Integrated applications for RF pulse design, spectral simulation and MRS data analysis.

Purpose: The Vespa package (Versatile Simulation, Pulses, and Analysis) is described and demonstrated. It provides workflows for developing and optimizing linear combination modeling (LCM) fitting for H MRS data using intuitive graphical user interface interfaces for RF pulse design, spectral simulation, and MRS data analysis. Command line interfaces for embedding workflows in MR manufacturer platforms and utilities for synthetic dataset creation are included.

NIfTI-MRS: A standard data format for magnetic resonance spectroscopy.

Purpose: Multiple data formats in the MRS community currently hinder data sharing and integration. NIfTI-MRS is proposed as a standard spectroscopy data format, implemented as an extension to the Neuroimaging informatics technology initiative (NIfTI) format. This standardized format can facilitate data sharing and algorithm development as well as ease integration of MRS analysis alongside other imaging modalities.

The association between language-based task-functional magnetic resonance imaging hemodynamics and baseline GABA+ and glutamate-glutamine measured in pre-supplementary motor area: A pilot study in an aging model.

Aging is a natural phenomenon that elicits slow and progressive cerebrovascular and neurophysiological changes that eventually lead to cognitive decline. The objective of this pilot study is to examine the association of GABA+ and glutamate-glutamine (Glx) complex with language-based blood oxygen level dependent (BOLD) hemodynamics in an aging model. More specifically, using standard BOLD we will first attempt to validate whether previously reported findings for BOLD amplitude and resting neurochemical relationships hold in an aging model.

Design and validation of a semi-automatic bone segmentation algorithm from MRI to improve research efficiency.

Segmentation of medical images into different tissue types is essential for many advancements in orthopaedic research; however, manual segmentation techniques can be time- and cost-prohibitive. The purpose of this work was to develop a semi-automatic segmentation algorithm that leverages gradients in spatial intensity to isolate the patella bone from magnetic resonance (MR) images of the knee that does not require a training set. The developed algorithm was validated in a sample of four human participants (in vivo) and three porcine stifle joints (ex vivo) using both magnetic resonance imaging (MRI) and computed tomography (CT).

Lumbar intervertebral disc diurnal deformations and T2 and T1rho relaxation times vary by spinal level and disc region.

Purpose: Magnetic resonance imaging (MRI) is routinely used to evaluate spine pathology; however, standard imaging findings weakly correlate to low back pain. Abnormal disc mechanical function is implicated as a cause of back pain but is not assessed using standard clinical MRI. Our objective was to utilize our established MRI protocol for measuring disc function to quantify disc mechanical function in a healthy cohort.

Influence of editing pulse flip angle on J-difference MR spectroscopy.

Purpose: To investigate the editing-pulse flip angle (FA) dependence of editing efficiency and ultimately to maximize the edited signal of commonly edited MR spectroscopy (MRS) signals, such as gamma-aminobutyric acid (GABA) and lactate.

Methods: Density-matrix simulations were performed for a range of spin systems to find the editing-pulse FA for maximal editing efficiency. Simulations were confirmed by phantom experiments and in vivo measurements in 10 healthy participants using a 3T Philips scanner.

Contribution of macromolecules to brain H MR spectra: Experts' consensus recommendations.

Proton MR spectra of the brain, especially those measured at short and intermediate echo times, contain signals from mobile macromolecules (MM). A description of the main MM is provided in this consensus paper. These broad peaks of MM underlie the narrower peaks of metabolites and often complicate their quantification but they also may have potential importance as biomarkers in specific diseases.

Global brain volume and N-acetyl-aspartate decline over seven decades of normal aging.

We characterize the whole-brain N-acetyl-aspartate (WBNAA) and brain tissue fractions across the adult lifespan and test the hypothesis that, despite age-related atrophy, neuronal integrity (reflected by WBNAA) is preserved in normal aging. Two-hundred-and-seven participants: 133 cognitively intact older adults (73.6 ± 7.

Advanced magnetic resonance spectroscopic neuroimaging: Experts' consensus recommendations.

Magnetic resonance spectroscopic imaging (MRSI) offers considerable promise for monitoring metabolic alterations associated with disease or injury; however, to date, these methods have not had a significant impact on clinical care, and their use remains largely confined to the research community and a limited number of clinical sites. The MRSI methods currently implemented on clinical MRI instruments have remained essentially unchanged for two decades, with only incremental improvements in sequence implementation. During this time, a number of technological developments have taken place that have already greatly benefited the quality of MRSI measurements within the research community and which promise to bring advanced MRSI studies to the point where the technique becomes a true imaging modality, while making the traditional review of individual spectra a secondary requirement.

T relaxation times of macromolecules and metabolites in the human brain at 9.4 T.

Purpose: Relaxation times can contribute to spectral assignment. In this study, effective T relaxation times ( ) of macromolecules are reported for gray and white matter-rich voxels in the human brain at 9.4 T.

Across-vendor standardization of semi-LASER for single-voxel MRS at 3T.

The semi-adiabatic localization by adiabatic selective refocusing (sLASER) sequence provides single-shot full intensity signal with clean localization and minimal chemical shift displacement error and was recommended by the international MRS Consensus Group as the preferred localization sequence at high- and ultra-high fields. Across-vendor standardization of the sLASER sequence at 3 tesla has been challenging due to the B requirements of the adiabatic inversion pulses and maximum B limitations on some platforms. The aims of this study were to design a short-echo sLASER sequence that can be executed within a B limit of 15 μT by taking advantage of gradient-modulated RF pulses, to implement it on three major platforms and to evaluate the between-vendor reproducibility of its perfomance with phantoms and in vivo.

Methodological consensus on clinical proton MRS of the brain: Review and recommendations.

Proton MRS ( H MRS) provides noninvasive, quantitative metabolite profiles of tissue and has been shown to aid the clinical management of several brain diseases. Although most modern clinical MR scanners support MRS capabilities, routine use is largely restricted to specialized centers with good access to MR research support. Widespread adoption has been slow for several reasons, and technical challenges toward obtaining reliable good-quality results have been identified as a contributing factor.

AutoVOI: real-time automatic prescription of volume-of-interest for single voxel spectroscopy.

Purpose: To develop a fast and automated volume-of-interest (VOI) prescription pipeline (AutoVOI) for single-voxel MRS that removes the need for manual VOI placement, allows flexible VOI planning in any brain region, and enables high inter- and intra-subject consistency of VOI prescription.

Methods: AutoVOI was designed to transfer pre-defined VOIs from an atlas to the 3D anatomical data of the subject during the scan. The AutoVOI pipeline was optimized for consistency in VOI placement (precision), enhanced coverage of the targeted tissue (accuracy), and fast computation speed.

A convolutional neural network to filter artifacts in spectroscopic MRI.

Purpose: Proton MRSI is a noninvasive modality capable of generating volumetric maps of in vivo tissue metabolism without the need for ionizing radiation or injected contrast agent. Magnetic resonance spectroscopic imaging has been shown to be a viable imaging modality for studying several neuropathologies. However, a key hurdle in the routine clinical adoption of MRSI is the presence of spectral artifacts that can arise from a number of sources, possibly leading to false information.

A magnetic resonance imaging framework for quantifying intervertebral disc deformation in vivo: Reliability and application to diurnal variations in lumbar disc shape.

Low back pain is a significant socioeconomic burden in the United States and lumbar intervertebral disc degeneration is frequently implicated as a cause. The discs play an important mechanical role in the spine, yet the relationship between disc function and back pain is poorly defined. The objective of this work was to develop a technique using magnetic resonance imaging (MRI) and three-dimensional modeling to measure in vivo disc deformations.

Whole brain neuronal abnormalities in focal epilepsy quantified with proton MR spectroscopy.

Objective: To test the hypothesis that localization-related epilepsy is associated with widespread neuronal dysfunction beyond the ictal focus, reflected by a decrease in patients' global concentration of their proton MR spectroscopy (H-MRS) observed marker, N-acetyl-aspartate (NAA).

Methods: Thirteen patients with localization-related epilepsy (7 men, 6 women) 40±13 (mean±standard-deviation)years old, 8.3±13.

Global brain metabolic quantification with whole-head proton MRS at 3 T.

Total N-acetyl-aspartate + N-acetyl-aspartate-glutamate (NAA), total creatine (Cr) and total choline (Cho) proton MRS ( H-MRS) signals are often used as surrogate markers in diffuse neurological pathologies, but spatial coverage of this methodology is limited to 1%-65% of the brain. Here we wish to demonstrate that non-localized, whole-head (WH) H-MRS captures just the brain's contribution to the Cho and Cr signals, ignoring all other compartments. Towards this end, 27 young healthy adults (18 men, 9 women), 29.

Quantifying global-brain metabolite level changes with whole-head proton MR spectroscopy at 3T.

Background And Purpose: To assess the sensitivity of non-localized, whole-head H-MRS to an individual's serial changes in total-brain NAA, Glx, Cr and Cho concentrations - metabolite metrics often used as surrogate markers in neurological pathologies.

Materials And Methods: In this prospective study, four back-to-back (single imaging session) and three serial (successive sessions) non-localizing, ~3min H-MRS (TE/TR/TI=5/10/940ms) scans were performed on 18 healthy young volunteers: 9 women, 9 men: 29.9±7.

Automated whole-brain N-acetylaspartate proton MRS quantification.

Concentration of the neuronal marker, N-acetylaspartate (NAA), a quantitative metric for the health and density of neurons, is currently obtained by integration of the manually defined peak in whole-head proton ((1) H)-MRS. Our goal was to develop a full spectral modeling approach for the automatic estimation of the whole-brain NAA concentration (WBNAA) and to compare the performance of this approach with a manual frequency-range peak integration approach previously employed. MRI and whole-head (1) H-MRS from 18 healthy young adults were examined.

Correlation between quantitative whole-body muscle magnetic resonance imaging and clinical muscle weakness in Pompe disease.

Introduction: Previous examination of whole-body muscle involvement in Pompe disease has been limited to physical examination and/or qualitative magnetic resonance imaging (MRI). In this study we assess the feasibility of quantitative proton-density fat-fraction (PDFF) whole-body MRI in late-onset Pompe disease (LOPD) and compare the results with manual muscle testing.

Methods: Seven LOPD patients and 11 disease-free controls underwent whole-body PDFF MRI.