On the noise in "augmented T1-weighted steady state magnetic resonance imaging".

Recently, Ye and colleagues proposed a method for "augmented T1-weighted imaging" (aT1 W). The key operation is a complex division of gradient-echo (GRE) images obtained with different flip angles. Ye and colleagues provide an equation for the standard deviation of the obtained aT1 W signal. Here, we show that this equation leads to wrong values of the standard deviation of such an aT1 W signal. This is demonstrated by Monte Carlo simulations. The derivation of the equation provided by Ye and colleagues is shown to be erroneous. The error consists of a wrong handling of random variables and their standard deviations and of the wrong assumption of correlated noise in independently acquired GRE images. Instead, the probability distribution obtained with the aT1 W-method should have been carefully analyzed, perhaps on the basis of previous literature on ratio distributions and their normal approximations.

Analysis of accelerated 4D flow MRI in the murine aorta by radial acquisition and compressed sensing reconstruction.

Preclinical 4D flow MRI remains challenging and is restricted for parallel imaging acceleration due to the limited number of available receive channels. A radial acquisition with combined parallel imaging and temporal compressed sensing reconstruction was implemented to achieve accelerated preclinical 4D flow MRI. In order to increase the accuracy of the measured velocities, a quantitative evaluation of different temporal regularization weights for the compressed sensing reconstruction based on velocity instead of magnitude data is performed. A 3D radial retrospectively triggered phase contrast sequence with a combined parallel imaging and compressed sensing reconstruction with temporal regularization was developed. It was validated in a phantom and in vivo (C57BL/6 J mice), against an established fully sampled Cartesian sequence. Different undersampling factors (USFs [12, 15, 20, 30, 60]) were evaluated, and the effect of undersampling was analyzed in detail for magnitude and velocity data. Temporal regularization weights λ were evaluated for different USFs. Acceleration factors of up to 20 compared with full Nyquist sampling were achieved. The peak flow differences compared with the Cartesian measurement were the following: USF 12, 3.38%; USF 15, 4.68%; USF 20, 0.95%. The combination of 3D radial center-out trajectories and compressed sensing reconstruction is robust against motion and flow artifacts and can significantly reduce measurement time to 30 min at a resolution of 180 µm3 . Concisely, radial acquisition with combined compressed sensing and parallel imaging proved to be an excellent method for analyzing complex flow patterns in mice.

Dynamic 2D and 3D mapping of hyperpolarized pyruvate to lactate conversion in vivo with efficient multi-echo balanced steady-state free precession at 3 T.

The aim of this study was to acquire the transient MRI signal of hyperpolarized tracers and their metabolites efficiently, for which specialized imaging sequences are required. In this work, a multi-echo balanced steady-state free precession (me-bSSFP) sequence with Iterative Decomposition with Echo Asymmetry and Least squares estimation (IDEAL) reconstruction was implemented on a clinical 3 T positron-emission tomography/MRI system for fast 2D and 3D metabolic imaging. Simulations were conducted to obtain signal-efficient sequence protocols for the metabolic imaging of hyperpolarized biomolecules. The sequence was applied in vitro and in vivo for probing the enzymatic exchange of hyperpolarized [1-13 C]pyruvate and [1-13 C]lactate. Chemical shift resolution was achieved using a least-square, iterative chemical species separation algorithm in the reconstruction. In vitro, metabolic conversion rate measurements from me-bSSFP were compared with NMR spectroscopy and free induction decay-chemical shift imaging (FID-CSI). In vivo, a rat MAT-B-III tumor model was imaged with me-bSSFP and FID-CSI. 2D metabolite maps of [1-13 C]pyruvate and [1-13 C]lactate acquired with me-bSSFP showed the same spatial distributions as FID-CSI. The pyruvate-lactate conversion kinetics measured with me-bSSFP and NMR corresponded well. Dynamic 2D metabolite mapping with me-bSSFP enabled the acquisition of up to 420 time frames (scan time: 180-350 ms/frame) before the hyperpolarized [1-13 C]pyruvate was relaxed below noise level. 3D metabolite mapping with a large field of view (180 × 180 × 48 mm3 ) and high spatial resolution (5.6 × 5.6 × 2 mm3 ) was conducted with me-bSSFP in a scan time of 8.2 seconds. It was concluded that Me-bSSFP improves the spatial and temporal resolution for metabolic imaging of hyperpolarized [1-13 C]pyruvate and [1-13 C]lactate compared with either of the FID-CSI or EPSI methods reported at 3 T, providing new possibilities for clinical and preclinical applications.

Comparative Analyses of the Self-Sealing Mechanisms in Leaves of Delosperma cooperi and Delosperma ecklonis (Aizoaceae).

Within the Aizoaceae, the genus Delosperma exhibits a vast diversification colonizing various ecological niches in South-Africa and showing evolutionary adaptations to dry habitats that might include rapid self-sealing. Leaves of Delosperma react to external damage by the bending or contraction of the entire leaf until wound edges are brought into contact. A study of leaf morphology and anatomy, biomechanics of entire leaves and individual tissues and self-sealing kinematics after a ring incision under low and high relative humidity (RH) was carried out comparing the closely related species Delosperma cooperi and Delosperma ecklonis, which are indigenous to semi-arid highlands and regions with an oceanic climate, respectively. For both species, the absolute contractions of the examined leaf segments ("apex", "incision", "base") were more pronounced at low RH levels. Independent of the given RH level, the absolute contractions within the incision region of D. cooperi were significantly higher than in all other segments of this species and of D. ecklonis. The more pronounced contraction of D. cooperi leaves was linked mainly to the elastic properties of the central vascular strand, which is approximately twice as flexible as that of D. ecklonis leaves.

Structural and functional imaging of large and opaque plant specimens.

Three- and four-dimensional imaging techniques are a prerequisite for spatially resolving the form-structure-function relationships in plants. However, choosing the right imaging method is a difficult and time-consuming process as the imaging principles, advantages and limitations, as well as the appropriate fields of application first need to be compared. The present study aims to provide an overview of three imaging methods that allow for imaging opaque, large and thick (>5 mm, up to several centimeters), hierarchically organized plant samples that can have complex geometries. We compare light microscopy of serial thin sections followed by 3D reconstruction (LMTS3D) as an optical imaging technique, micro-computed tomography (µ-CT) based on ionizing radiation, and magnetic resonance imaging (MRI) which uses the natural magnetic properties of a sample for image acquisition. We discuss the most important imaging principles, advantages, and limitations, and suggest fields of application for each imaging technique (LMTS, µ-CT, and MRI) with regard to static (at a given time; 3D) and dynamic (at different time points; quasi 4D) structural and functional plant imaging.

On the application of balanced steady-state free precession to MR microscopy.

OBJECTIVE: The applicability of the balanced steady-state free precession (bSSFP) sequence to the field of MR microscopy was investigated, since the potentially high SNR makes bSSFP attractive. However, particularly at ultra-high magnetic fields, a number of constraints emerge: the frequency sensitivity of the bSSFP signal, the duty cycle of the imaging gradients, and the intrinsic diffusion attenuation of the steady state due to the imaging gradients. MATERIALS AND METHODS: Optimization of the bSSFP sequence was performed on three imaging systems (7 T and 9.4 T) suited for MR microscopy. Since biological samples are often imaged in the very proximity of materials from sample containers/holder or devices such as electrodes, several microscopy phantoms representing such circumstances were fabricated and examined with 3D bSSFP. RESULTS: Artifact-free microscopic bSSFP images could be obtained with voxel sizes down to 16 µm × 16 µm × 78 µm and with an SNR gain of 25% over standard gradient echo images. CONCLUSION: With appropriate choice of phantom materials, optimization of the flip angle to the diffusion-attenuated steady state and protocols considering duty-cycle limitations, bSSFP can be a valuable tool in MR microscopy.

Pulseq: A rapid and hardware-independent pulse sequence prototyping framework.

PURPOSE: Implementing new magnetic resonance experiments, or sequences, often involves extensive programming on vendor-specific platforms, which can be time consuming and costly. This situation is exacerbated when research sequences need to be implemented on several platforms simultaneously, for example, at different field strengths. This work presents an alternative programming environment that is hardware-independent, open-source, and promotes rapid sequence prototyping. METHODS: A novel file format is described to efficiently store the hardware events and timing information required for an MR pulse sequence. Platform-dependent interpreter modules convert the file to appropriate instructions to run the sequence on MR hardware. Sequences can be designed in high-level languages, such as MATLAB, or with a graphical interface. Spin physics simulation tools are incorporated into the framework, allowing for comparison between real and virtual experiments. RESULTS: Minimal effort is required to implement relatively advanced sequences using the tools provided. Sequences are executed on three different MR platforms, demonstrating the flexibility of the approach. CONCLUSION: A high-level, flexible and hardware-independent approach to sequence programming is ideal for the rapid development of new sequences. The framework is currently not suitable for large patient studies or routine scanning although this would be possible with deeper integration into existing workflows. Magn Reson Med 77:1544-1552, 2017. © 2016 International Society for Magnetic Resonance in Medicine.

Initial investigation of glucose metabolism in mouse brain using enriched 17 O-glucose and dynamic 17 O-MRS.

In this initial work, the in vivo degradation of 17 O-labeled glucose was studied during cellular glycolysis. To monitor cellular glucose metabolism, direct 17 O-magnetic resonance spectroscopy (MRS) was used in the mouse brain at 9.4 T. Non-localized spectra were acquired with a custom-built transmit/receive (Tx/Rx) two-turn surface coil and a free induction decay (FID) sequence with a short TR of 5.4 ms. The dynamics of labeled oxygen in the anomeric 1-OH and 6-CH2 OH groups was detected using a Hankel-Lanczos singular value decomposition (HLSVD) algorithm for water suppression. Time-resolved 17 O-MRS (temporal resolution, 42/10.5 s) was performed in 10 anesthetized (1.25% isoflurane) mice after injection of a 2.2 M solution containing 2.5 mg/g body weight of differently labeled 17 O-glucose dissolved in 0.9% physiological saline. From a pharmacokinetic model fit of the H217 O concentration-time course, a mean apparent cerebral metabolic rate of 17 O-labeled glucose in mouse brain of CMRGlc  = 0.07 ± 0.02 µmol/g/min was extracted, which is of the same order of magnitude as a literature value of 0.26 ± 0.06 µmol/g/min reported by 18 F-fluorodeoxyglucose (18 F-FDG) positron emission tomography (PET). In addition, we studied the chemical exchange kinetics of aqueous solutions of 17 O-labeled glucose at the C1 and C6 positions with dynamic 17 O-MRS. In conclusion, the results of the exchange and in vivo experiments demonstrate that the C6-17 OH label in the 6-CH2 OH group is transformed only glycolytically by the enzyme enolase into the metabolic end-product H217 O, whereas C1-17 OH ends up in water via direct hydrolysis as well as glycolysis. Therefore, dynamic 17 O-MRS of highly labeled 17 O-glucose could provide a valuable non-radioactive alternative to FDG PET in order to investigate glucose metabolism.

A comparison of Lenz lenses and LC resonators for NMR signal enhancement.

High signal-to-noise ratio (SNR) of the NMR signal has always been a key target that drives massive research effort in many fields. Among several parameters, a high filling factor of the MR coil has proven to boost the SNR. In case of small-volume samples, a high filling factor and thus a high SNR can be achieved through miniaturizing the MR coil. However, under certain circumstances, this can be impractical. In this paper, we present an extensive theoretical and experimental investigation of the inductively coupled LC resonator and the magnetic Lenz lens as two candidate approaches that can enhance the SNR in such circumstances. The results demonstrate that the narrow-band LC resonator is superior in terms of SNR, while the non-tuned nature of the Lenz lens makes it preferable in broadband applications.

Revealing signal from noisy (19) F MR images by chemical shift artifact correction.

PURPOSE: The correction of chemical shift artifacts in MR images of fluorinated molecules with a multi-resonance spectrum is investigated. The goal is to find a deconvolution method which is capable of correcting the artifact, thereby enhancing signal-to-noise ratio (SNR) and revealing signal that vanishes in the noise in the original image. THEORY AND METHODS: Simulations for inspecting the influence of MRI acquisition parameters on the possibility to correct the artifact are performed. Artifact correction is studied on the spectrum of a perfluorocarbon compound by means of deconvolution of complex images with a measured or an optimized point spread function and by using lasso regularization. RESULTS: Distinct parameter settings for image acquisition are identified that should be avoided for successful deconvolution. With in vitro and in vivo images it is shown that the SNR of the corrected image can be increased significantly by 20-50% by a regularized deconvolution of the artifact image and (19) F signal can be revealed from noise. CONCLUSION: By deconvolution, SNR can be enhanced as compared to an image which only exploits the strongest peak of the spectrum. Thus, the limit of detection of the (19) F signal can be lowered by exciting all resonances and by means of correcting the chemical shift artifact.

Intrinsic diffusion sensitivity of the balanced steady-state free precession (bSSFP) imaging sequence.

The purpose of this work was to analyze the intrinsic diffusion sensitivity of the balanced steady-state free precession (bSSFP) imaging sequence, meaning the observation of diffusion-induced attenuation of the bSSFP steady-state signal due to the imaging gradients. Although these diffusion effects are usually neglected for most clinical gradient systems, such strong gradient systems are employed for high resolution imaging of small animals or MR Microscopy. The impact on the bSSFP signal of the imaging gradients characterized by their b-values was analyzed with simulations and experiments at a 7T animal scanner using a gradient system with maximum gradient amplitude of approx. 700 mT/m. It was found that the readout gradients have a stronger impact on the attenuation than the phase encoding gradients. Also, as the PE gradients are varying with each repetition interval, the diffusion effects induce strong modulations of the bSSFP signal over the sequence repetition cycles depending on the phase encoding gradient table. It is shown that a signal gain can be obtained through a change of flip angle as a new optimal flip angle maximizing the signal can be defined. The dependency of the diffusion effects on relaxation times and b-values were explored with simulations. The attenuation increases with T2. In conclusion, diffusion attenuation of the bSSFP signal becomes significant for high resolution imaging voxel size (roughly < 100 µm) of long T2 substances.

A continuous-flow, high-throughput, high-pressure parahydrogen converter for hyperpolarization in a clinical setting.

Pure parahydrogen (pH(2) ) is the prerequisite for optimal pH(2) -based hyperpolarization experiments, promising approaches to access the hidden orders of magnitude of MR signals. pH(2) production on-site in medical research centers is vital for the proliferation of these technologies in the life sciences. However, previously suggested designs do not meet our requirements for safety or production performance (flow rate, pressure or enrichment). In this article, we present the safety concept, design and installation of a pH(2) converter, operated in a clinical setting. The apparatus produces a continuous flow of four standard liters per minute of ≈98% enriched pH(2) at a pressure maximum of 50 bar. The entire production cycle, including cleaning and cooling to 25 K, takes less than 5 h, only ≈45 min of which are required for actual pH(2) conversion. A fast and simple quantification procedure is described. The lifetimes of pH(2) in a glass vial and aluminum storage cylinder are measured to be T(1C) (glass vial) =822 ± 29 min and T(1C) (Al cylinder) =129 ± 36 days, thus providing sufficiently long storage intervals and allowing the application of pH(2) on demand. A dependence of line width on pH(2) enrichment is observed. As examples, (1) H hyperpolarization of pyridine and (13) C hyperpolarization of hydroxyethylpropionate are presented.

Fourier transform temporal diffusion spectroscopy.

Temporal diffusion spectroscopy (TDS) currently uses the oscillating gradient spin echo (OGSE) experiment to measure the spectral density of translational velocity autocorrelation at single frequencies. Due to timing restrictions imposed by the transverse relaxation, the frequency selectivity and the sampling density of OGSE are limited, especially at low frequencies. We propose to overcome this problem by adopting the principles of Fourier transform spectroscopy. The new method of Fourier transform TDS (FTDS) uses two broadband gradient waveforms with different relative delays to make the spin echo attenuation sensitive to a broad range of diffusion frequencies with different harmonic modulations and calculates the spectrum by discrete Fourier transform. The method was validated by a measurement of diffusion spectra in highly restrictive tissues of a celery stalk and provided results consistent with OGSE, however, on a denser frequency grid.

Use of simulated annealing for the design of multiple repetition time balanced steady-state free precession imaging.

Balanced steady-state free precession is an ultrafast sequence with high signal-to-noise efficiency, but it also generates a strong fat signal which can mask important features. One method of fat suppression is to modify the balanced steady-state free precession spectrum using multiple repetition times to create a wide stopband over the fat frequency. However, with three or more pulse repetition times, the number of parameters creates a vast search space with many local minima of a cost function. We report on the initial results of using simulated annealing to find optimal sequences for two applications of multiple-pulse repetition time balanced steady-state free precession: positive contrast imaging and fat suppression.

Gradient echo imaging.

Magnetic resonance imaging (MRI) based on gradient echoes is used in a wide variety of imaging techniques and clinical applications. Gradient echo sequences form the basis for an essential group of imaging methods that find widespread use in clinical practice, particularly when fast imaging is important, as for example in cardiac MRI or contrast-enhanced MR angiography. However, the term "gradient echo sequence" is somewhat unspecific, as even images acquired with the most common sequences employing the gradient echo for data acquisition can significantly differ in signal, contrast, artifact behavior, and sensitivity to, eg, flow. This is due to the different use of sequence timing and basic sequence building blocks such as spoiler gradients or specific radiofrequency (RF) pulse phase patterns. In this article the basic principles of gradient echo formation compared to spin echo imaging are reviewed and the properties of gradient echo imaging in its simplest form (TR ≫ T(2)) are described. Further, the most common three variants of fast gradient echo sequences (TR < T(2)), namely, unbalanced gradient echo, RF spoiled gradient echo, and balanced steady state free precession; are discussed. For each gradient echo sequence type, examples of applications exploiting the specific properties of the individual technique are presented.

Dental MRI: imaging of soft and solid components without ionizing radiation.

PURPOSE: To evaluate the ability of conventional and ultra-short or zero echo time MRI for imaging of soft and solid dental components in and ex vivo. MATERIALS AND METHODS: Turbo spin echo (TSE), ultra-short echo time (UTE), and zero echo time (ZTE) MRI were performed on extracted (human and equine) teeth and in vivo using whole-body and small-bore MR systems at 3 T, 7T, and 9.4T, respectively. RESULTS: At an isotropic resolution of (600 µm)(3) , strong signal of soft-tissue, e.g., mucosa and nerves with excellent contrast was achieved using TSE at 3T in vivo. No signal, though, was obtained from solid components, e.g., teeth (due to short T(2) ). In contrast, dentin, cementum as well as enamel of extracted teeth were readily depicted using UTE and ZTE at a resolution of ≈ (150 µm)(3) at 7T and 9.4T. In particular, ZTE provided higher signal in enamel. CONCLUSION: As an alternative to X-ray based methods like cone-beam computed tomography (CT) or conventional CT, the presented results demonstrate the potential of ZTE and UTE MRI as a radiation-free imaging modality, delivering contrast of soft and solid components at the same time.

Diverging prefrontal cortex fiber connection routes to the subthalamic nucleus and the mesencephalic ventral tegmentum investigated with long range (normative) and short range (ex-vivo high resolution) 7T DTI.

Uncertainties concerning anatomy and function of cortico-subcortical projections have arisen during the recent years. A clear distinction between cortico-subthalamic (hyperdirect) and cortico-tegmental projections (superolateral medial forebrain bundle, slMFB) so far is elusive. Deep Brain Stimulation (DBS) of the slMFB (for major depression, MD and obsessive compulsive disorders, OCD) has on the one hand been interpreted as actually involving limbic (prefrontal) hyperdirect pathways. On the other hand slMFB's stimulation region in the mesencephalic ventral tegmentum is said to impact on other structures too, going beyond the antidepressant (or anti OCD) efficacy of sole modulation of the cortico-tegmental reward-associated pathways. We have here used a normative diffusion MRT template (HCP, n = 80) for long-range tractography and augmented this dataset with ex-vivo high resolution data (n = 1) in a stochastic brain space. We compared this data with histological information and used the high resolution ex-vivo data set to scrutinize the mesencephalic tegmentum for small fiber pathways present. Our work resolves an existing ambiguity between slMFB and prefrontal hyperdirect pathways which-for the first time-are described as co-existent. DBS of the slMFB does not appear to modulate prefrontal hyperdirect cortico-subthalamic but rather cortico-tegmental projections. Smaller fiber structures in the target region-as far as they can be discerned-appear not to be involved in slMFB DBS. Our work enfeebles previous anatomical criticism and strengthens the position of the slMFB DBS target for its use in MD and OCD.

Increasing spoiling efficiency in RF-spoiled gradient echo sequences by averaging of RF phase-cycle-adapted k-spaces.

A method is presented that improves the effectiveness of RF-spoiling whenever an image consists of the averaging of several identical single acquisitions. Using this method, it becomes possible to reduce the necessary moment of the spoiler gradient by a factor equal to the number of averages. The idea is to perform the collection of k-space lines such that the averaging takes over a part of the spoiling process. The number of sequence cycles played out between two acquisitions of a certain k-space line is adjusted based on both the number of total averages of this line and the phase-cycling pattern of the RF-pulse train of a RF-spoiled gradient echo sequence. In this way, ghost artifacts visible in the single images add to zero in the averaged image while the depiction of the object experiences normal averaging with enhanced signal-to-noise ratio.

Three-directional acceleration phase mapping of myocardial function.

An optimized acceleration encoded phase contrast method termed "acceleration phase mapping" for the assessment of regional myocardial function is presented. Based on an efficient gradient waveform design using two-sided encoding for in vivo three-directional acceleration mapping, echo and repetition times TE = 12-14 ms and TR = 15-17 ms for low accelerations sensitivity aenc = 5-8 m/s(2) were achieved. In addition to phantom validation, the technique was applied in a study with 10 healthy volunteers at 1.5T and 3T to evaluate its feasibility to assess regional myocardial acceleration at 1.5T and 3T. Results of the acceleration measurements were compared with the temporal derivative of myocardial velocities from three-directional velocity encoded standard phase contrast MRI in the same volunteers. The feasibility to assess myocardial acceleration along the radial, circumferential, and longitudinal direction of the left ventricle was demonstrated. Despite improved signal-to-noise-ratio at 3T (34% increase compared with 1.5T), image quality with respect to susceptibility artifacts was better 1.5T compared with 3T. Analysis of global and regional left ventricular acceleration showed characteristic patterns of systolic and diastolic acceleration and deceleration. Comparisons of directly measured and derived myocardial acceleration dynamics over the cardiac cycle revealed good correlation (r = 0.45-0.68, P < 0.01) between both methods.

Morphology and Anatomy of Branch-Branch Junctions in Opuntia ficus-indica and Cylindropuntia bigelovii: A Comparative Study Supported by Mechanical Tissue Quantification.

The Opuntioideae include iconic cacti whose lateral branch-branch junctions are intriguing objects from a mechanical viewpoint. We have compared Opuntia ficus-indica, which has stable branch connections, with Cylindropuntia bigelovii, whose side branches abscise under slight mechanical stress. To determine the underlying structures and mechanical characteristics of these stable versus shedding cacti junctions, we conducted magnetic resonance imaging, morphometric and anatomical analyses of the branches and tensile tests of individual tissues. The comparison revealed differences in geometry, shape and material properties as follows: (i) a more pronounced tapering of the cross-sectional area towards the junctions supports the abscission of young branches of C. bigelovii. (ii) Older branches of O. ficus-indica form, initially around the branch-branch junctions, collar-shaped periderm tissue. This secondary coverage mechanically stiffens the dermal tissue, giving a threefold increase in strength and a tenfold increase in the elastic modulus compared with the epidermis. (iii) An approximately 200-fold higher elastic modulus of the vascular bundles of O. ficus-indica is a prerequisite for the stable junction of its young branches. Our results provide, for both biological and engineered materials systems, important insights into the geometric characteristics and mechanical properties of branching joints that are either stable or easily detachable.