Pulse sequence programming in a dynamic visual environment: SequenceTree

Three contrasts in 3 min: Rapid, high-resolution, and bone-selective UTE MRI for craniofacial imaging with automated deep-learning skull segmentation

PURPOSE

Ultrashort echo time (UTE) MRI can be a radiation-free alternative to CT for craniofacial imaging of pediatric patients. However, unlike CT, bone-specific MR imaging is limited by long scan times, relatively low spatial resolution, and a time-consuming bone segmentation workflow.

METHODS

A rapid, high-resolution UTE technique for brain and skull imaging in conjunction with an automatic segmentation pipeline was developed. A dual-RF, dual-echo UTE sequence was optimized for rapid scan time (3 min) and smaller voxel size (0.65 mm3). A weighted least-squares conjugate gradient method for computing the bone-selective image improves bone specificity while retaining bone sensitivity. Additionally, a deep-learning U-Net model was trained to automatically segment the skull from the bone-selective images. Ten healthy adult volunteers (six male, age 31.5 ± 10 years) and three pediatric patients (two male, ages 12 to 15 years) were scanned at 3 T. Clinical CT for the three patients were obtained for validation. Similarities in 3D skull reconstructions relative to clinical standard CT were evaluated based on the Dice similarity coefficient and Hausdorff distance. Craniometric measurements were used to assess geometric accuracy of the 3D skull renderings.

RESULTS

The weighted least-squares method produces images with enhanced bone specificity, suppression of soft tissue, and separation from air at the sinuses when validated against CT in pediatric patients. Dice similarity coefficient overlap was 0.86 ± 0.05, and the 95th percentile Hausdorff distance was 1.77 ± 0.49 mm between the full-skull binary masks of the optimized UTE and CT in the testing dataset.

CONCLUSION

An optimized MRI acquisition, reconstruction, and segmentation workflow for craniofacial imaging was developed.

Reduced cross-scanner variability using vendor-agnostic sequences for single-shell diffusion MRI

PURPOSE

To reduce the inter-scanner variability of diffusion MRI (dMRI) measures between scanners from different vendors by developing a vendor-neutral dMRI pulse sequence using the open-source vendor-agnostic Pulseq platform.

METHODS

We implemented a standard EPI based dMRI sequence in Pulseq. We tested it on two clinical scanners from different vendors (Siemens Prisma and GE Premier), systematically evaluating and comparing the within- and inter-scanner variability across the vendors, using both the vendor-provided and Pulseq dMRI sequences. Assessments covered both a diffusion phantom and three human subjects, using standard error (SE) and Lin's concordance correlation to measure the repeatability and reproducibility of standard DTI metrics including fractional anisotropy (FA) and mean diffusivity (MD).

RESULTS

Identical dMRI sequences were executed on both scanners using Pulseq. On the phantom, the Pulseq sequence showed more than a 2.5× reduction in SE (variability) across Siemens and GE scanners. Furthermore, Pulseq sequences exhibited markedly reduced SE in-vivo, maintaining scan-rescan repeatability while delivering lower variability in FA and MD (more than 50% reduction in cortical/subcortical regions) compared to vendor-provided sequences.

CONCLUSION

The Pulseq diffusion sequence reduces the cross-scanner variability for both phantom and in-vivo data, which will benefit multi-center neuroimaging studies and improve the reproducibility of neuroimaging studies.

Quantification of whole-organ individual and bilateral renal metabolic rate of oxygen

PURPOSE

Renal metabolic rate of oxygen (rMRO2 ) is a potentially important biomarker of kidney function. The key parameters for rMRO2 quantification include blood flow rate (BFR) and venous oxygen saturation (SvO2 ) in a draining vessel. Previous approaches to quantify renal metabolism have focused on the single organ. Here, both kidneys are considered as one unit to quantify bilateral rMRO2 . A pulse sequence to facilitate bilateral rMRO2 quantification is introduced.

METHODS

To quantify bilateral rMRO2 , measurements of BFR and SvO2 are made along the inferior vena cava (IVC) at suprarenal and infrarenal locations. From the continuity equation, these four parameters can be related to derive an expression for bilateral rMRO2 . The recently reported K-MOTIVE pulse sequence was implemented at four locations: left kidney, right kidney, suprarenal IVC, and infrarenal IVC. A dual-band variant of K-MOTIVE (db-K-MOTIVE) was developed by incorporating simultaneous-multi-slice imaging principles. The sequence simultaneously measures BFR and SvO2 at suprarenal and infrarenal locations in a single pass of 21 s, yielding bilateral rMRO2 .

RESULTS

SvO2 and BFR are higher in suprarenal versus infrarenal IVC, and the renal veins are highly oxygenated (SvO2  >90%). Bilateral rMRO2 quantified in 10 healthy subjects (8 M, 30 ± 8 y) was found to be 291 ± 247 and 349 ± 300 (μmolO2 /min)/100 g, derived from K-MOTIVE and db-K-MOTIVE, respectively. In comparison, total rMRO2 from combining left and right was 329 ± 273 (μmolO2 /min)/100 g.

CONCLUSION

The present work demonstrates that bilateral rMRO2 quantification is feasible with fair reproducibility and physiological plausibility. The indirect method is a promising approach to compute bilateral rMRO2 when individual rMRO2 quantification is difficult.

MRI-based quantification of whole-organ renal metabolic rate of oxygen

During the early stages of diabetes, kidney oxygen utilization increases. The mismatch between oxygen demand and supply contributes to tissue hypoxia, a key driver of chronic kidney disease. Thus, whole-organ renal metabolic rate of oxygen (rMRO2 ) is a potentially valuable biomarker of kidney function. The key parameters required to determine rMRO2 include the renal blood flow rate (RBF) in the feeding artery and oxygen saturation in the draining renal vein (SvO2 ). However, there is currently no noninvasive method to quantify rMRO2 in absolute physiologic units. Here, a new MRI pulse sequence, Kidney Metabolism of Oxygen via T2 and Interleaved Velocity Encoding (K-MOTIVE), is described, along with evaluation of its performance in the human kidney in vivo. K-MOTIVE interleaves a phase-contrast module before a background-suppressed T2 -prepared balanced steady-state-free-precession (bSSFP) readout to measure RBF and SvO2 in a single breath-hold period of 22 s, yielding rMRO2 via Fick's principle. Variants of K-MOTIVE to evaluate alternative bSSFP readout strategies were studied. Kidney mass was manually determined from multislice gradient recalled echo images. Healthy subjects were recruited to quantify rMRO2 of the left kidney at 3-T field strength (N = 15). Assessments of repeat reproducibility and comparisons with individual measurements of RBF and SvO2 were performed, and the method's sensitivity was evaluated with a high-protein meal challenge (N = 8). K-MOTIVE yielded the following metabolic parameters: T2  = 157 ± 19 ms; SvO2  = 92% ± 6%; RBF = 400 ± 110 mL/min; and rMRO2  = 114 ± 117(μmol O2 /min)/100 g tissue. Reproducibility studies of T2 and RBF (parameters directly measured by K-MOTIVE) resulted in coefficients of variation less than 10% and intraclass correlation coefficients more than 0.75. The high-protein meal elicited an increase in rMRO2 , which was corroborated by serum biomarkers. The K-MOTIVE sequence measures SvO2 and RBF, the parameters necessary to quantify whole-organ rMRO2 , in a single breath-hold. The present work demonstrates that rMRO2 quantification is feasible with good reproducibility. rMRO2 is a potentially valuable physiological biomarker.

Six-minute, in vivo MRI quantification of proximal femur trabecular bone 3D microstructure

BACKGROUND

Assessment of proximal femur trabecular bone microstructure in vivo by magnetic resonance imaging has recently been validated for acquiring information independent of bone mineral density in osteoporotic patients. However, the requisite signal-to-noise ratio (SNR) and resolution for interrogation of the trabecular microstructure at this anatomical location prolongs the scan duration and renders the imaging protocol clinically infeasible. Parallel imaging and compressed sensing (PICS) techniques can reduce the scan duration of the imaging protocol without substantially compromising image quality. The present work investigates the limits of acceleration for a commonly used PICS technique, ℓ1-ESPIRiT, for the purpose of quantifying measures of trabecular bone microarchitecture. Based on a desired error tolerance, a six-minute, prospectively accelerated variant of the imaging protocol was developed and assessed for intersession reproducibility and agreement with the longer reference scan.

PURPOSE

To investigate the limits of acceleration for MRI-based trabecular bone quantification by parallel imaging and compressed sensing reconstruction, and to develop a prototypical imaging protocol for assessing the proximal femur microstructure in a clinically practical scan time.

METHODS

Healthy participants (n = 11) were scanned by a 3D balanced steady-state free precession (bSSFP) sequence satisfying the Nyquist criterion with a scan duration of about 18 min. The raw data were retrospectively undersampled and reconstructed to mimic various acceleration factors ranging from 2 to 6. Trabecular volumes-of-interest in four major femoral regions (greater trochanter, intertrochanteric region, femoral neck, and femoral head) were analyzed and six relevant measures of trabecular bone microarchitecture (bone volume fraction, surface-to-curve ratio, erosion index, elastic modulus, trabecular thickness, plates-to-rods ratio) were obtained for images of all accelerations. To assess agreement, median percent error and intraclass correlation coefficients (ICCs) were computed using the fully-sampled data as reference. Based on this analysis, a prospectively 3-fold accelerated sequence with a duration of about 6 min was developed and the analysis was repeated.

RESULTS

A prospective acceleration factor of 3 demonstrated comparable performance in reproducibility and absolute agreement to the fully-sampled scan. The median CoV over all image-derived metrics was generally <6 % and ICCs >0.70. Also, measurements from prospectively 3-fold accelerated scans demonstrated in general median percent errors of <7 % and ICCs >0.70.

CONCLUSION

The present work proposes a method to make in vivo quantitative assessment of proximal femur trabecular microstructure with a clinically practical scan duration of about 6 min.

Superior sagittal sinus flow as a proxy for tracking global cerebral blood flow dynamics during wakefulness and sleep

Sleep, a state of reduced consciousness, affects brain oxygen metabolism and lowers cerebral metabolic rate of oxygen (CMRO2). Previously, we quantified CMRO2 during sleep via Fick's Principle, with a single-band MRI sequence measuring both hemoglobin O2 saturation (SvO2) and superior sagittal sinus (SSS) blood flow, which was upscaled to obtain total cerebral blood flow (tCBF). The procedure involves a brief initial calibration scan to determine the upscaling factor (fc), assumed state-invariant. Here, we used a dual-band sequence to simultaneously provide SvO2 in SSS and tCBF in the neck every 16 seconds, allowing quantification of fc dynamically. Ten healthy subjects were scanned by MRI with simultaneous EEG for 80 minutes, yielding 300 temporal image frames per subject. Four volunteers achieved slow-wave sleep (SWS), as evidenced by increased δ-wave activity (per American Academy of Sleep Medicine criteria). SWS was maintained for 13.5 ± 7.0 minutes, with CMRO2 28.6 ± 5.5% lower than pre-sleep wakefulness. Importantly, there was negligible bias between tCBF obtained by upscaling SSS-blood flow, and tCBF measured directly in the inflowing arteries of the neck (intra-class correlation 0.95 ± 0.04, averaged across all subjects), showing that the single-band approach is a valid substitute for quantifying tCBF, simplifying image data collection and analysis without sacrificing accuracy.

AI-driven and automated MRI sequence optimization in scanner-independent MRI sequences formulated by a domain-specific language

Introduction

The complexity of Magnetic Resonance Imaging (MRI) sequences requires expert knowledge about the underlying contrast mechanisms to select from the wide range of available applications and protocols. Automation of this process using machine learning (ML) can support the radiologists and MR technicians by complementing their experience and finding the optimal MRI sequence and protocol for certain applications.

Methods

We define domain-specific languages (DSL) both for describing MRI sequences and for formulating clinical demands for sequence optimization. By using various abstraction levels, we allow different key users exact definitions of MRI sequences and make them more accessible to ML. We use a vendor-independent MRI framework (gammaSTAR) to build sequences that are formulated by the DSL and export them using the generic file format introduced by the Pulseq framework, making it possible to simulate phantom data using the open-source MR simulation framework JEMRIS to build a training database that relates input MRI sequences to output sets of metrics. Utilizing ML techniques, we learn this correspondence to allow efficient optimization of MRI sequences meeting the clinical demands formulated as a starting point.

Results

ML methods are capable of capturing the relation of input and simulated output parameters. Evolutionary algorithms show promising results in finding optimal MRI sequences with regards to the training data. Simulated and acquired MRI data show high correspondence to the initial set of requirements.

Discussion

This work has the potential to offer optimal solutions for different clinical scenarios, potentially reducing exam times by preventing suboptimal MRI protocol settings. Future work needs to cover additional DSL layers of higher flexibility as well as an optimization of the underlying MRI simulation process together with an extension of the optimization method.

Open and reproducible neuroimaging: From study inception to publication

Empirical observations of how labs conduct research indicate that the adoption rate of open practices for transparent, reproducible, and collaborative science remains in its infancy. This is at odds with the overwhelming evidence for the necessity of these practices and their benefits for individual researchers, scientific progress, and society in general. To date, information required for implementing open science practices throughout the different steps of a research project is scattered among many different sources. Even experienced researchers in the topic find it hard to navigate the ecosystem of tools and to make sustainable choices. Here, we provide an integrated overview of community-developed resources that can support collaborative, open, reproducible, replicable, robust and generalizable neuroimaging throughout the entire research cycle from inception to publication and across different neuroimaging modalities. We review tools and practices supporting study inception and planning, data acquisition, research data management, data processing and analysis, and research dissemination. An online version of this resource can be found at https://oreoni.github.io. We believe it will prove helpful for researchers and institutions to make a successful and sustainable move towards open and reproducible science and to eventually take an active role in its future development.

Metabolite patterns associated with individual response to supervised exercise therapy in patients with intermittent claudication

Objective

Supervised exercise therapy (SET) is the first line treatment for intermittent claudication owing to peripheral arterial disease. Despite multiple randomized controlled trials proving the efficacy of SET, there are large differences in individual patient's responses. We used plasma metabolomics to identify potential metabolic influences on the individual response to SET.

Methods

Primary metabolites, complex lipids, and lipid mediators were measured on plasma samples taken at before and after Gardner graded treadmill walking tests that were administered before and after 12 weeks of SET. We used an ensemble modeling approach to identify metabolites or changes in metabolites at specific time points that associated with interindividual variability in the functional response to SET. Specific time points analyzed included baseline metabolite levels before SET, dynamic metabolomics changes before SET, the difference in pre- and post-SET baseline metabolomics, and the difference (pre- and post-SET) of the dynamic (pre- and post-treadmill).

Results

High levels of baseline anandamide levels pre- and post-SET were associated with a worse response to SET. Increased arachidonic acid (AA) and decreased levels of the AA precursor dihomo-γ-linolenic acid across SET were associated with a worse response to SET. Participants who were able to tolerate large increases in AA during acute exercise had longer, or better, walking times both before and after SET.

Conclusions

We identified two pathways of relevance to individual response to SET that warrant further study: anandamide synthesis may activate endocannabinoid receptors, resulting in worse treadmill test performance. SET may train patients to withstand higher levels of AA, and inflammatory signaling, resulting in longer walking times.

Clinical Relevance

This manuscript describes the use of metabolomic techniques to measure the interindividual effects of SET in patients with peripheral artery disease (PAD). We identified high levels of AEA are linked to CB1 signaling and activation of inflammatory pathways. This alters energy expenditure in myoblasts by decreasing glucose uptake and may induce an acquired skeletal muscle myopathy. SET may also help participants tolerate increased levels of AA and inflammation produced during exercise, resulting in longer walking times. This data will enhance understanding of the pathophysiology of PAD and the mechanism by which SET improves walking intolerance.

Metabolism of oxygen via T2 and interleaved velocity encoding: A rapid method to quantify whole-brain cerebral metabolic rate of oxygen

PURPOSE

Cerebral metabolic rate of oxygen (CMRO2 ) is an important biomarker of brain function. Key physiological parameters required to quantify CMRO2 include blood flow rate in the feeding arteries and venous oxygen saturation (SvO2 ) in the draining vein. Here, a pulse sequence, metabolism of oxygen via T2 and interleaved velocity encoding (MOTIVE), was developed to measure both parameters simultaneously and enable CMRO2 quantification in a single pass.

METHODS

The MOTIVE sequence interleaves a phase-contrast module between a nonselective saturation and a background-suppressed T2 -prepared EPI readout (BGS-EPI) to measure T2 of blood water protons and cerebral blood flow in 20 s or less. The MOTIVE and standalone BGS-EPI sequences were compared against TRUST ("T2 relaxation under spin tagging") in the brain in healthy subjects (N = 24). Variants of MOTIVE to enhance resolution or shorten scan time were explored. Intrasession and intersession reproducibility studies were performed.

RESULTS

MOTIVE experiments yielded an average SvO2 of 61 ± 6% in the superior sagittal sinus of the brain and an average cerebral blood flow of 56 ± 10 ml/min/100 g. The bias in SvO2 of MOTIVE and BGS-EPI to TRUST was +2 ± 4% and +1 ± 3%, respectively. The bias in cerebral blood flow of MOTIVE to Cartesian phase-contrast reference was +1 ± 6 ml/min/100 g.

CONCLUSIONS

The MOTIVE sequence is an advance over existing T2 -based oximetric methods. It does not require a control image and simultaneously measures SvO2 and flow velocity. The measurements agree well with TRUST and reference phase-contrast sequences. This noninvasive technique enables CMRO2 quantification in under 20 s and is reproducible for in vivo applications.

qMRI-BIDS: An extension to the brain imaging data structure for quantitative magnetic resonance imaging data

The Brain Imaging Data Structure (BIDS) established community consensus on the organization of data and metadata for several neuroimaging modalities. Traditionally, BIDS had a strong focus on functional magnetic resonance imaging (MRI) datasets and lacked guidance on how to store multimodal structural MRI datasets. Here, we present and describe the BIDS Extension Proposal 001 (BEP001), which adds a range of quantitative MRI (qMRI) applications to the BIDS. In general, the aim of qMRI is to characterize brain microstructure by quantifying the physical MR parameters of the tissue via computational, biophysical models. By proposing this new standard, we envision standardization of qMRI through multicenter dissemination of interoperable datasets. This way, BIDS can act as a catalyst of convergence between qMRI methods development and application-driven neuroimaging studies that can help develop quantitative biomarkers for neural tissue characterization. In conclusion, this BIDS extension offers a common ground for developers to exchange novel imaging data and tools, reducing the entrance barrier for qMRI in the field of neuroimaging.

Vendor-neutral sequences and fully transparent workflows improve inter-vendor reproducibility of quantitative MRI

PURPOSE

We developed an end-to-end workflow that starts with a vendor-neutral acquisition and tested the hypothesis that vendor-neutral sequences decrease inter-vendor variability of T1, magnetization transfer ratio (MTR), and magnetization transfer saturation-index (MTsat) measurements.

METHODS

We developed and deployed a vendor-neutral 3D spoiled gradient-echo (SPGR) sequence on three clinical scanners by two MRI vendors. We then acquired T1 maps on the ISMRM-NIST system phantom, as well as T1, MTR, and MTsat maps in three healthy participants. We performed hierarchical shift function analysis in vivo to characterize the differences between scanners when the vendor-neutral sequence is used instead of commercial vendor implementations. Inter-vendor deviations were compared for statistical significance to test the hypothesis.

RESULTS

In the phantom, the vendor-neutral sequence reduced inter-vendor differences from 8% to 19.4% to 0.2% to 5% with an overall accuracy improvement, reducing ground truth T1 deviations from 7% to 11% to 0.2% to 4%. In vivo, we found that the variability between vendors is significantly reduced (p = 0.015) for all maps (T1, MTR, and MTsat) using the vendor-neutral sequence.

CONCLUSION

We conclude that vendor-neutral workflows are feasible and compatible with clinical MRI scanners. The significant reduction of inter-vendor variability using vendor-neutral sequences has important implications for qMRI research and for the reliability of multicenter clinical trials.

Whole-brain 3D mapping of oxygen metabolism using constrained quantitative BOLD

Quantitative BOLD (qBOLD) MRI permits noninvasive evaluation of hemodynamic and metabolic states of the brain by quantifying parametric maps of deoxygenated blood volume (DBV) and hemoglobin oxygen saturation level of venous blood (Y_v), and along with a measurement of cerebral blood flow (CBF), the cerebral metabolic rate of oxygen (CMRO₂). The method, thus should have potential to provide important information on many neurological disorders as well as normal cerebral physiology. One major challenge in qBOLD is to separate de-oxyhemoglobin’s contribution to R₂′ from other sources modulating the voxel signal, for instance, R₂, R₂′ from non-heme iron (R′_2,nh), and macroscopic magnetic field variations. Further, even with successful separation of the several confounders, it is still challenging to extract DBV and Y_v from the heme-originated R₂′ because of limited sensitivity of the qBOLD model. These issues, which have not been fully addressed in currently practiced qBOLD methods, have so far precluded 3D whole-brain implementation of qBOLD. Thus, the purpose of this work was to develop a new 3D MRI oximetry technique that enables robust qBOLD parameter mapping across the entire brain. To achieve this goal, we employed a rapid, R₂′-sensitive, steady-state 3D pulse sequence (termed ‘AUSFIDE’) for data acquisition, and implemented a prior-constrained qBOLD processing pipeline that exploits a plurality of preliminary parameters obtained via AUSFIDE, along with additionally measured cerebral venous blood volume. Numerical simulations and in vivo studies at 3 T were performed to evaluate the performance of the proposed, constrained qBOLD mapping in comparison to the parent qBOLD method. Measured parameters (Y_v, DBV, R′_2,nh, nonblood magnetic susceptibility) in ten healthy subjects demonstrate the expected contrast across brain territories, while yielding group-averages of 64.0 ± 2.3 % and 62.2 ± 3.1 % for Y_v and 2.8 ± 0.5 % and 1.8 ± 0.4 % for DBV in cortical gray and white matter, respectively. Given the Y_v measurements, additionally quantified CBF in seven of the ten study subjects enabled whole-brain 3D CMRO₂ mapping, yielding group averages of 134.2 ± 21.1 and 79.4 ± 12.6 µmol/100 g/min for cortical gray and white matter, in good agreement with literature values. The results suggest feasibility of the proposed method as a practical and reliable means for measuring neurometabolic parameters over an extended brain coverage.

A framework for validating open-source pulse sequences

Open-source pulse sequence programs offer an accessible and transparent approach to sequence development and deployment. However, a common framework for testing, documenting, and sharing open-source sequences is still needed to ensure sequence usability and repeatability. We propose and demonstrate such a framework by implementing two sequences, Inversion Recovery Spin Echo (IRSE) and Turbo Spin Echo (TSE), with PyPulseq, and testing them on a commercial 3 T scanner. We used the ACR and ISMRM/NIST phantoms for qualitative imaging and T₁/T₂ mapping, respectively. The qualitative sequences show good agreement with vendor-provided counterparts (mean Structural Similarity Index Measure (SSIM) = 0.810 for IRSE and 0.826 for TSE). Both sequences passed five out of the seven standard ACR tests, performing at similar levels to vendor counterparts. Compared to reference values, the coefficient of determination R² was 0.9946 for IRSE T₁ mapping and 0.9331 for TSE T₂ mapping. All sequences passed the scanner safety check for a 70 kg, 175 cm subject. The framework was demonstrated by packaging the sequences and sharing them on GitHub with data and documentation on the file generation, acquisition, reconstruction, and post-processing steps. The same sequences were tested at a second site using a 1.5 T scanner with the information shared. PDF templates for both sequence developers and users were created and filled.

MRI-derived porosity index is associated with whole-bone stiffness and mineral density in human cadaveric femora

Ultrashort echo time (UTE) magnetic resonance imaging (MRI) measures proton signals in cortical bone from two distinct water pools, bound water, or water that is tightly bound to bone matrix, and pore water, or water that is freely moving in the pore spaces in bone. By isolating the signal contribution from the pore water pool, UTE biomarkers can directly quantify cortical bone porosity in vivo. The Porosity Index (PI) is one non-invasive, clinically viable UTE-derived technique that has shown strong associations in the tibia with μCT porosity and other UTE measures of bone water. However, the efficacy of the PI biomarker has never been examined in the proximal femur, which is the site of the most catastrophic osteoporotic fractures. Additionally, the loads experienced during a sideways fall are complex and the femoral neck is difficult to image with UTE, so the usefulness of the PI in the femur was unknown. Therefore, the aim of this study was to examine the relationships between the PI measure in the proximal cortical shaft of human cadaveric femora specimens compared to (1) QCT-derived bone mineral density (BMD) and (2) whole bone stiffness obtained from mechanical testing mimicking a sideways fall. Fifteen fresh, frozen whole cadaveric femora specimens (age 72.1 ± 15.0 years old, 10 male, 5 female) were scanned on a clinical 3-T MRI using a dual-echo UTE sequence. Specimens were then scanned on a clinical CT scanner to measure volumetric BMD (vBMD) and then non-destructively mechanically tested in a sideways fall configuration. The PI in the cortical shaft demonstrated strong correlations with bone stiffness (r = -0.82, P = 0.0014), CT-derived vBMD (r = -0.64, P = 0.0149), and with average cortical thickness (r = -0.60, P = 0.0180). Furthermore, a hierarchical regression showed that PI was a strong predictor of bone stiffness which was independent of the other parameters. The findings from this study validate the MRI-derived porosity index as a useful measure of whole-bone mechanical integrity and stiffness.

Alternating unbalanced SSFP for 3D R 2 ' mapping of the human brain

PURPOSE

Measuring the transverse-relaxation rate R 2 ' provides valuable information in quantitative evaluation of tissue microstructure, for example, in terms of oxygenation levels. Here, we propose an alternating unbalanced SSFP pulse sequence for rapid whole-brain 3D R 2 ' mapping.

METHODS

Unlike currently practiced, spin echo-based R 2 ' measurement techniques, the proposed method alternates between SSFP-FID and SSFP-ECHO modes for rapid 3D encoding of transverse relaxation rates expressed as R₂ + R 2 ' and R₂ - R 2 ' . Z-shimming gradients embedded into multi-echo trains of each SSFP module are designed to achieve relative immunity to large-scale magnetic-field variations (ΔB₀ ). Appropriate models for the temporal evolution of the two groups of SSFP signals were constructed with ΔB₀ -induced modulations accounted for, leading to ΔB₀ -corrected estimation of R₂ , R 2 ' , and R 2 ∗ (= R₂ + R 2 ' ). Additionally, relative magnetic susceptibility (Δχ) maps were obtained by quantitative susceptibility mapping of the phase data. Numerical simulations were performed to optimize scan parameters, followed by in vivo studies at 3 T in 7 healthy subjects. Measured parameters were evaluated in six brain regions, and subjected to interparameter correlation analysis.

RESULTS

The resultant maps of R 2 ' and additionally derived R₂ , R 2 ∗ , and Δχ all demonstrated the expected contrast across brain territories (eg, deep brain structures versus cortex), with the measured values in good agreement with previous reports. Furthermore, regression analyses yielded strong linear relationships for the transverse relaxation parameters ( R 2 ' , R₂ , and R 2 ∗ ) against Δχ.

CONCLUSION

Results suggest feasibility of the proposed method as a practical and reliable means for measuring R 2 ' , R₂ , R 2 ∗ , and Δχ across the entire brain.

Venous cerebral blood volume mapping in the whole brain using venous-spin-labeled 3D turbo spin echo

PURPOSE

Venous cerebral blood volume (CBVv ) is a major contributor to BOLD contrast, and therefore is an important parameter for understanding the underlying mechanism. Here, we propose a velocity-selective venous spin labeling (VS-VSL)-prepared 3D turbo spin echo pulse sequence for whole-brain baseline CBVv mapping.

METHODS

Unlike previous CBVv measurement techniques that exploit the interrelationship between BOLD signals and CBVv , in the proposed VS-VSL technique both arterial blood and cerebrospinal fluid (CSF) signals were suppressed before the VS pulse train for exclusive labeling of venous blood, while a single-slab 3D turbo spin echo readout was used because of its relative immunity to magnetic field variations. Furthermore, two approximations were made to the VS-VSL signal model for simplified derivation of CBVv . In vivo studies were performed at 3T field strength in 8 healthy subjects. The performance of the proposed VS-VSL method in baseline CBVv estimation was first evaluated in comparison to the existing, hyperoxia-based method. Then, data were also acquired using VS-VSL under hypercapnic and hyperoxic gas breathing challenges for further validation of the technique.

RESULTS

The proposed technique yielded physiologically plausible baseline CBVv values, and when compared with the hyperoxia-based method, showed no statistical difference. Furthermore, data acquired using VS-VSL yielded average CBVv of 2.89%/1.78%, 3.71%/2.29%, and 2.88%/1.76% for baseline, hypercapnia, and hyperoxia, respectively, in gray/white matter regions. As expected, hyperoxia had negligible effect (P > .8), whereas hypercapnia demonstrated vasodilation (P << .01).

CONCLUSION

Upon further validation of the quantification model, the method is expected to have merit for 3D CBVv measurements across the entire brain.

Self-Navigated Three-Dimensional Ultrashort Echo Time Technique for Motion-Corrected Skull MRI

Ultrashort echo time (UTE) MRI is capable of detecting signals from protons with very short T₂ relaxation times, and thus has potential for skull-selective imaging as a radiation-free alternative to computed tomography. However, relatively long scan times make the technique vulnerable to artifacts from involuntary subject motion. Here, we developed a self-navigated, three-dimensional (3D) UTE pulse sequence, which builds on dual-RF, dual-echo UTE imaging, and a retrospective motion correction scheme for motion-resistant skull MRI. Full echo signals in the second readout serve as a self-navigator that yields a time-course of center of mass, allowing for adaptive determination of motion states. Furthermore, golden-means based k-space trajectory was employed to achieve a quasi-uniform distribution of sampling views on a spherical k-space surface for any subset of the entire data collected, thereby allowing reconstruction of low-resolution images pertaining to each motion state for subsequent estimation of rigid-motion parameters. Finally, the extracted trajectory of the head was used to make the whole k-space datasets motion-consistent, leading to motion-corrected, high-resolution images. Additionally, we posit that hardware-related k-space trajectory errors, if uncorrected, result in obscured bone contrast. Thus, a calibration scan was performed once to measure k-space encoding locations, subsequently used during image reconstruction of actual imaging data. In vivo studies were performed to evaluate the effectiveness of the proposed correction schemes in combination with approaches to accelerated bone-selective imaging. Results illustrating effective removal of motion artifacts and clear depiction of skull bone voxels suggest that the proposed method is robust to intermittent head motions during scanning.

Multi-site harmonization of 7 tesla MRI neuroimaging protocols

Increasing numbers of 7 T (7 T) magnetic resonance imaging (MRI) scanners are in research and clinical use. 7 T MRI can increase the scanning speed, spatial resolution and contrast-to-noise-ratio of many neuroimaging protocols, but technical challenges in implementation have been addressed in a variety of ways across sites. In order to facilitate multi-centre studies and ensure consistency of findings across sites, it is desirable that 7 T MRI sites implement common high-quality neuroimaging protocols that can accommodate different scanner models and software versions.

With the installation of several new 7 T MRI scanners in the United Kingdom, the UK7T Network was established with an aim to create a set of harmonized structural and functional neuroimaging sequences and protocols. The Network currently includes five sites, which use three different scanner platforms, provided by two different vendors.

Here we describe the harmonization of functional and anatomical imaging protocols across the three different scanner models, detailing the necessary changes to pulse sequences and reconstruction methods. The harmonized sequences are fully described, along with implementation details. Example datasets acquired from the same subject on all Network scanners are made available. Based on these data, an evaluation of the harmonization is provided. In addition, the implementation and validation of a common system calibration process is described.

Portable and platform-independent MR pulse sequence programs

PURPOSE

To introduce a new sequence description format for vendor-independent MR sequences that include all calculation logic portably. To introduce a new MRI sequence development approach which utilizes flexibly reusable modules.

METHODS

The proposed sequence description contains a sequence module hierarchy for loop and group logic, which is enhanced by a novel strategy for performing efficient parameter and pulse shape calculation. These calculations are powered by a flow graph structure. By using the flow graph, all calculations are performed with no redundancy and without requiring preprocessing. The generation of this interpretable structure is a separate step that combines MRI techniques while actively considering their context. The driver interface is slim and highly flexible through scripting support. The sequences do not require any vendor-specific compiling or processing step. A vendor-independent frontend for sequence configuration can be used. Tests that ensure physical feasibility of the sequence are integrated into the calculation logic.

RESULTS

The framework was used to define a set of standard sequences. Resulting images were compared to respective images acquired with sequences provided by the device manufacturer. Images were acquired using a standard commercial MRI system.

CONCLUSIONS

The approach produces configurable, vendor-independent sequences, whose configurability enables rapid prototyping. The transparent data structure simplifies the process of sharing reproducible sequences, modules, and techniques.

Acute Effects of Electronic Cigarette Aerosol Inhalation on Vascular Function Detected at Quantitative MRI

Background Previous studies showed that nicotinized electronic cigarettes (hereafter, e-cigarettes) elicit systemic oxidative stress and inflammation. However, the effect of the aerosol alone on endothelial function is not fully understood. Purpose To quantify surrogate markers of endothelial function in nonsmokers after inhalation of aerosol from nicotine-free e-cigarettes. Materials and Methods In this prospective study (from May to September 2018), nonsmokers underwent 3.0-T MRI before and after inhaling nicotine-free e-cigarette aerosol. Peripheral vascular reactivity to cuff-induced ischemia was quantified by temporally resolving blood flow velocity and oxygenation (SvO2) in superficial femoral artery and vein, respectively, along with artery luminal flow-mediated dilation. Precuff occlusion, resistivity index, baseline blood flow velocity, and SvO2 were evaluated. During reactive hyperemia, blood flow velocity yielded peak velocity, time to peak, and acceleration rate (hyperemic index); SvO2 yielded washout time of oxygen-depleted blood, rate of resaturation, and maximum SvO2 increase (overshoot). Cerebrovascular reactivity was assessed in the superior sagittal sinus, evaluating the breath-hold index. Central arterial stiffness was measured via aortic pulse wave velocity. Differences before versus after e-cigarette vaping were tested with Hotelling T2 test. Results Thirty-one healthy never-smokers (mean age, 24.3 years ± 4.3; 14 women) were evaluated. After e-cigarette vaping, resistivity index was higher (0.03 of 1.30 [2.3%]; P < .05), luminal flow-mediated dilation severely blunted (-3.2% of 9.4% [-34%]; P < .001), along with reduced peak velocity (-9.9 of 56.6 cm/sec [-17.5%]; P < .001), hyperemic index (-3.9 of 15.1 cm/sec2 [-25.8%]; P < .001), and delayed time to peak (2.1 of 7.1 sec [29.6%]; P = .005); baseline SvO2 was lower (-13 of 65 %HbO2 [-20%]; P < .001) and overshoot higher (10 of 19 %HbO2 [52.6%]; P < .001); and aortic pulse wave velocity marginally increased (0.19 of 6.05 m/sec [3%]; P = .05). Remaining parameters did not change after aerosol inhalation. Conclusion Inhaling nicotine-free electronic cigarette aerosol transiently impacted endothelial function in healthy nonsmokers. Further studies are needed to address the potentially adverse long-term effects on vascular health. © RSNA, 2019 Online supplemental material is available for this article.

coreMRI: A high-performance, publicly available MR simulation platform on the cloud

Introduction

A Cloud-ORiented Engine for advanced MRI simulations (coreMRI) is presented in this study. The aim was to develop the first advanced MR simulation platform delivered as a web service through an on-demand, scalable cloud-based and GPU-based infrastructure. We hypothesized that such an online MR simulation platform could be utilized as a virtual MRI scanner but also as a cloud-based, high-performance engine for advanced MR simulations in simulation-based quantitative MR (qMR) methods.

Methods and results

The simulation framework of coreMRI was based on the solution of the Bloch equations and utilized a ground-up-approach design based on the principles already published in the literature. The development of a front-end environment allowed the connection of the end-users to the GPU-equipped instances on the cloud. The coreMRI simulation platform was based on a modular design where individual modules (such as the Gadgetron reconstruction framework and a newly developed Pulse Sequence Designer) could be inserted in the main simulation framework. Different types and sources of pulse sequences and anatomical models were utilized in this study revealing the flexibility that the coreMRI simulation platform offers to the users. The performance and scalability of coreMRI were also examined on multi-GPU configurations on the cloud, showing that a multi-GPU computer on the cloud equipped with a newer generation of GPU cards could significantly mitigate the prolonged execution times that accompany more realistic MRI and qMR simulations.

Conclusions

coreMRI is available to the entire MR community, whereas its high performance and scalability allow its users to configure advanced MRI experiments without the constraints imposed by experimentation in a true MRI scanner (such as time constraint and limited availability of MR scanners), without upfront investment for purchasing advanced computer systems and without any user expertise on computer programming or MR physics. coreMRI is available to the users through the webpage https://www.coreMRI.org.

Spin-Scenario: A flexible scripting environment for realistic MR simulations

In this paper we present a new open source package, Spin-Scenario, aimed at developing an intuitive, flexible and unique scripting framework able to cover many aspects of simulations in both MR imaging and MR spectroscopy. For this purpose, we adopted the Liouville space model as the standard computing engine and let the consequent computational burden be afforded by parallel computing techniques. Benefitting from the powerful Lua scripting language, the pulse sequence programming syntax was specially designed to offer an extremely concise way of scripting. Moreover, the built-in dataflow graph based optimal control scheme enables an efficient optimization of shaped pulses or multiple cooperative pulses for real-life experiment evaluations. As the name states, the users are expected to be able to realize their creative ideas like a scenarist that creates a scenario script and looks at the spin actors acting accordingly. The validation of the framework was demonstrated with several examples within MR imaging and MR spectroscopy. Spin-Scenario is available for download at https://github.com/spin-scenario.

Rapid dual-RF, dual-echo, 3D ultrashort echo time craniofacial imaging: A feasibility study

PURPOSE

To develop a dual-radiofrequency (RF), dual-echo, 3D ultrashort echo-time (UTE) pulse sequence and bone-selective image reconstruction for rapid high-resolution craniofacial MRI.

METHODS

The proposed pulse sequence builds on recently introduced dual-RF UTE imaging. While yielding enhanced bone specificity by exploiting high sensitivity of short T₂ signals to variable RF pulse widths, the parent technique exacts a 2-fold scan time penalty relative to standard dual-echo UTE. In the proposed method, the parent sequence's dual-RF scheme was incorporated into dual-echo acquisitions while radial view angles are varied every pulse-to-pulse repetition period. The resulting 4 echoes (2 for each RF) were combined by view-sharing to construct 2 sets of k-space data sets, corresponding to short and long TEs, respectively, leading to a 2-fold increase in imaging efficiency. Furthermore, by exploiting the sparsity of bone signals in echo-difference images, acceleration was achieved by solving a bone-sparsity constrained image reconstruction problem. In vivo studies were performed to evaluate the effectiveness of the proposed acceleration approaches in comparison to the parent method.

RESULTS

The proposed technique achieves 1.1-mm isotropic skull imaging in 3 minutes without visual loss of image quality, compared to the parent technique (scan time = 12 minutes). Bone-specific images and corresponding 3D renderings of the skull were found to depict the expected craniofacial anatomy over the entire head.

CONCLUSION

The proposed method is able to achieve high-resolution volumetric craniofacial images in a clinically practical imaging time, and thus may prove useful as a potential alternative to computed tomography.

In vivo bone 31 P relaxation times and their implications on mineral quantification

PURPOSE

The intersubject variations in bone phosphorus-31 (³¹ P) T₁ and <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow><mml:msubsup><mml:mi>T</mml:mi> <mml:mn>2</mml:mn> <mml:mo>*</mml:mo></mml:msubsup> </mml:mrow> </mml:math> , as well as the implications on in vivo ³¹ P MRI-based bone mineral quantification, were investigated at 3T field strength.

METHODS

A technique that isolates the bone signal from the composite in vivo ³¹ P spectrum was first evaluated via simulation and experiments ex vivo and subsequently applied to measure the T₁ of bone ³¹ P collectively with a spectroscopic saturation recovery sequence in a group of healthy subjects aged 26 to 76 years. <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow><mml:msubsup><mml:mi>T</mml:mi> <mml:mn>2</mml:mn> <mml:mo>*</mml:mo></mml:msubsup> </mml:mrow> </mml:math> was derived from the bone signal linewidth. The density of bone ³¹ P was derived for all subjects from ³¹ P zero TE images acquired in the same scan session using the measured relaxation times. Test-retest experiments were also performed to evaluate repeatability of this in vivo MRI-based bone mineral quantification protocol.

RESULTS

The T₁ obtained in vivo using the proposed spectral separation method combined with saturation recovery sequence is 38.4 ± 1.5 s for the subjects studied. Average ³¹ P density found was 6.40 ± 0.58 mol/L (corresponding to 1072 ± 98 mg/cm³ mineral density), in good agreement with an earlier study in specimens from donors of similar age range. Neither the relaxation times (P = 0.18 for T₁ , P = 0.99 for <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow><mml:msubsup><mml:mi>T</mml:mi> <mml:mn>2</mml:mn> <mml:mo>*</mml:mo></mml:msubsup> </mml:mrow> </mml:math> ) nor ³¹ P density (P = 0.55) were found to correlate with subject age. Average coefficients of variation for the repeat study were 1.5%, 2.6%, and 4.4% for bone ³¹ P T₁ , <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow><mml:msubsup><mml:mi>T</mml:mi> <mml:mn>2</mml:mn> <mml:mo>*</mml:mo></mml:msubsup> </mml:mrow> </mml:math> , and density, respectively.

CONCLUSION

Neither ³¹ P T₁ nor <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow><mml:msubsup><mml:mi>T</mml:mi> <mml:mn>2</mml:mn> <mml:mo>*</mml:mo></mml:msubsup> </mml:mrow> </mml:math> varies significantly in healthy adults across a 50-year age range, therefore obviating the need for subject-specific measurements.

Interleaved quantitative BOLD: Combining extravascular R2' - and intravascular R2-measurements for estimation of deoxygenated blood volume and hemoglobin oxygen saturation

Quantitative BOLD (qBOLD), a non-invasive MRI method for assessment of hemodynamic and metabolic properties of the brain in the baseline state, provides spatial maps of deoxygenated blood volume fraction (DBV) and hemoglobin oxygen saturation (HbO₂) by means of an analytical model for the temporal evolution of free-induction-decay signals in the extravascular compartment. However, mutual coupling between DBV and HbO₂ in the signal model results in considerable estimation uncertainty precluding achievement of a unique set of solutions. To address this problem, we developed an interleaved qBOLD method (iqBOLD) that combines extravascular R₂' and intravascular R₂ mapping techniques so as to obtain prior knowledge for the two unknown parameters. To achieve these goals, asymmetric spin echo and velocity-selective spin-labeling (VSSL) modules were interleaved in a single pulse sequence. Prior to VSSL, arterial blood and CSF signals were suppressed to produce reliable estimates for cerebral venous blood volume fraction (CBV_v) as well as venous blood R₂ (to yield HbO₂). Parameter maps derived from the VSSL module were employed to initialize DBV and HbO₂ in the qBOLD processing. Numerical simulations and in vivo experiments at 3 T were performed to evaluate the performance of iqBOLD in comparison to the parent qBOLD method. Data obtained in eight healthy subjects yielded plausible values averaging 60.1 ± 3.3% for HbO₂ and 3.1 ± 0.5 and 2.0 ± 0.4% for DBV in gray and white matter, respectively. Furthermore, the results show that prior estimates of CBV_v and HbO₂ from the VSSL component enhance the solution stability in the qBOLD processing, and thus suggest the feasibility of iqBOLD as a promising alternative to the conventional technique for quantifying neurometabolic parameters.

TOPPE: A framework for rapid prototyping of MR pulse sequences

PURPOSE

To introduce a framework for rapid prototyping of MR pulse sequences.

METHODS

We propose a simple file format, called "TOPPE", for specifying all details of an MR imaging experiment, such as gradient and radiofrequency waveforms and the complete scan loop. In addition, we provide a TOPPE file "interpreter" for GE scanners, which is a binary executable that loads TOPPE files and executes the sequence on the scanner. We also provide MATLAB scripts for reading and writing TOPPE files and previewing the sequence prior to hardware execution. With this setup, the task of the pulse sequence programmer is reduced to creating TOPPE files, eliminating the need for hardware-specific programming. No sequence-specific compilation is necessary; the interpreter only needs to be compiled once (for every scanner software upgrade). We demonstrate TOPPE in three different applications: k-space mapping, non-Cartesian PRESTO whole-brain dynamic imaging, and myelin mapping in the brain using inhomogeneous magnetization transfer.

RESULTS

We successfully implemented and executed the three example sequences. By simply changing the various TOPPE sequence files, a single binary executable (interpreter) was used to execute several different sequences.

CONCLUSION

The TOPPE file format is a complete specification of an MR imaging experiment, based on arbitrary sequences of a (typically small) number of unique modules. Along with the GE interpreter, TOPPE comprises a modular and flexible platform for rapid prototyping of new pulse sequences. Magn Reson Med 79:3128-3134, 2018. © 2017 International Society for Magnetic Resonance in Medicine.

In vivo whole-blood T2 versus HbO2 calibration by modulating blood oxygenation level in the femoral vein through intermittent cuff occlusion

PURPOSE

To investigate the feasibility of estimating calibration constants (K and T_2o ) in vivo for converting whole-blood T₂ to blood hemoglobin oxygen saturation (HbO₂ ) according to the Luz-Meiboom model, 1/T2=1/T2o+K(1-HbO2)2, where K and T_2o are relaxivity and transverse relaxation time of fully saturated blood, respectively.

METHODS

A range of HbO₂ values was achieved in the superficial femoral vein with intermittent cuff occlusion in seven healthy adults (four males) to establish a calibration curve between blood T₂ and HbO₂ at 1.5T. HbO₂ was derived via MR susceptometry, a technique previously validated, and the transverse relaxation time was quantified with an optimized T₂ -prepared balanced steady-state free precession pulse sequence. To evaluate the accuracy of the in vivo calibration method, T₂ and HbO₂ were quantified in the superior sagittal sinus in six additional subjects and compared with susceptometry.

RESULTS

Two sets of gender-specific calibration constants were derived, one for each gender corresponding to hematocrits of 0.47 ± 0.02 for males and 0.38 ± 0.01 for females, yielding K/T_2o  = 41 Hz/260 ms and 26 Hz/280 ms, respectively. The in vivo calibration returned physiologically plausible superior sagittal sinus SvO₂ values (65 ± 5% HbO₂ ), and there was no significant difference between the results from the two methods (average difference -0.3% HbO₂ ).

CONCLUSION

The results show feasibility of performing in vivo calibration for converting whole-blood T₂ to HbO₂ . The proposed approach bypasses the involved and cumbersome processes associated with in vitro calibration. Magn Reson Med 79:2290-2296, 2018. © 2017 International Society for Magnetic Resonance in Medicine.

Simultaneous measurement of macro- and microvascular blood flow and oxygen saturation for quantification of muscle oxygen consumption

PURPOSE

To investigate the relationship between blood flow and oxygen consumption in skeletal muscle, a technique called "Velocity and Perfusion, Intravascular Venous Oxygen saturation and T2*" (vPIVOT) is presented. vPIVOT allows the quantification of feeding artery blood flow velocity, perfusion, draining vein oxygen saturation, and muscle T2*, all at 4-s temporal resolution. Together, the measurement of blood flow and oxygen extraction can yield muscle oxygen consumption ( V˙O2) via the Fick principle.

METHODS

In five subjects, vPIVOT-derived results were compared with those obtained from stand-alone sequences during separate ischemia-reperfusion paradigms to investigate the presence of measurement bias. Subsequently, in 10 subjects, vPIVOT was applied to assess muscle hemodynamics and V˙O2 following a bout of dynamic plantar flexion contractions.

RESULTS

From the ischemia-reperfusion paradigm, no significant differences were observed between data from vPIVOT and comparison sequences. After exercise, the macrovascular flow response reached a maximum 8 ± 3 s after relaxation; however, perfusion in the gastrocnemius muscle continued to rise for 101 ± 53 s. Peak V˙O2 calculated based on mass-normalized arterial blood flow or perfusion was 15.2 ± 6.7 mL O₂ /min/100 g or 6.0 ± 1.9 mL O₂ /min/100 g, respectively.

CONCLUSIONS

vPIVOT is a new method to measure blood flow and oxygen saturation, and therefore to quantify muscle oxygen consumption. Magn Reson Med 79:846-855, 2018. © 2017 International Society for Magnetic Resonance in Medicine.

High-speed whole-brain oximetry by golden-angle radial MRI

PURPOSE

To determine whole-brain cerebral metabolic rate of oxygen (CMRO₂ ), an improved imaging approach, based on radial encoding, termed radial OxFlow (rOxFlow), was developed to simultaneously quantify draining vein venous oxygen saturation (SvO₂ ) and total cerebral blood flow (tCBF).

METHODS

To evaluate the efficiency and precision of the rOxFlow sequence, 10 subjects were studied during a paradigm of repeated breath-holds with both rOxFlow and Cartesian OxFlow (cOxFlow) sequences. CMRO₂ was calculated at baseline from OxFlow-measured data assuming an arterial O₂ saturation of 97%, and the SvO₂ and tCBF breath-hold responses were quantified.

RESULTS

Average neurometabolic-vascular parameters across the 10 subjects for cOxFlow and rOxFlow were, respectively: SvO₂ (%) baseline: 64.6 ± 8.0 versus 64.2 ± 6.6; SvO₂ peak: 70.5 ± 8.5 versus 72.6 ± 5.4; tCBF (mL/min/100 g) baseline: 39.2 ± 3.8 versus 40.6 ± 8.0; tCBF peak: 53.2 ± 5.1 versus 56.1 ± 11.7; CMRO₂ (µmol O₂ /min/100 g) baseline: 111.5 ± 26.8 versus 120.1 ± 19.6. The above measures were not significantly different between sequences (P > 0.05).

CONCLUSION

There was good agreement between the two methods in terms of the physiological responses measured. Comparing the two, rOxFlow provided higher temporal resolution and greater flexibility for reconstruction while maintaining high SNR. Magn Reson Med 79:217-223, 2018. © 2017 International Society for Magnetic Resonance in Medicine.

Multiplexed MRI methods for rapid estimation of global cerebral metabolic rate of oxygen consumption

The global cerebral metabolic rate of oxygen (CMRO₂), which reflects metabolic activity of the brain under various physiologic conditions, can be quantified using a method, referred to as 'OxFlow', which simultaneously measures hemoglobin oxygen saturation in a draining vein (Y_v) and total cerebral blood flow (tCBF). Conventional OxFlow (Conv-OxFlow) entails four interleaves incorporated in a single pulse sequence - two for phase-contrast based measurement of tCBF in the supplying arteries of the neck, and two to measure the intra- to extravascular phase difference in the superior sagittal sinus to derive Y_v [Jain et al., JCBFM 2010]. However, this approach limits achievable temporal resolution thus precluding capture of rapid changes of brain metabolic states such as the response to apneic stimuli. Here, we developed a time-efficient, multiplexed OxFlow method and evaluated its potential for measuring dynamic alterations in global CMRO₂ during a breath-hold challenge. Two different implementations of multiplexed OxFlow were investigated: 1) simultaneous-echo-refocusing based OxFlow (SER-OxFlow) and 2) simultaneous-multi-slice imaging-based dual-band OxFlow (DB-OxFlow). The two sequences were implemented on 3T scanners (Siemens TIM Trio and Prisma) and their performance was evaluated in comparison to Conv-OxFlow in ten healthy subjects for baseline CMRO₂ quantification. Comparison of measured parameters (Y_v, tCBF, CMRO₂) revealed no significant bias of SER-OxFlow and DB-OxFlow, with respect to the reference Conv-OxFlow while improving temporal resolution two-fold (12.5 versus 25s). Further acceleration shortened scan time to 8 and 6s for SER and DB-OxFlow, respectively, for time-resolved CMRO₂ measurement. The two sequences were able of capturing smooth transitions of Y_v, tCBF, and CMRO₂ over the time course consisting of 30s of normal breathing, 30s of volitional apnea, and 90s of recovery. While both SER- and DB-OxFlow techniques provide significantly improved temporal resolution (by a factor of 3 - 4 relative to Conv-OxFlow), DB-OxFlow was found to be superior for the study of short physiologic stimuli.

Fast Realistic MRI Simulations Based on Generalized Multi-Pool Exchange Tissue Model

We present MRiLab, a new comprehensive simulator for large-scale realistic MRI simulations on a regular PC equipped with a modern graphical processing unit (GPU). MRiLab combines realistic tissue modeling with numerical virtualization of an MRI system and scanning experiment to enable assessment of a broad range of MRI approaches including advanced quantitative MRI methods inferring microstructure on a sub-voxel level. A flexible representation of tissue microstructure is achieved in MRiLab by employing the generalized tissue model with multiple exchanging water and macromolecular proton pools rather than a system of independent proton isochromats typically used in previous simulators. The computational power needed for simulation of the biologically relevant tissue models in large 3D objects is gained using parallelized execution on GPU. Three simulated and one actual MRI experiments were performed to demonstrate the ability of the new simulator to accommodate a wide variety of voxel composition scenarios and demonstrate detrimental effects of simplified treatment of tissue micro-organization adapted in previous simulators. GPU execution allowed  ∼ 200× improvement in computational speed over standard CPU. As a cross-platform, open-source, extensible environment for customizing virtual MRI experiments, MRiLab streamlines the development of new MRI methods, especially those aiming to infer quantitatively tissue composition and microstructure.

Measurement of skeletal muscle perfusion dynamics with pseudo-continuous arterial spin labeling (pCASL): Assessment of relative labeling efficiency at rest and during hyperemia, and comparison to pulsed arterial spin labeling (PASL)

PURPOSE

To compare calf skeletal muscle perfusion measured with pulsed arterial spin labeling (PASL) and pseudo-continuous arterial spin labeling (pCASL) methods, and to assess the variability of pCASL labeling efficiency in the popliteal artery throughout an ischemia-reperfusion paradigm.

MATERIALS AND METHODS

At 3T, relative pCASL labeling efficiency was experimentally assessed in five subjects by measuring the signal intensity of blood in the popliteal artery just distal to the labeling plane immediately following pCASL labeling or control preparation pulses, or without any preparation pulses throughout separate ischemia-reperfusion paradigms. The relative label and control efficiencies were determined during baseline, hyperemia, and recovery. In a separate cohort of 10 subjects, pCASL and PASL sequences were used to measure reactive hyperemia perfusion dynamics.

RESULTS

Calculated pCASL labeling and control efficiencies did not differ significantly between baseline and hyperemia or between hyperemia and recovery periods. Relative to the average baseline, pCASL label efficiency was 2 ± 9% lower during hyperemia. Perfusion dynamics measured with pCASL and PASL did not differ significantly (P > 0.05). Average leg muscle peak perfusion was 47 ± 20 mL/min/100g or 50 ± 12 mL/min/100g, and time to peak perfusion was 25 ± 3 seconds and 25 ± 7 seconds from pCASL and PASL data, respectively. Differences of further metrics parameterizing the perfusion time course were not significant between pCASL and PASL measurements (P > 0.05).

CONCLUSION

No change in pCASL labeling efficiency was detected despite the almost 10-fold increase in average blood flow velocity in the popliteal artery. pCASL and PASL provide precise and consistent measurement of skeletal muscle reactive hyperemia perfusion dynamics. J. MAGN. RESON. IMAGING 2016;44:929-939.

Rapid High-resolution, Self-registered, Dual Lumen-contrast MRI Method for Vessel-wall Assessment in Peripheral Artery Disease:: A Preliminary Investigation

RATIONALE AND OBJECTIVES

Contrast-enhanced angiographic evaluation by magnetic resonance imaging (MRI) and computed tomography (CT) is the reference standard for assessing peripheral artery disease (PAD). However, because PAD and diabetes often coexist, the prevalence of renal insufficiency is a major challenge to contrast-based angiography. The objective of this work is to describe and demonstrate a new application of three-dimensional double-echo steady-state (3D DESS) as a noncontrast vascular MRI method for evaluating peripheral atherosclerosis at 3 Tesla (3T).

MATERIALS AND METHODS

A water-selective 3D DESS pulse sequence was designed to simultaneously collect two steady-state free-precession signals (free induction decay and Echo) yielding "black blood" (BB) and "gray blood" (GB) images. For completeness Bloch equation, simulations were performed to characterize DESS signals of various tissues including blood at different velocities and to assess two healthy subjects for the purpose of pulse sequence optimization. Exploratory studies were performed as an add-on protocol to an existing study involving patients with PAD. To evaluate the method's specificity for detecting calcification, images from select patients were compared against CT angiography.

RESULTS

Simulations agreed qualitatively with in vivo images supporting DESS' potential for generating distinct lumen contrast (GB vs BB). Lesions representing calcium were easily identifiable on the basis of signal void occurring on both image types and were confirmed by CT angiography. Further, BB allowed visualization of stent restenosis, and data suggest its ability to visualize acute thrombus by virtue of T2 weighting.

CONCLUSION

Preliminary investigation and results suggest noncontrast 3D DESS to have the potential to improve diagnosis of PAD patients by providing detailed structural assessment of vessel-wall architecture.

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 2.2% (P=0.18, two-tailed t-test), 3.4% (P=0.08, two-tailed t-test), and 2.0% (P=0.56, two-tailed t-test) for SvO2, CBF, and CMRO2, respectively. F-OxFlow's potential to monitor dynamic changes in SvO2, CBF, and CMRO2 is illustrated in a paradigm of volitional apnea applied to five of the study subjects. The sequence captured an average increase in SvO2, CBF, and CMRO2 of 10.1±2.5%, 43.2±9.2%, and 7.1±2.2%, respectively, in good agreement with literature values. The method may therefore be suited for monitoring alterations in CBF and SvO2 in response to neurovascular stimuli.

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 = 30.2 ± 0.7 years), young smokers (YS: N = 39 mean age 32.1 ± 0.7 years), older non-smokers (ONS: N = 45, mean age = 57.8 ± 0.6 years), and older smokers (OS: N = 40, mean age = 56.3 ± 0.6 years), all without overt cardiovascular disease. Vascular reactivity was evaluated following cuff-induced hyperemia via time-resolved blood flow velocity and oxygenation (SvO2) in the femoral artery and vein, respectively. SvO2 dynamics yielded washout time (time to minimum SvO2), resaturation rate (upslope) and maximum change from baseline (overshoot). Arterial parameters included pulse ratio (PR), hyperemic index (HI) and duration of hyperemia (TFF). Pulse-wave velocity (PWV) was assessed in aortic arch, thoracoabdominal aorta and iliofemoral arteries. Ultrasound-based carotid intimal-medial thickness (IMT) and brachial flow-mediated dilation were measured for comparison.

RESULTS

Age and smoking status were independent for all parameters. Smokers had reduced upslope (-28.4%, P < 0.001), increased washout time (+15.3%, P < 0.01), and reduced HI (-19.5%, P < 0.01). Among non-smokers, older subjects had lower upslope (-22.7%, P < 0.01) and overshoot (-29.4%, P < 0.01), elevated baseline pulse ratio (+14.9%, P < 0.01), central and peripheral PWV (all P < 0.05). Relative to YNS, YS had lower upslope (-23.6%, P < 0.01) and longer washout time (13.5%, P < 0.05). Relative to ONS, OS had lower upslope (-33.0%, P < 0.01). IMT was greater in ONS than in YNS (+45.6%, P < 0.001), and also in YS compared to YNS (+14.7%, P < 0.05).

CONCLUSIONS

Results suggest CMR biomarkers of endothelial function to be sensitive to age and smoking independent of each other.

Combined measurement of perfusion, venous oxygen saturation, and skeletal muscle T2* during reactive hyperemia in the leg

BACKGROUND

The function of the peripheral microvascular may be interrogated by measuring perfusion, tissue oxygen concentration, or venous oxygen saturation (SvO2) recovery dynamics following induced ischemia. The purpose of this work is to develop and evaluate a magnetic resonance (MR) technique for simultaneous measurement of perfusion, SvO2, and skeletal muscle T2*.

METHODS

Perfusion, Intravascular Venous Oxygen saturation, and T2* (PIVOT) is comprised of interleaved pulsed arterial spin labeling (PASL) and multi-echo gradient-recalled echo (GRE) sequences. During the PASL post-labeling delay, images are acquired with a multi-echo GRE to quantify SvO2 and T2* at a downstream slice location. Thus time-courses of perfusion, SvO2, and T2* are quantified simultaneously within a single scan. The new sequence was compared to separately measured PASL or multi-echo GRE data during reactive hyperemia in five young healthy subjects. To explore the impairment present in peripheral artery disease patients, five patients were evaluated with PIVOT.

RESULTS

Comparison of PIVOT-derived data to the standard techniques shows that there was no significant bias in any of the time-course-derived metrics. Preliminary data show that PAD patients exhibited alterations in perfusion, SvO2, and T2* time-courses compared to young healthy subjects.

CONCLUSION

Simultaneous quantification of perfusion, SvO2, and T2* is possible with PIVOT. Kinetics of perfusion, SvO2, and T2* during reactive hyperemia may help to provide insight into the function of the peripheral microvasculature in patients with PAD.

Spectrally selective 3D TSE imaging of phosphocreatine in the human calf muscle at 3 T

Quantitative information about concentrations of several metabolites in human skeletal muscle can be obtained through localized (31)P magnetic resonance spectroscopy methods. However, these methods have shortcomings: long acquisition times, limited volume coverage, and coarse resolution. Significantly higher spatial and temporal resolution of imaging of single metabolites can be achieved through spectrally selective three-dimensional imaging methods. This study reports the implementation of a three-dimensional spectrally selective turbo spin-echo sequence, on a 3T clinical system, to map the concentration of phosphocreatine in the human calf muscle with significantly increased spatial resolution and in a clinically feasible scan time. Absolute phosphocreatine quantification was performed with the use of external phantoms after relaxation and flip angle correction of the turbo spin-echo voxel signal. The mean ± standard deviation of the phosphocreatine concentration measured in five healthy volunteers was 29.4 ± 2.5 mM with signal-to-noise ratio of 14:1 and voxel size of 0.52 mL.

Time-resolved absolute velocity quantification with projections

Quantitative information on time-resolved blood velocity along the femoral/popliteal artery can provide clinical information on peripheral arterial disease and complement MR angiography as not all stenoses are hemodynamically significant. The key disadvantages of the most widely used approach to time-resolve pulsatile blood flow by cardiac-gated velocity-encoded gradient-echo imaging are gating errors and long acquisition time. Here, we demonstrate a rapid nontriggered method that quantifies absolute velocity on the basis of phase difference between successive velocity-encoded projections after selectively removing the background static tissue signal via a reference image. The tissue signal from the reference image's center k-space line is isolated by masking out the vessels in the image domain. The performance of the technique, in terms of reproducibility and agreement with results obtained with conventional phase contrast-MRI was evaluated at 3 T field strength with a variable-flow rate phantom and in vivo of the triphasic velocity waveforms at several segments along the femoral and popliteal arteries. Additionally, time-resolved flow velocity was quantified in five healthy subjects and compared against gated phase contrast-MRI results. To illustrate clinical feasibility, the proposed method was shown to be able to identify hemodynamic abnormalities and impaired reactivity in a diseased femoral artery. For both phantom and in vivo studies, velocity measurements were within 1.5 cm/s, and the coefficient of variation was less than 5% in an in vivo reproducibility study. In five healthy subjects, the average differences in mean peak velocities and their temporal locations were within 1 cm/s and 10 ms compared to gated phase contrast-MRI. In conclusion, the proposed method provides temporally resolved arterial velocity with a temporal resolution of 20 ms with minimal post processing.

Evaluation of cuff-induced ischemia in the lower extremity by magnetic resonance oximetry

OBJECTIVES

The aim of this study was to evaluate vascular function in the lower extremities by making direct time-course measurement of oxygen saturation in the femoral/popliteal arteries and veins during cuff-induced reactive hyperemia with magnetic resonance imaging-based oximetry.

BACKGROUND

Magnetic resonance imaging-based oximetry is a new calibration-free technique taking advantage of the paramagnetic nature of blood that depends on the volume fraction of deoxyhemoglobin in red blood cells.

METHODS

We compared post-occlusive blood oxygenation time-course of femoral/popliteal vessels in: 1) young healthy subjects (YH) (n = 10; mean ankle-brachial index [ABI] 1.0 +/- 0.1, mean age 30 +/- 7 years); 2) peripheral arterial disease (PAD) patients (n = 12; mean ABI 0.6 +/- 0.1, mean age 71 +/- 9 years); and 3) age-matched healthy control subjects (AHC) (n = 8; mean ABI 1.1 +/- 0.1, mean age 68 +/- 9 years). Blood oxygenation was quantified at 3.0-T field strength with a field mapping pulse sequence yielding the magnetic susceptibility difference between blood in the vessels and surrounding muscle tissue from which the intravascular blood oxygen saturation is computed as %HbO(2).

RESULTS

Significantly longer washout time (42 +/- 16 s vs. 14 +/- 4 s; p < 0.0001) and lower upslope (0.60 +/- 0.20 %HbO(2)/s vs. 1.32 +/- 0.41 %HbO(2)/s; p = 0.0008) were observed for PAD patients compared with healthy subjects (YH and AHC combined). Furthermore, greater overshoot was observed in YH than in AHC (21 +/- 8 %HbO(2) vs. 10 +/- 5 %HbO(2); p = 0.0116).

CONCLUSIONS

Post-occlusive transient changes in venous blood oxygenation might provide a new measure of vascular competence, which was found to be reduced in subjects with abnormal ABI, manifesting in prolonged recovery during the early phase of hyperemia.

Accuracy and precision of MR blood oximetry based on the long paramagnetic cylinder approximation of large vessels

An accurate noninvasive method to measure the hemoglobin oxygen saturation (%HbO(2)) of deep-lying vessels without catheterization would have many clinical applications. Quantitative MRI may be the only imaging modality that can address this difficult and important problem. MR susceptometry-based oximetry for measuring blood oxygen saturation in large vessels models the vessel as a long paramagnetic cylinder immersed in an external field. The intravascular magnetic susceptibility relative to surrounding muscle tissue is a function of oxygenated hemoglobin (HbO(2)) and can be quantified with a field-mapping pulse sequence. In this work, the method's accuracy and precision was investigated theoretically on the basis of an analytical expression for the arbitrarily oriented cylinder, as well as experimentally in phantoms and in vivo in the femoral artery and vein at 3T field strength. Errors resulting from vessel tilt, noncircularity of vessel cross-section, and induced magnetic field gradients were evaluated and methods for correction were designed and implemented. Hemoglobin saturation was measured at successive vessel segments, differing in geometry, such as eccentricity and vessel tilt, but constant blood oxygen saturation levels, as a means to evaluate measurement consistency. The average standard error and coefficient of variation of measurements in phantoms were <2% with tilt correction alone, in agreement with theory, suggesting that high accuracy and reproducibility can be achieved while ignoring noncircularity for tilt angles up to about 30 degrees . In vivo, repeated measurements of %HbO(2) in the femoral vessels yielded a coefficient of variation of less than 5%. In conclusion, the data suggest that %HbO(2) can be measured reproducibly in vivo in large vessels of the peripheral circulation on the basis of the paramagnetic cylinder approximation of the incremental field.

Retrospective correction for induced magnetic field inhomogeneity in measurements of large-vessel hemoglobin oxygen saturation by MR susceptometry

MR susceptometry-based blood oximetry relies on phase mapping to measure the difference in magnetic susceptibility between intravascular blood and surrounding tissue. The main source of error in MR susceptometry is the static field inhomogeneity caused by an interface between air and tissue or between adjacent tissue types. High-pass filtering has previously been used in conjunction with shimming to reduce the effect of low spatial-frequency modulations of the phase caused by large-scale induced magnetic fields. We demonstrate that high-pass filtering is not optimum for MR susceptometry because the results are sensitive to filter size. We propose an alternative method that acquires data without scanner-implemented default shimming, and fits, after appropriate weighting and masking, the static field inhomogeneity to a second-order polynomial. Compared to shimming the retrospective correction technique improved agreement between hemoglobin saturations measured in different segments of a vessel (femoral versus popliteal artery and vein) from three standard errors to less than one.