A multi-imaging modality study of bone density, bone structure and the muscle - bone unit in end-stage renal disease.

End stage renal disease (ESRD) is associated with sarcopenia and skeletal fragility. The objectives of this cross-sectional study were to (1) characterize body composition, bone mineral density (BMD) and bone structure in hemodialysis patients compared with controls, (2) assess whether DXA areal BMD (aBMD) correlates with peripheral quantitative CT (pQCT) measures of volumetric BMD (vBMD), cortical dimensions and MRI measures of trabecular microarchitecture, and (3) determine the magnitude of bone deficits in ESRD after adjustment for muscle mass. Thirty ESRD participants, ages 25 to 64 years, were compared with 403 controls for DXA and pQCT outcomes and 104 controls for MRI outcomes; results were expressed as race- and sex- specific Z-scores relative to age.

High-Density, Long-Lasting, and Multi-region Electrophysiological Recordings Using Polymer Electrode Arrays.

The brain is a massive neuronal network, organized into anatomically distributed sub-circuits, with functionally relevant activity occurring at timescales ranging from milliseconds to years. Current methods to monitor neural activity, however, lack the necessary conjunction of anatomical spatial coverage, temporal resolution, and long-term stability to measure this distributed activity. Here we introduce a large-scale, multi-site, extracellular recording platform that integrates polymer electrodes with a modular stacking headstage design supporting up to 1,024 recording channels in freely behaving rats.

A Fully Automated Approach to Spike Sorting.

Understanding the detailed dynamics of neuronal networks will require the simultaneous measurement of spike trains from hundreds of neurons (or more). Currently, approaches to extracting spike times and labels from raw data are time consuming, lack standardization, and involve manual intervention, making it difficult to maintain data provenance and assess the quality of scientific results. Here, we describe an automated clustering approach and associated software package that addresses these problems and provides novel cluster quality metrics.

Validation of neural spike sorting algorithms without ground-truth information.

Background: The throughput of electrophysiological recording is growing rapidly, allowing thousands of simultaneous channels, and there is a growing variety of spike sorting algorithms designed to extract neural firing events from such data. This creates an urgent need for standardized, automatic evaluation of the quality of neural units output by such algorithms.

New Method: We introduce a suite of validation metrics that assess the credibility of a given automatic spike sorting algorithm applied to a given dataset.

Selective in vivo bone imaging with long-T suppressed PETRA MRI.

Purpose: To design and evaluate an optimized PETRA (point-wise encoding time reduction with radial acquisition) sequence with long-T suppression at 3 Tesla.

Methods: An adiabatic inversion recovery-based scheme was used to null the long-T signal. To minimize scan time, the signal was sampled multiple times after each inversion with variable excitation flip angles designed to yield constant short-T signal amplitude.

Method for rapid MRI quantification of global cerebral metabolic rate of oxygen.

A recently reported quantitative magnetic resonance imaging (MRI) method denoted OxFlow has been shown to be able to quantify whole-brain cerebral metabolic rate of oxygen (CMRO2) by simultaneously measuring oxygen saturation (SvO2) in the superior sagittal sinus and cerebral blood flow (CBF) in the arteries feeding the brain in 30 seconds, which is adequate for measurement at baseline but not necessarily in response to neuronal activation. Here, we present an accelerated version of the method (referred to as F-OxFlow) that quantifies CMRO2 in 8 seconds scan time under full retention of the parent method's capabilities and compared it with its predecessor at baseline in 10 healthy subjects. Results indicate excellent agreement between both sequences, with mean bias of 2.

Effects of age and smoking on endothelial function assessed by quantitative cardiovascular magnetic resonance in the peripheral and central vasculature.

Background: Both age and smoking promote endothelial dysfunction and impair vascular reactivity. Here, we tested this hypothesis by quantifying new cardiovascular magnetic resonance (CMR)-based biomarkers in smokers and nonsmokers.

Methods: Study population: young non-smokers (YNS: N = 45, mean age = 30.

Pulse sequence programming in a dynamic visual environment: SequenceTree.

Purpose: To describe SequenceTree, an open source, integrated software environment for implementing MRI pulse sequences and, ideally, exporting them to actual MRI scanners. The software is a user-friendly alternative to vendor-supplied pulse sequence design and editing tools and is suited for programmers and nonprogrammers alike.

Methods: The integrated user interface was programmed using the Qt4/C++ toolkit.

Rapid T2- and susceptometry-based CMRO2 quantification with interleaved TRUST (iTRUST).

Susceptometry-based oximetry (SBO) and T2-relaxation-under-spin-tagging (TRUST) are two promising methods for quantifying the cerebral metabolic rate of oxygen (CMRO2), a critical parameter of brain function. We present a combined method, interleaved TRUST (iTRUST), which achieves rapid, simultaneous quantification of both susceptometry- and T2-based CMRO2 via insertion of a flow-encoded, dual-echo gradient-recalled echo (OxFlow) module within the T1 recovery portion of the TRUST sequence. In addition to allowing direct comparison between SBO- and TRUST-derived venous oxygen saturation (Yv) values, iTRUST substantially improves TRUST temporal resolution for CMRO2 quantification and obviates the need for a separate blood flow measurement following TRUST acquisition.

Comparison of MRI methods for measuring whole-brain venous oxygen saturation.

Purpose: In this work, we compare susceptometry-based oximetry (SBO) and two T2 -based methods for estimating resting baseline SvO2 in the superior sagittal sinus (SSS).

Methods: SBO is a field-mapping technique whereas in T2 -based methods the intravascular blood signal is isolated either with velocity-encoded projections [projection-based T2 (PT2 )] or a tag-control scheme [T2 -relaxation under spin tagging (TRUST)] after T2 -preparation. The measurements were performed on twelve healthy subjects (mean age = 33 ± 6 years) at 3 Tesla field strength.

Registration-based autofocusing technique for automatic correction of motion artifacts in time-series studies of high-resolution bone MRI.

Purpose: To develop a registration-based autofocusing (RAF) motion correction technique for high-resolution trabecular bone (TB) imaging and to evaluate its performance on in vivo MR data.

Materials And Methods: The technique combines serial registration with a previously developed motion correction technique - autofocusing - for automatic correction of subject movement degradation of MR images acquired in longitudinal studies. The method was tested on in vivo images of the distal radius to measure improvements in serial reproducibility of parameters in 12 women (ages 50-75 years), and to compare with the navigator echo-based correction and autofocusing.

Correction of excitation profile in Zero Echo Time (ZTE) imaging using quadratic phase-modulated RF pulse excitation and iterative reconstruction.

Zero-echo Time (ZTE) imaging is a promising technique for magnetic resonance imaging (MRI) of short-T2 tissue nuclei in tissues. A problem inherent to the method currently hindering its translation to the clinic is the presence of a spatial encoding gradient during excitation, which causes the hard pulse to become spatially selective, resulting in blurring and shadow artifacts in the image. While shortening radio-frequency (RF) pulse duration alleviates this problem the resulting elevated RF peak power and specific absorption rate (SAR) in practice impede such a solution.

Assessment of trabecular bone yield and post-yield behavior from high-resolution MRI-based nonlinear finite element analysis at the distal radius of premenopausal and postmenopausal women susceptible to osteoporosis.

Rationale And Objectives: To assess the performance of a nonlinear microfinite element model on predicting trabecular bone yield and post-yield behavior based on high-resolution in vivo magnetic resonance images via the serial reproducibility.

Materials And Methods: The nonlinear model captures material nonlinearity by iteratively adjusting tissue-level modulus based on tissue-level effective strain. It enables simulations of trabecular bone yield and post-yield behavior from micro magnetic resonance images at in vivo resolution by solving a series of nonlinear systems via an iterative algorithm on a desktop computer.

The shear modulus of the nucleus pulposus measured using magnetic resonance elastography: a potential biomarker for intervertebral disc degeneration.

Purpose: This study aims to: (1) measure the shear modulus of nucleus pulposus (NP) in intact human vertebra-disc-vertebra segments using a magnetic resonance elastography setup for a 7T whole-body scanner, (2) quantify the effect of disc degeneration on the NP shear modulus measured using magnetic resonance elastography, and (3) compare the NP shear modulus to other magnetic resonance-based biomarkers of dis degeneration.

Methods: Thirty intact human disc segments were classified as normal, mild, or severely degenerated. The NP shear modulus was measured using a custom-made setup that included a novel inverse method less sensitive to noisy displacements.

Potential of in vivo MRI-based nonlinear finite-element analysis for the assessment of trabecular bone post-yield properties.

Purpose: Bone strength is the key factor impacting fracture risk. Assessment of bone strength from high-resolution (HR) images have largely relied on linear micro-finite element analysis (μFEA) even though failure always occurs beyond the yield point, which is outside the linear regime. Nonlinear μFEA may therefore be more informative in predicting failure behavior.

Task-correlated facial and head movements in classifier-based real-time FMRI.

Background: Real-time fMRI is especially vulnerable to task-correlated movement artifacts because statistical methods normally available in conventional analyses to remove such signals cannot be used in the context of real-time fMRI. Multi-voxel classifier-based methods, although advantageous in many respects, are particularly sensitive. Here we systematically studied various movements of the head and face to determine to what extent these can "masquerade" as signal in multi-voxel classifiers.

Computationally-optimized bone mechanical modeling from high-resolution structural images.

Image-based mechanical modeling of the complex micro-structure of human bone has shown promise as a non-invasive method for characterizing bone strength and fracture risk in vivo. In particular, elastic moduli obtained from image-derived micro-finite element (μFE) simulations have been shown to correlate well with results obtained by mechanical testing of cadaveric bone. However, most existing large-scale finite-element simulation programs require significant computing resources, which hamper their use in common laboratory and clinical environments.

Micro-MR imaging-based computational biomechanics demonstrates reduction in cortical and trabecular bone strength after renal transplantation.

Purpose: To examine the ability of three-dimensional micro-magnetic resonance (MR) imaging-based computational biomechanics to detect mechanical alterations in trabecular bone and cortical bone in the distal tibia of incident renal transplant recipients 6 months after renal transplantation and compare them with bone mineral density (BMD) outcomes.

Materials And Methods: The study was approved by the institutional review board and complied with HIPAA guidelines. Written informed consent was obtained from all subjects.

Predicting trabecular bone elastic properties from measures of bone volume fraction and fabric on the basis of micromagnetic resonance images.

The relationship between fabric (a measure of structural anisotropy) and elastic properties of trabecular bone was examined by invoking morphology and homogenization theory on the basis of micromagnetic resonance images from the distal tibia in specimens (N = 30) and human subjects (N = 16) acquired at a 160 × 160 × 160 μm(3) voxel size. The fabric tensor was mapped in 7.5 × 7.

Comparison of optimized soft-tissue suppression schemes for ultrashort echo time MRI.

Ultrashort echo time (UTE) imaging with soft-tissue suppression reveals short-T(2) components (typically hundreds of microseconds to milliseconds) ordinarily not captured or obscured by long-T(2) tissue signals on the order of tens of milliseconds or longer. Therefore, the technique enables visualization and quantification of short-T(2) proton signals such as those in highly collagenated connective tissues. This work compares the performance of the three most commonly used long-T(2) suppression UTE sequences, i.

Accuracy of the cylinder approximation for susceptometric measurement of intravascular oxygen saturation.

Susceptometry-based MR oximetry has previously been shown suitable for quantifying hemoglobin oxygen saturation in large vessels for studying vascular reactivity and quantification of global cerebral metabolic rate of oxygen utilization. A key assumption underlying this method is that large vessels can be modeled as long paramagnetic cylinders. However, bifurcations, tapering, noncircular cross-section, and curvature of these vessels produce substantial deviations from cylindrical geometry, which may lead to errors in hemoglobin oxygen saturation quantification.

On the significance of motion degradation in high-resolution 3D μMRI of trabecular bone.

Rationale And Objectives: Subtle subject movement during high-resolution three-dimensional micro-magnetic resonance imaging of trabecular bone (TB) causes blurring, thereby rendering the data unreliable for quantitative analysis. In this work, the effects of translational and rotational motion displacements were evaluated qualitatively and quantitatively.

Materials And Methods: In experiment 1, motion was induced by applying various simulated and previously observed in vivo trajectories as phase shifts to k-space or rotation angles to k-space segments of a virtually motion-free data set.

Rapid magnetic resonance measurement of global cerebral metabolic rate of oxygen consumption in humans during rest and hypercapnia.

The effect of hypercapnia on cerebral metabolic rate of oxygen consumption (CMRO(2)) has been a subject of intensive investigation and debate. Most applications of hypercapnia are based on the assumption that a mild increase in partial pressure of carbon dioxide has negligible effect on cerebral metabolism. In this study, we sought to further investigate the vascular and metabolic effects of hypercapnia by simultaneously measuring global venous oxygen saturation (S(v)O(2)) and total cerebral blood flow (tCBF), with a temporal resolution of 30 seconds using magnetic resonance susceptometry and phase-contrast techniques in 10 healthy awake adults.

Helmholtz-pair transmit coil with integrated receive array for high-resolution MRI of trabecular bone in the distal tibia at 7T.

A Helmholtz-pair local transmit RF coil with an integrated four-element receive array RF coil and foot immobilization platform was designed and constructed for imaging the distal tibia in a whole-body 7T MRI scanner. Simulations and measurements of the B(1) field distribution of the transmit coil are described, along with SAR considerations for operation at 7T. Results of imaging the trabecular bone of three volunteers at 1.

Performance of μMRI-Based virtual bone biopsy for structural and mechanical analysis at the distal tibia at 7T field strength.

Purpose: To assess the performance of a 3D fast spin echo (FSE) pulse sequence utilizing out-of-slab cancellation through phase alternation and micro-magnetic resonance imaging (μMRI)-based virtual bone biopsy processing methods to probe the serial reproducibility and sensitivity of structural and mechanical parameters of the distal tibia at 7.0T.

Materials And Methods: The distal tibia of five healthy subjects was imaged at three timepoints with a 3D FSE sequence at 137 × 137 × 410 μm(3) voxel size.