gr-MRI: A software package for magnetic resonance imaging using software defined radios

Bringing MRI to low- and middle-income countries: Directions, challenges and potential solutions

The global disparity of magnetic resonance imaging (MRI) is a major challenge, with many low- and middle-income countries (LMICs) experiencing limited access to MRI. The reasons for limited access are technological, economic and social. With the advancement of MRI technology, we explore why these challenges still prevail, highlighting the importance of MRI as the epidemiology of disease changes in LMICs. In this paper, we establish a framework to develop MRI with these challenges in mind and discuss the different aspects of MRI development, including maximising image quality using cost-effective components, integrating local technology and infrastructure and implementing sustainable practices. We also highlight the current solutions-including teleradiology, artificial intelligence and doctor and patient education strategies-and how these might be further improved to achieve greater access to MRI.

Open-source magnetic resonance imaging: Improving access, science, and education through global collaboration

Open-source practices and resources in magnetic resonance imaging (MRI) have increased substantially in recent years. This trend started with software and data being published open-source and, more recently, open-source hardware designs have become increasingly available. These developments towards a culture of sharing and establishing nonexclusive global collaborations have already improved the reproducibility and reusability of code and designs, while providing a more inclusive approach, especially for low-income settings. Community-driven standardization and documentation efforts are further strengthening and expanding these milestones. The future of open-source MRI is bright and we have just started to discover its full collaborative potential. In this review we will give an overview of open-source software and open-source hardware projects in human MRI research.

MaRGE: A graphical environment for MaRCoS

The open-source console MaRCoS, which stands for "Magnetic Resonance Control System", combines hardware, firmware and software elements for integral control of Magnetic Resonance Imaging (MRI) scanners. Previous developments have focused on making the system robust and reliable, rather than on users, who have been somewhat overlooked. This work describes a Graphical User Interface (GUI) designed for intuitive control of MaRCoS, as well as compatibility with clinical environments. The GUI is based on an arrangement of tabs and a renewed Application Program Interface (API). Compared to the previous versions, the MaRGE package ("MaRCoS Graphical Environment") includes new functionalities such as the possibility to export images to standard DICOM formats, create and manage clinical protocols, or display and process image reconstructions, among other features conceived to simplify the operation of MRI scanners. All prototypes in our facilities are commanded by MaRCoS and operated with the new GUI. Here we report on its performance on an experimental 0.2 T scanner designed for hard-tissue, as well as a 72 mT portable scanner presently installed in the radiology department of a large hospital. The possibility to customize, adapt and streamline processes has substantially improved our workflows and overall experience.

Tackling SNR at low-field: a review of hardware approaches for point-of-care systems

OBJECTIVE

To review the major hardware components of low-field point-of-care MRI systems which affect the overall sensitivity.

METHODS

Designs for the following components are reviewed and analyzed: magnet, RF coils, transmit/receive switches, preamplifiers, data acquisition system, and methods for grounding and mitigating electromagnetic interference.

RESULTS

High homogeneity magnets can be produced in a variety of different designs including C- and H-shaped as well as Halbach arrays. Using Litz wire for RF coil designs enables unloaded Q values of ~ 400 to be reached, with body loss representing about 35% of the total system resistance. There are a number of different schemes to tackle issues arising from the low coil bandwidth with respect to the imaging bandwidth. Finally, the effects of good RF shielding, proper electrical grounding, and effective electromagnetic interference reduction can lead to substantial increases in image signal-to-noise ratio.

DISCUSSION

There are many different magnet and RF coil designs in the literature, and to enable meaningful comparisons and optimizations to be performed it would be very helpful to determine a standardized set of sensitivity measures, irrespective of design.

MaRCoS, an open-source electronic control system for low-field MRI

Every magnetic resonance imaging (MRI) device requires an electronic control system that handles pulse sequences and signal detection and processing. Here we provide details on the architecture and performance of MaRCoS, a MAgnetic Resonance COntrol System developed by an open international community of low-field MRI researchers. MaRCoS is inexpensive and can handle cycle-accurate sequences without hard length limitations, rapid bursts of events, and arbitrary waveforms. It has also been readily adapted to meet the requirements of the various academic and private institutions participating in its development. We describe the MaRCoS hardware, firmware and software that enable all of the above, including a Python-based graphical user interface for pulse sequence implementation, data processing and image reconstruction.

Benchmarking the performance of a low-cost magnetic resonance control system at multiple sites in the open MaRCoS community

PURPOSE

To describe the current properties and capabilities of an open-source hardware and software package that is being developed by many sites internationally with the aim of providing an inexpensive yet flexible platform for low-cost MRI.

METHODS

This article describes three different setups from 50 to 360 mT in different settings, all of which used the MaRCoS console for acquiring data, and different types of software interface (custom-built GUI or Pulseq overlay) to acquire it.

RESULTS

Images are presented both from phantoms and in vivo from healthy volunteers to demonstrate the image quality that can be obtained from the MaRCoS hardware/software interfaced to different low-field magnets.

CONCLUSIONS

The results presented here show that a number of different sequences commonly used in the clinic can be programmed into an open-source system relatively quickly and easily, and can produce good quality images even at this early stage of development. Both the hardware and software will continue to develop, and it is an aim of this article to encourage other groups to join this international consortium.

External Dynamic InTerference Estimation and Removal (EDITER) for low field MRI

PURPOSE

Point-of-care MRI requires operation outside of Faraday shielded rooms normally used to block image-degrading electromagnetic interference (EMI). To address this, we introduce the EDITER method (External Dynamic InTerference Estimation and Removal), an external sensor-based method to retrospectively remove image artifacts from time-varying external interference sources.

THEORY AND METHODS

The method acquires data from multiple EMI detectors (tuned receive coils as well as untuned electrodes placed on the body) simultaneously with the primary MR coil during and between image data acquisition. We calculate impulse response functions dynamically that map the data from the detectors to the time varying artifacts then remove the transformed detected EMI from the MR data. Performance of the EDITER algorithm was assessed in phantom and in vivo imaging experiments in an 80 mT portable brain MRI in a controlled EMI environment and with an open 47.5 mT MRI scanner in an uncontrolled EMI setting.

RESULTS

In the controlled setting, the effectiveness of the EDITER technique was demonstrated for specific types of introduced EMI sources with up to a 97% reduction of structured EMI and up to 76% reduction of broadband EMI in phantom experiments. In the uncontrolled EMI experiments, we demonstrate EMI reductions of up to 99% using an electrode and pick-up coil in vivo. We demonstrate up to a nine-fold improvement in image SNR with the method.

CONCLUSION

The EDITER technique is a flexible and robust method to improve image quality in portable MRI systems with minimal passive shielding and could reduce the reliance of MRI on shielded rooms and allow for truly portable MRI.

Digital Doppler-Cancellation Servo for Ultrastable Optical Frequency Dissemination Over Fiber

Progress made in optical references, including ultrastable Fabry-Perot cavities, optical frequency combs, and optical atomic clocks, has driven the need for ultrastable optical fiber networks. Telecom-wavelength ultrapure optical signal transport has been demonstrated on distances ranging from the laboratory scale to the continental scale. In this article, we present a Doppler-cancellation setup based on a digital phase-locked loop (PLL) for ultrastable optical signal dissemination over fiber. The optical phase stabilization setup is based on a usual heterodyne Michelson-interferometer setup, while the software-defined radio (SDR) implementation of the PLL is based on a compact commercial board embedding a field-programmable gate array and analog-to-digital and digital-to-analog converters. Using three different configurations, including an undersampling method, we demonstrate a 20-m-long fiber link with residual fractional frequency instability as low as 10^-18 at 1000 s and optical phase noise of -70 dBc/Hz at 1 Hz with a telecom frequency carrier.

Nuclear magnetic resonance measurements in dynamically controlled field pulse

We present the architecture of the versatile nuclear magnetic resonance (NMR) spectrometer with software-defined radio technology and its application to the dynamically controlled pulsed magnetic fields. The pulse-field technology is the only solution to access magnetic fields greater than 50 T, but the NMR experiment in the pulsed magnetic field was difficult because of the continuously changing field strength. The dynamically controlled field pulse allows us to perform NMR experiment in a quasi-steady field condition by creating a constant magnetic field for a short time around the peak of the field pulse. We confirmed the reproducibility of the field pulses using the NMR spectroscopy as a high precision magnetometer. With the highly reproducible field strength, we succeeded in measuring the nuclear spin-lattice relaxation rate 1/T₁, which had never been measured by the pulse-field NMR experiment without dynamic field control. We also implement the NMR spectrum measurement with both the frequency-sweep and field-sweep modes and discuss the appropriate choices of these modes depending on the magnetic properties of the sample to be measured. This development, with further improvement at a long-duration field pulse, will innovate the microscopic measurement in extremely high magnetic fields.

Low-cost low-field NMR and MRI: Instrumentation and applications

While NMR and MRI are often thought of as expensive techniques requiring large institutional investment, opportunities for low-cost, low-field NMR and MRI abound. We discuss a number of approaches to performing magnetic resonance experiments with inexpensive, easy to find or build components, aimed at applications in industry, education, and research. Opportunities that aim to make NMR accessible to a broad community are highlighted. We describe and demonstrate some projects from our laboratory, including a new prototype instrument for measurements at frequencies up to ∼200 kHz and demonstrate its application to the study of the rapidly advancing technique known as inhomogeneous magnetization transfer imaging, a promising method for characterizing myelin in vivo.

Machine learning assistive rapid, label-free molecular phenotyping of blood with two-dimensional NMR correlational spectroscopy

Translation of the findings in basic science and clinical research into routine practice is hampered by large variations in human phenotype. Developments in genotyping and phenotyping, such as proteomics and lipidomics, are beginning to address these limitations. In this work, we developed a new methodology for rapid, label-free molecular phenotyping of biological fluids (e.g., blood) by exploiting the recent advances in fast and highly efficient multidimensional inverse Laplace decomposition technique. We demonstrated that using two-dimensional T1-T2 correlational spectroscopy on a single drop of blood (<5 μL), a highly time- and patient-specific 'molecular fingerprint' can be obtained in minutes. Machine learning techniques were introduced to transform the NMR correlational map into user-friendly information for point-of-care disease diagnostic and monitoring. The clinical utilities of this technique were demonstrated through the direct analysis of human whole blood in various physiological (e.g., oxygenated/deoxygenated states) and pathological (e.g., blood oxidation, hemoglobinopathies) conditions.

Low-cost and portable MRI

Research in MRI technology has traditionally expanded diagnostic benefit by developing acquisition techniques and instrumentation to enable MRI scanners to "see more." This typically focuses on improving MRI's sensitivity and spatiotemporal resolution, or expanding its range of biological contrasts and targets. In complement to the clear benefits achieved in this direction, extending the reach of MRI by reducing its cost, siting, and operational burdens also directly benefits healthcare by increasing the number of patients with access to MRI examinations and tilting its cost-benefit equation to allow more frequent and varied use. The introduction of low-cost, and/or truly portable scanners, could also enable new point-of-care and monitoring applications not feasible for today's scanners in centralized settings. While cost and accessibility have always been considered, we have seen tremendous advances in the speed and spatial-temporal capabilities of general-purpose MRI scanners and quantum leaps in patient comfort (such as magnet length and bore diameter), but only modest success in the reduction of cost and siting constraints. The introduction of specialty scanners (eg, extremity, brain-only, or breast-only scanners) have not been commercially successful enough to tilt the balance away from the prevailing model: a general-purpose scanner in a centralized healthcare location. Portable MRI scanners equivalent to their counterparts in ultrasound or even computed tomography have not emerged and MR monitoring devices exist only in research laboratories. Nonetheless, recent advances in hardware and computational technology as well as burgeoning markets for MRI in the developing world has created a resurgence of interest in the topic of low-cost and accessible MRI. This review examines the technical forces and trade-offs that might facilitate a large step forward in the push to "jail-break" MRI from its centralized location in healthcare and allow it to reach larger patient populations and achieve new uses. Level of Evidence: 5 Technical Efficacy Stage: 6 J. Magn. Reson. Imaging 2019. J. Magn. Reson. Imaging 2020;52:686-696.

A Signal Acquisition Setup for Ultrashort Echo Time Imaging Operating in Parallel on Unmodified Clinical MRI Scanners Achieving an Acquisition Delay of [Formula: see text]

Ultrashort echo time imaging on clinical systems is still limited by the rather long radio frequency switching times achievable with standard front end concepts. In this contribution, an independent parallel receive-only system is interfaced to an unmodified clinical MRI system, enabling imaging of species with ultrashort relaxation times, such as bone, tendon, teeth, or lung tissue. Synchronization of the system is achieved by an electronically decoupled one-way trigger line, a clock reference signal, and RF pulse tracking, thus ensuring minimal interference with the host system. With the proposed system, an acquisition delay of [Formula: see text] is experimentally demonstrated.

Magnetic Microdevices for MRI-Based Detection of SARS-CoV-2 Viruses

Goal: To develop a micron-scale device that can operate as an MRI-based reporter for the presence of SARS-CoV-2 virus. Methods: Iron rod microdevices were constructed via template-guided synthesis and suspended in phosphate buffered saline (PBS). Heat-inactivated SARS-CoV-2 viruses were added to the samples and imaged with low-field MRI. Results: MRI of microdevices and viruses showed decreased signal intensity at low concentrations of viruses that recovered at higher concentrations. Electron micrographs suggest that reduced MRI intensity may be due to concentration-dependent shielding of water protons from local magnetic inhomogeneities caused by the iron microdevices. Conclusions: The preliminary results presented in this letter provide justification for further studies exploring the potential diagnostic role of magnetic microdevices in assessing the presence and concentration of SARS-CoV-2 viruses.

Design and implementation of a low-cost, tabletop MRI scanner for education and research prototyping

While access to a laboratory MRI system is ideal for teaching MR physics as well as many aspects of signal processing, providing multiple MRI scanners can be prohibitively expensive for educational settings. To address this need, we developed a small, low-cost, open-interface tabletop MRI scanner for academic use. We constructed and tested 20 of these scanners for parallel use by teams of 2-3 students in a teaching laboratory. With simplification and down-scaling to a 1 cm FOV, fully-functional scanners were achieved within a budget of $10,000 USD each. The design was successful for teaching MR principles and basic signal processing skills and serves as an accessible testbed for more advanced MR research projects. Customizable GUIs, pulse sequences, and reconstruction code accessible to the students facilitated tailoring the scanner to the needs of laboratory exercise. The scanners have been used by >800 students in 6 different courses and all designs, schematics, sequences, GUIs, and reconstruction code is open-source.

Geometrically-differential NMR in a stripline front-end

A major challenge facing the development of portable, low-cost NMR is the development of robust yet sensitive transceivers, for which several trade-offs in scalability, performance and complexity are usually necessary. Here we report on a stripline-based NMR detector that overcomes previous limitations. It features a sensitivity of 5.7×10^-4 TA^-1Ω^-0.5 over a sample volume of 10 mm × 10 mm × 3 mm, an exceptionally high B₁ homogeneity of A₄₅₀/A₉₀=98.4%, intrinsic electromagnetic shielding of 27 dB from environmental influences, and a total signal gain of 68 dB in the presence of a noise factor of 1.28, without any exterior shielding. The new dual-coil arrangement offers a downscalable geometry optimised for gap magnets, and it is voltage-tunable and plug-in compatible with commercial software-defined radio spectrometer boards. Exceptionally, it features both common-mode and novel differential-mode NMR measurement abilities.

Three-dimensional MRI in a homogenous 27 cm diameter bore Halbach array magnet

Modern clinical MRI systems utilise very high magnetic fields strengths to produce high resolution images of the human body. The high up-front and maintenance cost of these systems means that much of the world lacks access to this technology. In this paper we propose a low cost, head-only, homogenous Halbach magnet array with the potential for paediatric neuroimaging in low-resource settings. The homogeneity of the Halbach array is improved by allowing the diameter of the Halbach array to vary along its length, and also adding smaller internal shim magnets. The constructed magnet has a bore diameter of 27 cm, mean B₀ field strength of 50.4 mT and a homogeneity of 2400 ppm over a 20 cm diameter spherical volume. The level of homogeneity of the system means that coil-based gradients can be used for spatial encoding which greatly increases the flexibility in image acquisition. 3D images of a "brain phantom" were acquired over a 22 × 22 × 22 cm field of view with a 3.5 mm isotropic resolution using a spin-echo sequence. Future development of a low-cost gradient amplifier and an open-source spectrometer has the potential of offering a fully open-source, low-cost MRI system for paediatric neuroimaging in low-resource settings.

Deconstructing and reconstructing MRI hardware

Three topics concerning future hardware development for clinical MRI are discussed, with the general theme of operational simplification.

Omics Meeting Onics: Towards the Next Generation of Spectroscopic-Based Technologies in Personalized Medicine

This article aims to discuss the recent development of integrated point-of-care spectroscopic-based technologies that are paving the way for the next generation of diagnostic monitoring technologies in personalized medicine. Focusing on the nuclear magnetic resonance (NMR) technologies as the leading example, we discuss the emergence of -onics technologies (e.g., photonics and electronics) and how their coexistence with -omics technologies (e.g., genomics, proteomics, and metabolomics) can potentially change the future technological landscape of personalized medicine. The idea of an open-source (e.g., hardware and software) movement is discussed, and we argue that technology democratization will not only promote the dissemination of knowledge and inspire new applications, but it will also increase the speed of field implementation.

The MR Cap: A single-sided MRI system designed for potential point-of-care limited field-of-view brain imaging

PURPOSE

The size, cost, and siting requirements of conventional MRI systems limit their availability and preclude usage as monitoring or point-of-care devices. To address this, we developed a lightweight MRI for point-of-care brain imaging over a reduced field of view (FOV).

METHODS

The B₀ magnet was designed with a genetic algorithm optimizing homogeneity over a 3 × 8 × 8 cm FOV and a built-in gradient for slice selection or readout encoding. An external pair of gradient coils enables phase encoding in the other two directions and a radiofrequency (RF) coil provides excitation and detection. The system was demonstrated with high-resolution 1D "depth profiling" and 3D phantom imaging.

RESULTS

The lightweight B₀ magnet achieved a 64-mT average field over the imaging region at a materials cost of <$450 USD. The weight of the magnet, gradient, and RF coil was 8.3 kg. Depth profiles were obtained at high resolution (0.89 mm) and multislice rapid acquisition with refocused echoes (RARE) images were obtained with a resolution ~2 mm in-plane and ~6-mm slice thickness, each in an imaging time of 11 min.

CONCLUSION

The system demonstrates the feasibility of a lightweight brain MRI system capable of 1D to 3D imaging within a reduced FOV. The proposed system is low-cost and small enough to be used in point-of-care applications.

Magnetic resonance imaging with RF encoding on curved natural slices

While the idea of using spatial encoding fields (SEM) for image formation has been proven, conventional wisdom still holds that a magnetic resonance imaging (MRI) system begins with a highly uniform magnetic field. In particular, radio frequency (RF) encoding MRIs designed and tested to date have largely used uniform magnetic fields. Here we demonstrate magnetic resonance imaging in a magnetic field with a built-in gradient that gives non-planar slices - curved surfaces - when the nuclear spins are excited with narrow band RF pulses. Image encoding on these naturally occurring non-planar slices was accomplished with RF encoding using a non-linear spatially varying B₁ phase gradient. The imaging methods were demonstrated on a small prototype MRI instrument. The MRI has no switched magnetic field gradients - it is "gradient-free". A low field gradient-free MRI with low mass permanent magnets and simple, low power, RF encoding hardware is ideal for deployment on the International Space Station for the study of astronaut muscle and bone mass loss. Gradient-free natural slice encoding MRI designs would also be portable enough for application in remote terrestrial locations, in emergency rooms and in operating rooms where they can be used with minimally invasive and robotic surgery.