Advances in spiral fMRI: A high-resolution dataset

We present data collected for the research article "Advances in Spiral fMRI: A High-resolution Study with Single-shot Acquisition" (Kasper et al. 2022). All data was acquired on a 7T ultra-high field MR system (Philips Achieva), equipped with a concurrent magnetic field monitoring setup based on 16 NMR probes. For task-based fMRI, a visual quarterfield stimulation paradigm was employed, alongside physiological monitoring via peripheral recordings. This data collection contains different datasets pertaining to different purposes: (1) Measured magnetic field dynamics (k0, spiral k-space trajectories, 2nd order spherical harmonics, concomitant fields) during ultra-high field fMRI sessions from six subjects, as well as concurrent temperature curves of the gradient coil, to explore MR system and subject-induced variability of field fluctuations and assess the impact of potential correction methods. (2) MR Raw Data, i.e., coil and concurrent encoding magnetic field (trajectory) data, of a single subject, as well as nominal spiral gradient waveforms, precomputed B0 and coil sensitivity maps, to enable testing of alternative image reconstruction approaches for spiral fMRI data. (3) Reconstructed image time series of the same subject alongside behavioral and physiological logfiles, to reproduce the fMRI preprocessing and analysis, as well as figures presented in the research article related to this article, using the published analysis code repository. All data is provided in standardized formats for the respective research area. In particular, ISMRMRD (HDF5) is used to store raw coil data and spiral trajectories, as well as measured field dynamics. Likewise, the NIfTI format is used for all imaging data (anatomical MRI and spiral fMRI, B0 and coil sensitivity maps).

T-Hex: Tilted hexagonal grids for rapid 3D imaging

PURPOSE

The purpose of this work is to devise and demonstrate an encoding strategy for 3D MRI that reconciles high speed with flexible segmentation, uniform k-space density, and benign T 2 ∗ effects.

METHODS

Fast sampling of a 3D k-space is typically accomplished by 2D readouts per shot using EPI trains or spiral readouts. Tilted hexagonal (T-Hex) sampling is a way of acquiring more k-space volume per excitation while maintaining uniform sampling density and a smooth T 2 ∗ filter. The k-space volume covered per shot is controlled by the tilting angle. Image reconstruction is performed with a 3D extension of the iterative SENSE approach, incorporating actual field dynamics and static off-resonance. T-Hex imaging is compared with established 3D schemes in terms of speed and noise performance.

RESULTS

Tilted hexagonal acquisition is found to achieve greater imaging speed than known alternatives, particularly in combination with spiral trajectories. The interplay of the proposed 3D trajectories, array detection, and off-resonance is successfully addressed by iterative inversion of the full signal model. Enhanced coverage per shot is of greatest utility for high speed in an intermediate resolution regime of 1 to 4 mm. T-Hex EPI combines the benefits of extended coverage per shot with increased robustness against off-resonance effects.

CONCLUSION

Sampling of tilted hexagonal grids is a feasible means of gaining 3D imaging speed with near-optimal SNR efficiency and benign depiction properties. It is a particularly promising technique for time-resolved applications such as fMRI.

A Reconfigurable Platform for Magnetic Resonance Data Acquisition and Processing

Developments in magnetic resonance imaging (MRI) in the last decades show a trend towards a growing number of array coils and an increasing use of a wide variety of sensors. Associated cabling and safety issues have been addressed by moving data acquisition closer to the coil. However, with the increasing number of radio-frequency (RF) channels and trend towards higher acquisition duty-cycles, the data amount is growing, which poses challenges for throughput and data handling. As it is becoming a limitation, early compression and preprocessing is becoming ever more important. Additionally, sensors deliver diverse data, which require distinct and often low-latency processing for run-time updates of scanner operation. To address these challenges, we propose the transition to reconfigurable hardware with an application tailored assembly of interfaces and real-time processing resources. We present an integrated solution based on a system-on-chip (SoC), which offers sufficient throughput and hardware-based parallel processing power for very challenging applications. It is equipped with fiber-optical modules serving as versatile interfaces for modular systems with in-field operation. We demonstrate the utility of the platform on the example of concurrent imaging and field sensing with hardware-based coil compression and trajectory extraction. The preprocessed data are then used in expanded encoding model based image reconstruction of single-shot and segmented spirals as used in time-series and anatomical imaging respectively.

An In-Bore Receiver for Magnetic Resonance Imaging

In magnetic resonance imaging, the use of array detection and the number of detector elements have seen a steady increase over the past two decades. As a result, per-channel analog connection via long coaxial cable, as commonly used, poses an increasing challenge in terms of handling, safety, and coupling among cables. This situation is exacerbated when complementary recording of radiofrequency transmission or NMR-based magnetic field sensing further add to channel counts. A generic way of addressing this trend is the transition to digital signal transmission, enabled by digitization and first-level digital processing close to detector coils and sensors in the magnet bore. The foremost challenge that comes with this approach is to achieve high dynamic range, linearity, and phase stability despite interference by strong static, audiofrequency, and radiofrequency fields. The present work reports implementation of a 16-channel in-bore receiver, performing signal digitization and processing with subsequent optical transmission over fiber. Along with descriptions of the system design and construction, performance evaluation is reported. The resulting device is fully MRI compatible providing practically equal performance and signal quality compared to state-of-the-art RF digitizers operating outside the magnet. Its use is demonstrated by examples of head imaging and magnetic field recording.

High-resolution short-T2 MRI using a high-performance gradient

PURPOSE

To achieve high resolution in imaging of short-T₂ materials and tissues by using a high-performance human-sized gradient insert with strength up to 200 mT/m and 100% duty cycle.

METHODS

Dedicated short-T₂ methodology and hardware are used, such as the pointwise encoding time reduction with radial acquisition (PETRA) technique with modulated excitation pulses, optimized radio-frequency hardware, and a high-performance gradient insert. A theoretical analysis of actual spatial resolution and SNR is provided to support the choice of scan parameters and interpretation of the results. Imaging is performed in resolution phantoms, animal specimen, and human volunteers at both conventional and maximum available gradient strengths and compared using image subtraction.

RESULTS

Calculations suggest that increasing gradient strength beyond conventional values considerably improves both actual resolution and SNR efficiency in short-T₂ imaging. Resolution improvements are confirmed in all investigated samples, in particular 2 mm slots were resolved in a hard-plastic plate with T₂ ≈ 10 μs and in vivo musculoskeletal images were acquired at isotropic 200 μm resolution. Expected improvements in signal yield are realized in fine structures benefitting from high resolution but to less extent in regions of low contrast where decay-related blurring leads to signal overlap between neighboring locations.

CONCLUSION

Strong gradients with high duty cycle enable short-T₂ imaging at unprecedentedly high resolution, holding the potential for improving MRI of, eg, bone, tendon, lung, or teeth. Moreover, it allows direct access of tissues with T₂ of tens of microseconds such as myelin or collagen.

Gradient Response Harvesting for Continuous System Characterization During MR Sequences

MRI gradient systems are required to generate magnetic field gradient waveforms with very high fidelity. This is commonly implemented by gradient system calibration and pre-emphasis. However, a number of mechanisms, particularly thermal changes, cause variation in the gradient response over time, which cannot be addressed by calibration approaches. To overcome this limitation, we present a novel method termed gradient response harvesting, where the gradient response is continuously characterized during the course of a normal MR sequence. Snippets of field measurements are repeatedly acquired during an MR sequence, and from these multiple field measurements and the known nominal MR sequence gradients, the gradient response and gradient/field offsets are calculated. The calculation is implemented in a model-based and a model-free variant. The method is demonstrated for EPI with high gradient duty-cycle, where the continuous gradient characterization is used to obtain k-space trajectory estimates that are employed in the subsequent image reconstruction. During the course of the MR sequence, changes in both the envelope and the phase of the gradient response functions were observed, including shifts of mechanical resonances. The gradient response changes were also reflected in the calculated uninterrupted gradient waveforms and thus in the k-space trajectories. Using the updated encoding information in the image reconstruction removed ghosting artifacts, that otherwise impaired the image quality. We introduced the concept of gradient response harvesting and demonstrated its feasibility. The obtained gradient response functions may be used for quality assurance/preventive maintenance, real-time adaptation of gradient pre-emphasis or to calculate uninterrupted gradient field evolutions.

Automatic Resonance Frequency Retuning of Stretchable Liquid Metal Receive Coil for Magnetic Resonance Imaging

Stretchable magnetic resonance (MR) receive coils show shifts in their resonance frequency when stretched. An in-field receiver measures the frequency response of a stretchable coil. The receiver and coil are designed to operate at 128 MHz for a 3T MR scanner. Based on the measured frequency response, we are able to detect the changes of the resonance frequency of the coil. We show a proportional-integral-derivative controller that tracks the changes in resonance frequency and retunes the stretchable coil. The settling time of the control loop is less than 3.8ms. The retuning system reduces the loss in signal-to-noise ratio of phantom images from 1.6 dB to 0.3 dB, when the coil is stretched by 40% and the coil is retuned to 128 MHz.

On the Bending and Stretching of Liquid Metal Receive Coils for Magnetic Resonance Imaging

The eGaIn coil on neoprene demonstrated in this paper presents a stretchable radio frequency receive coil for magnetic resonance imaging (MRI). The coil with dimensions [Formula: see text] is tuned to resonate at 128 MHz for 3 T MRI. We investigate the effect of stretching (up to 40% strain) and bending (50 mm radius of curvature) of the coil on the coil's resistance and resonance frequency. Measurements and simulations show a decrease in resonance frequency of 2.5 MHz per 10% strain. The higher resistivity of liquid metal compared to copper reduces the SNR of MRI scans by 34%; therefore, a tradeoff between flexibility and performance remains. Nevertheless, we have successfully performed MRI scans with the liquid metal coil.

Multi-Rate Acquisition for Dead Time Reduction in Magnetic Resonance Receivers: Application to Imaging With Zero Echo Time

For magnetic resonance imaging of tissues with very short transverse relaxation times, radio-frequency excitation must be immediately followed by data acquisition with fast spatial encoding. In zero-echo-time (ZTE) imaging, excitation is performed while the readout gradient is already on, causing data loss due to an initial dead time. One major dead time contribution is the settling time of the filters involved in signal down-conversion. In this paper, a multi-rate acquisition scheme is proposed to minimize dead time due to filtering. Short filters and high output bandwidth are used initially to minimize settling time. With increasing time since the signal onset, longer filters with better frequency selectivity enable stronger signal decimation. In this way, significant dead time reduction is accomplished at only a slight increase in the overall amount of output data. Multi-rate acquisition was implemented with a two-stage filter cascade in a digital receiver based on a field-programmable gate array. In ZTE imaging in a phantom and in vivo, dead time reduction by multi-rate acquisition is shown to improve image quality and expand the feasible bandwidth while increasing the amount of data collected by only a few percent.

A Fully Integrated Dual-Channel On-Coil CMOS Receiver for Array Coils in 1.5-10.5 T MRI

Magnetic resonance imaging (MRI) is among the most important medical imaging modalities. Coil arrays and receivers with high channel counts (16 and more) have to be deployed to obtain the image quality and acquisition speed required by modern clinical protocols. In this paper, we report the theoretical analysis, the system-level design, and the circuit implementation of the first receiver IC (RXIC) for clinical MRI fully integrated in a modern CMOS technology. The dual-channel RXIC sits directly on the sensor coil, thus eliminating any RF cable otherwise required to transport the information out of the magnetic field. The first stage LNA was implemented using a noise-canceling architecture providing a highly reflective input used to decouple the individual channels of the array. Digitization is performed directly on-chip at base-band by means of a delta-sigma modulator, allowing the subsequent optical transmission of data. The presented receiver, implemented in a CMOS technology, is compatible with MRI scanners up to . It reaches sub- noise figure for MRI units and features a dynamic range up to at a power consumption below per channel, with an area occupation of . Mounted on a small-sized printed circuit board (PCB), the receiver IC has been employed in a commercial MRI scanner to acquire in-vivo images matching the quality of traditional systems, demonstrating the first step toward multichannel wearable MRI array coils.

Adsorbed Eutectic GaIn Structures on a Neoprene Foam for Stretchable MRI Coils

Stretchable conductors based on eutectic gallium-indium (eGaIn) alloy are patterned on a polychloroprene substrate (neoprene foam) using stencil printing. By tuning the amount of eGaIn on the neoprene substrate, different strain-sensitivity of electrical resistance is achieved. Conductors with a layer of eGaIn, which adsorbs to the walls of 60-100 µm wide neoprene cells, change their electrical resistance for 5% at 100% strain. When the amount of eGaIn is increased, the cells are filled with eGaIn and the strain-sensitivity of the electrical resistance rises to 300% at 100% strain. The developed conductors are patterned as stretchable on-body coils for receiving magnetic signals in a clinical magnetic resonance imaging setup. First images with a stretchable coil are acquired on an orange and compared to the images that are recorded using a rigid copper coil of the same size.

A wearable bluetooth LE sensor for patient monitoring during MRI scans

This paper presents a working prototype of a wearable patient monitoring device capable of recording the heart rate, blood oxygen saturation, surface temperature and humidity during an magnetic resonance imaging (MRI) experiment. The measured values are transmitted via Bluetooth low energy (LE) and displayed in real time on a smartphone on the outside of the MRI room. During 7 MRI image acquisitions of at least 1 min and a total duration of 25 min no Bluetooth data packets were lost. The raw measurements of the light intensity for the photoplethysmogram based heart rate measurement shows an increased noise floor by 50LSB (least significant bit) during the MRI operation, whereas the temperature and humidity readings are unaffected. The device itself creates a magnetic resonance (MR) signal loss with a radius of 14 mm around the device surface and shows no significant increase in image noise of an acquired MRI image due to its radio frequency activity. This enables continuous and unobtrusive patient monitoring during MRI scans.

Symmetrically biased T/R switches for NMR and MRI with microsecond dead time

For direct NMR detection and imaging of compounds with very short coherence life times the dead time between radio-frequency (RF) pulse and reception of the free induction decay (FID) is a major limiting factor. It is typically dominated by the transient and recovery times of currently available transmit-receive (T/R) switches and amplification chains. A novel PIN diode-based T/R switch topology is introduced allowing for fast switching by high bias transient currents but nevertheless producing a very low video leakage signal and insertion loss (0.5dB). The low transient spike level in conjunction with the high isolation (75dB) prevent saturation of the preamplifier entirely which consequently does not require time for recovery. Switching between transmission and reception is demonstrated within less than 1μs in bench tests as well as in acquisitions of FIDs and zero echo time (ZTE) images with bandwidths up to 500kHz at 7T. Thereby the 2kW switch exhibited a rise-time of 350ns (10-99%) producing however a total video leakage of below 20mV peak-to-peak and less than -89dBm in-band. The achieved switching time renders the RF pulse itself the dominant contribution to the dead time in which a coherence cannot be observed, thus making pulsed NMR experiments almost time-optimal even for compounds with very short signal life times.

Using sex pheromone trapping to explore threats to wheat from Hessian fly (Diptera: Cecidomyiidae) in the Upper Great Plains

Before embarking on the 5-10 yr effort it can take to transfer plant resistance (R) genes to adapted crop cultivars, a question must be asked: is the pest a sufficient threat to warrant this effort? We used the recently discovered female-produced sex pheromone of the Hessian fly, Mayetiola destructor (Say) (Diptera: Cecidomyiidae),to explore this question for populations in the Upper Great Plains. Methods for pheromone trapping were established and trapping data were used to explore geographic distribution, phenology, and density. The pheromone lure remained attractive for up to 10 d and only attracted male Hessian flies. Traps placed within the crop canopy caught flies but traps placed above the crop canopy did not. Hessian flies were trapped throughout North Dakota starting in the spring and continuing through the summer and autumn. Densities were low in the spring but increased greatly during the early part of the summer, with peak adult emergence taking place at a time (July/August) when spring wheat was being harvested and winter wheat had not yet been planted. In the autumn, adults were found at a time when winter wheat seedlings are growing. The discovery of flies on Conservation Reserve Program land supports the idea that pasture grasses serve as alternate hosts. We conclude that the Hessian fly is a risk to wheat in the Upper Great Plains and predict that global warming and the increasing cultivation of winter wheat will add to this risk.

A reproductive fitness cost associated with Hessian fly (Diptera: Cecidomyiidae) virulence to wheat's H gene-mediated resistance

We studied whether adaptation of the Hessian fly, Mayetiola destructor (Say) (Diptera: Cecidomyiidae), to plant resistance incurs fitness costs. In this gene-for-gene interaction, adaptation to a single H resistance gene occurs via loss of a single effector encoded by an Avirulence gene. By losing the effector, the adapted larva now survives on the H gene plant, presumably because it evades the plant's H gene-mediated surveillance system. The problem is the Hessian fly larva needs its effectors for colonization. Thus, for adapted individuals, there may be a cost for losing the effector, with this then creating a trade-off between surviving on H-resistant plants and growing on plants that lack H genes. In two different tests, we used wheat lacking H genes to compare the survival and growth of a nonadapted strain to two H-adapted strains. The two adapted strains differed in that one had been selected for adaptation to H9, whereas the other strain had been selected for adaptation to H13. Tests showed that two H-adapted strains were similar to the nonadapted strain in egg-to-adult survival but that they differed in producing adults with smaller wings. By using known relationships between wing length and reproductive potential, we found that losses in wing length underestimate losses in reproductive potential. For example, H9- and H13-adapted females had 9 and 3% wing losses, respectively, but they were estimated to have 32 and 12% losses in egg production. Fitness costs of adaptation will be investigated further via selection experiments comparing Avirulence allele frequencies for Hessian fly populations exposed or not exposed to H genes.

The use of X-terminals as clinical workstations

The Medical Computer Facility at the Fox Chase Cancer Center has installed X-terminals in patient examination rooms and at nursing stations for clinical data access by physicians and nurses. The X-terminals are connected to UNIX operating system RISC processors via Ethernet. The RISC processors communicate with databases on a minicomputer cluster. Simultaneous presentation of textual (e.g., pathology and radiology reports) and graphical (e.g., clinical laboratory results) clinical data is provided under X-Windows. CT and MRI images can also be displayed in windows. Our experiences implementing X-terminal clinical workstations in a production environment will be discussed.

Myo-Inositol transport in Klebsiella aerogenes. scyllo-Inositol, a non-metabolizable substrate for the study of the myo-inositol transport system

1. Scyllo-Inositol is transported against a concentration gradient by Klebsiella aerogenes, but is not metabolized. 2. The apparent KT of scyllo-inositol is 0.05 X 10(-3) M while that of myo-inositol is 0.23 X 10(-3) M. The V values are respectively 32 and 12 nmol min(-1) mg cells(-1) (dry weight). 3. Both cyclitols bind to the same carrier, since typical competitive inhibition kinetics are observed. 4. Neither phosphoenolpyruvate phosphotransferase nor a periplasmic binding protein seems to be involved in the scyllo-inositol transport system. 5. The induction of the transport system is not repressed by malate, furmarate, citrate, succinate or pyruvate; however, acetate represses the induction. The activity of the transport system is increased when the growth medium is supplemented with adenosine 3':5'-monophosphate.