Automated analysis of low-field brain MRI in cerebral malaria

A central challenge of medical imaging studies is to extract biomarkers that characterize disease pathology or outcomes. Modern automated approaches have found tremendous success in high-resolution, high-quality magnetic resonance images. These methods, however, may not translate to low-resolution images acquired on magnetic resonance imaging (MRI) scanners with lower magnetic field strength. In low-resource settings where low-field scanners are more common and there is a shortage of radiologists to manually interpret MRI scans, it is critical to develop automated methods that can augment or replace manual interpretation, while accommodating reduced image quality. We present a fully automated framework for translating radiological diagnostic criteria into image-based biomarkers, inspired by a project in which children with cerebral malaria (CM) were imaged using low-field 0.35 Tesla MRI. We integrate multiatlas label fusion, which leverages high-resolution images from another sample as prior spatial information, with parametric Gaussian hidden Markov models based on image intensities, to create a robust method for determining ventricular cerebrospinal fluid volume. We also propose normalized image intensity and texture measurements to determine the loss of gray-to-white matter tissue differentiation and sulcal effacement. These integrated biomarkers have excellent classification performance for determining severe brain swelling due to CM.     

High-field magnetic resonance techniques for brain research

High-field magnetic resonance imaging scanners with a static magnetic field of 3 Tesla or higher are becoming ubiquitous in clinical and basic neurosciences. Given the high cost and complexity of operation, it is important to ask whether or not and how the use of high-field magnets can be beneficial for the neurosciences. What new questions can be addressed? Which new insights can we expect from these new tools? In addition, what are the limitations of these new techniques? This review discusses the three most important applications of the high-field magnetic resonance techniques for the neuroscience community: first, functional magnetic resonance imaging, second, in vivo spectroscopy, and third, in vivo fiber tracking on the basis of diffusion tensor imaging.     

Measuring three-dimensional knee kinematics under torsional loading

Excessive knee joint laxity is often used as an indicator of joint disease or injury. Clinical assessment devices are currently limited to anterior–posterior drawer measurements, while tools used to measure movement in the remaining degrees of freedom are either invasive or prone to soft tissue artefact. The objective of this work was, therefore, to develop a methodology whereby in vivo knee joint kinematics could be measured in three dimensions under torsional loading while still maintaining a non-invasive procedure. A device designed to administer a subject-normalized torque in the transverse plane of the knee was securely fastened to the outer frame of an open magnetic resonance imaging (MRI) magnet. Low resolution 3D T1-weighted images (6.25 mm slice thickness) were generated by the 0.2 Tesla MRI scanner in less than 3 min while the joint was under load. The 3D image volume was then shape-matched to a high resolution image volume (1.56 mm slice thickness) scanned in a no-load position. Three-dimensional rotations and translations of the tibia with respect to the femur were calculated by comparing the transformation matrices before and after torque was applied. Results from six subjects showed that this technique was repeatable over five trials with the knee in extended and flexed positions. Differences in range of rotation were shown between subjects and between knee positions, suggesting that this methodology has sufficient utility for further application in clinical studies.     

Imaging of interstitial cryotherapy--an in vitro comparison of ultrasound, computed tomography, and magnetic resonance imaging.

RATIONALE AND OBJECTIVES: To evaluate the imaging capabilities of ultrasound (US), computed tomography (CT), and magnetic resonance imaging (MRI) in monitoring interstitial cryotherapy and to compare them with visual control. METHODS: An experimental MR-compatible, vacuum-insulated and liquid nitrogen-cooled cryoprobe was inserted under in vitro conditions into a porcine liver, which was kept at a temperature of 37 +/- 1 degrees C, in a water bath with continuous stirring. The freezing procedure was controlled macroscopically, by US (Toshiba Sonolayer, 7.5-MHz linear array transducer), by CT (Siemens Somatom Plus, slice thickness 2-8 mm, 165-210 mA at 120 kV), and by MRI (Philips Gyroscan ACS-NT, FFE TR/TE/FA = 15/5.4/25 degrees, T1-SE 550/20, T2-TSE 1800/100) after the iceball reached its maximum size. RESULTS: The maximum iceball diameter around the probe tip was 12.0 mm by visual control, 12.4 mm by US, 12.7 mm by CT, and within 12.8 mm by spin echo sequences and 11 mm by gradient echo sequence. Due to the nearly signal-free appearance of the frozen tissue on MR images, the ice/tissue contrast on T1-weighted and gradient echo images was superior to T2-weighted images and CT images. Sonographically, the ice formation appeared as a hyperechoic sickle with nearly complete acoustic shadowing. CONCLUSION: Due to the better ice/tissue contrast, T1-weighted or gradient echo MR images were superior to CT and US in monitoring interstitial cryotherapy. Gradient echo sequences generally underestimated the ice diameter by 15%.     

Preliminary studies on the use of magnetic resonance imaging with Gd-DTPA to monitor ovarian function in subhuman primates

These studies were initiated to explore the use of magnetic resonance imaging (MRI) to investigate follicular growth in subhuman primates. Four adult cynomolgus monkeys received an i.v. injection of a magnetic resonance (MR) contrast agent, gadolinium diethylenetriaminepentaacetic acid (Gd-DTPA), and ovaries were removed 1-20 min later. Gd-DTPA is an extracellular fluid marker that is readily detectable in MRI. Individual ovaries were imaged using a 3-in (7.62 cm) radiofrequency surface coil and a 1.5 Tesla magnet. MR images of these ovaries provided a high resolution visualization of follicles with diameters of 1 mm and greater. Results obtained with MRI were similar to hematoxylin/eosin-stained sections of the same ovaries photographed at low magnification. These results demonstrate that MRI provides excellent resolution of ovarian follicles in macaques and thus may be suitable to monitor follicular growth and atresia in this species.     

Combined study of 1H-magnetic resonance imaging and depth-selected, EKG-gated 31P-magnetic resonance spectroscopy of the heart in vivo

NMR is useful for both 1H-magnetic resonance imaging (MRI) and magnetic resonance spectroscopy (MRS). We undertook to combine these two merits of NMR for in vivo characterization of living rat heart in wide bore (9 cm) superconducting magnet under high magnetic field (6.4 Tesla). Spatial resolution of 1H-MRI attained 0.1 mm by spin warp method. Then, depth-selected, EKG-gated 31P-MRS was performed, adjusting the detection area to cover the heart that was identified by the preceding 1H-MRI. Three evidences that 31P-SMR signal chiefly originated from the heart without cross talk of adjacent organs indicated that combination of 1H-MRI and in vivo 31P-MRS under high magnetic field in whole animal is promising for more accurate evaluation of cardiac muscle metabolism.     

The role of low-field strength magnetic resonance imaging in bladder cancer staging

This article shows the role of magnetic resonance imaging (MRI) in complex diagnostics of urinary bladder cancer. The paper analyzes the authors' own data of urinary bladder MRI in 40 patients with histologically proven bladder cancer. This study demonstrates the additional capacities of low-field strength MRI with enhanced technique including conventional T1-, T2-weighted images along with FLAIR and PD images.     

Synthesis of magnetic resonance-, X-ray- and ultrasound-visible alginate microcapsules for immunoisolation and noninvasive imaging of cellular therapeutics

Cell therapy has the potential to treat or cure a wide variety of diseases. Non-invasive cell tracking techniques are, however, necessary to translate this approach to the clinical setting. This protocol details methods to create microcapsules that are visible by X-ray, ultrasound (US) or magnetic resonance (MR) for the encapsulation and immunoisolation of cellular therapeutics. Three steps are generally used to encapsulate cellular therapeutics in an alginate matrix: (i) droplets of cell-containing liquid alginate are extruded, using an electrostatic generator, through a needle tip into a solution containing a dissolved divalent cation salt to form a solid gel; (ii) the resulting gelled spheres are coated with polycations as a cross-linker; and (iii) these complexes are then incubated in a second solution of alginate to form a semipermeable membrane composed of an inner and an outer layer of alginate. The microcapsules can be rendered visible during the first step by adding contrast agents to the primary alginate layer. Such contrast agents include superparamagnetic iron oxide for detection by (1)H MR imaging (MRI); the radiopaque agents barium or bismuth sulfate for detection by X-ray modalities; or perfluorocarbon emulsions for multimodal detection by (19)F MRI, X-ray and US imaging. The entire synthesis can be completed within 2 h.     

In vivo High Angular Resolution Diffusion-Weighted Imaging of Mouse Brain at 16.4 Tesla

Magnetic Resonance Imaging (MRI) of the rodent brain at ultra-high magnetic fields (> 9.4 Tesla) offers a higher signal-to-noise ratio that can be exploited to reduce image acquisition time or provide higher spatial resolution. However, significant challenges are presented due to a combination of longer T ₁ and shorter T ₂/T₂* relaxation times and increased sensitivity to magnetic susceptibility resulting in severe local-field inhomogeneity artefacts from air pockets and bone/brain interfaces. The Stejskal-Tanner spin echo diffusion-weighted imaging (DWI) sequence is often used in high-field rodent brain MRI due to its immunity to these artefacts. To accurately determine diffusion-tensor or fibre-orientation distribution, high angular resolution diffusion imaging (HARDI) with strong diffusion weighting (b >3000 s/mm²) and at least 30 diffusion-encoding directions are required. However, this results in long image acquisition times unsuitable for live animal imaging. In this study, we describe the optimization of HARDI acquisition parameters at 16.4T using a Stejskal-Tanner sequence with echo-planar imaging (EPI) readout. EPI segmentation and partial Fourier encoding acceleration were applied to reduce the echo time (TE), thereby minimizing signal decay and distortion artefacts while maintaining a reasonably short acquisition time. The final HARDI acquisition protocol was achieved with the following parameters: 4 shot EPI, b = 3000 s/mm², 64 diffusion-encoding directions, 125×150 μm² in-plane resolution, 0.6 mm slice thickness, and 2h acquisition time. This protocol was used to image a cohort of adult C57BL/6 male mice, whereby the quality of the acquired data was assessed and diffusion tensor imaging (DTI) derived parameters were measured. High-quality images with high spatial and angular resolution, low distortion and low variability in DTI-derived parameters were obtained, indicating that EPI-DWI is feasible at 16.4T to study animal models of white matter (WM) diseases.     

Measurement of grey parrot (Psittacus erithacus) trachea via magnetic resonance imaging,dissection, and electron beam computed tomography

To produce a model to explain the acoustic properties of human speech sounds produced by Grey parrots (Psittacus erithacus) and to compare these properties across species (e.g., with humans, other psittacine and nonpsittacine mimics), researchers need adequate measurements of the chambers that constitute the parrot vocal tract. Various methods can provide such data. Here we compare results for tracheal measurements provided by a) magnetic resonance imaging (MRI) of a live bird, b) caliper measurements of four preserved specimens, and c) electron beam computed tomography (EBCT) of three of these preserved specimens. We find that EBCT scans provide data that correspond to the inner area of the dissected trachea, whereas MRI results correspond to area measurements that include tracheal ring thickness. We briefly discuss how these data may predict formant values for Grey parrot reproduction of human vowels. Our results suggest how noninvasive techniques can be used for cross-species comparisons, including the coevolution of structure and function in avian mimicry. J. Morphol. 238:81–91, 1998. © 1998 Wiley-Liss, Inc.     

Design of an MRI-compatible robotic stereotactic device for minimally invasive interventions in the breast

The objective of this work was to develop a robotic device to perform biopsy and therapeutic interventions in the breast with real-time magnetic resonance imaging (MRI) guidance. The device was designed to allow for (i) stabilization of the breast by compression, (ii) definition of the interventional probe trajectory by setting the height and pitch of a probe insertion apparatus, and (iii) positioning of an interventional probe by setting the depth of insertion. The apparatus is fitted with five computer-controlled degrees of freedom for delivering an interventional procedure. The entire device is constructed of MR compatible materials, i.e. nonmagnetic and non-conductive, to eliminate artifacts and distortion of the MR images. The apparatus is remotely controlled by means of ultrasonic motors and a graphical user interface, providing real-time MR-guided planning and monitoring of the operation. Joint motion measurements found probe placement in less than 50 s and sub-millimeter repeatability of the probe tip for same-direction point-to-point movements. However, backlash in the rotation joint may incur probe tip positional errors of up to 5 mm at a distance of 40 mm from the rotation axis, which may occur for women with large breasts. The imprecision caused by this backlash becomes negligible as the probe tip nears the rotation axis. Real-time MR-guidance will allow the physician to correct this error Compatibility of the device within the MR environment was successfully tested on a 4 Tesla MR human scanner     

Geometric inaccuracy and co-registration errors for CT,DynaCT and MRI images used in robotic stereotactic radiosurgery treatment planning

PurposeTo measure the combined errors due to geometric inaccuracy and image co-registration on secondary images (dynamic CT angiography (dCTA), 3D DynaCT angiography (DynaCTA), and magnetic resonance images (MRI)) that are routinely used to aid in target delineation and planning for stereotactic radiosurgery (SRS).MethodsThree phantoms (one commercial and two in-house built) and two different analysis approaches (commercial and MATLAB based) were used to quantify the magnitude of geometric image distortion and co-registration errors for different imaging modalities within CyberKnife’s MultiPlan treatment planning software. For each phantom, the combined errors were reported as a mean target registration error (TRE). The mean TRE’s for different intramodality imaging parameters (e.g., mAs, kVp, and phantom set-ups) and for dCTA, DynaCTA, and MRI systems were measured.ResultsOnly X-ray based imaging can be performed with the commercial phantom, and the mean TRE ± standard deviation values were large compared to the in-house analysis using MATLAB. With the 3D printed phantom, even drastic changes in treatment planning CT imaging protocols did not greatly influence the mean TRE (<0.5 mm for a 1 mm slice thickness CT). For all imaging modalities, the largest mean TRE was found on DynaCT, followed by T2-weighted MR images (albeit all <1 mm).ConclusionsThe user may overestimate the mean TRE if the commercial phantom and MultiPlan were used solely. The 3D printed phantom design is a sensitive and suitable quality assurance tool for measuring 3D geometric inaccuracy and co-registration errors across all imaging modalities.     

Noninvasive magnetic resonance imaging of the development of individual colon cancer tumors in rat liver

Monitoring tumor development is essential for the understanding of mechanisms involved in tumor progression and to determine efficacy of therapy. One of the evolving approaches is longitudinal noninvasive magnetic resonance imaging (MRI) of tumors in experimental models. We applied high-resolution MRI at 7 Tesla to study the development of colon cancer tumors in rat liver. MRI acquisition was triggered to the respiratory cycle to minimize motion artifacts. A special radio frequency (RF) coil was designed to acquire detailed T1-weighted and T2-weighted images of the liver. T2-weighted images identified hyperintense lesions representing tumors with a minimum diameter of 2 mm, enabling the determination of growth rates and morphological aspects of individual tumors. It is concluded that high-resolution MRI using a dedicated RF coil and triggering to the respiratory cycle is an excellent tool for quantitative and morphological analysis of individual diffusely distributed tumors throughout the liver. However, at present, MRI requires expensive equipment and expertise and is a time-consuming methodology. Therefore, it should preferably be used for dedicated applications rather than for high-throughput assessment of total tumor load in animals.     

A Computer-Simulation Study on the Effects of MRI Voxel Dimensions on Carotid Plaque Lipid-Core and Fibrous Cap Segmentation and Stress Modeling

Background

The benefits of a decreased slice thickness and/or in-plane voxel size in carotid MRI for atherosclerotic plaque component quantification accuracy and biomechanical peak cap stress analysis have not yet been investigated in detail because of practical limitations.

Methods

In order to provide a methodology that allows such an investigation in detail, numerical simulations of a T1-weighted, contrast-enhanced, 2D MRI sequence were employed. Both the slice thickness (2 mm, 1 mm, and 0.5 mm) and the in plane acquired voxel size (0.62x0.62 mm² and 0.31x0.31 mm²) were varied. This virtual MRI approach was applied to 8 histology-based 3D patient carotid atherosclerotic plaque models.

Results

A decreased slice thickness did not result in major improvements in lumen, vessel wall, and lipid-rich necrotic core size measurements. At 0.62x0.62 mm² in-plane, only a 0.5 mm slice thickness resulted in improved minimum fibrous cap thickness measurements (a 2–3 fold reduction in measurement error) and only marginally improved peak cap stress computations. Acquiring voxels of 0.31x0.31 mm² in-plane, however, led to either similar or significantly larger improvements in plaque component quantification and computed peak cap stress.

Conclusions

This study provides evidence that for currently-used 2D carotid MRI protocols, a decreased slice thickness might not be more beneficial for plaque measurement accuracy than a decreased in-plane voxel size. The MRI simulations performed indicate that not a reduced slice thickness (i.e. more isotropic imaging), but the acquisition of anisotropic voxels with a relatively smaller in-plane voxel size could improve carotid plaque quantification and computed peak cap stress accuracy.     

Potentialities of low-field magnetic resonance tomography in the diagnosis and treatment of invasive cancer of cervix uteri

The aim of the study was to evaluate the efficiency of low-field (0.14 T) magnetic resonance imaging (MRI) in the diagnosis and treatment of cancer of the cervix uteri. MATERIALS AND METHODS: Low-field MRI was performed in 39 patients with cancer of the cervix uteri to define the stage of the tumor and to follow up the outcomes of their treatment. Particular emphasis was laid on the determination of the size of the tumor and the presence of parametral invasion and on metastatic lesions of lymph nodes. MRI data were compared with clinical, morphological, and surgical staging results. In detecting the stage of cancer of the cervix uteri, the accuracy of MRI was 72% whereas that of clinical study was 51%. In determining parametral invasion, the accuracy of clinical study and low-field MRI was 71 and 90%, respectively. The sensitivity and specificity of MRI were 83 and 92%, respectively. The anterioposterior tumor size was an important prognostic factor in following up the outcomes of treatment as there was its close association and the incidence of tumor recurrences. The present study has indicated that the high efficiency of low-field MRI in detecting the stage of invasive cancer of cervix uteri makes it the method of choice in planning treatment and monitoring the outcomes of combined radiation therapy.     

A case of endometriosis in the macaque diagnosed by nuclear magnetic resonance imaging.

A case of spontaneous endometriosis was diagnosed in the pigtailed macaque (Macaca nemestrina nemestrina) with the aid of high-field (2.35 T), T2-weighted (TE50), C1H2-suppressed, oblique nuclear magnetic resonance imaging (MRI). Postmortem histology was obtained. A variety of endometriotic lesions was seen with MRI, including extrauterine hyperintense apparently cystic regions, extrauterine hypointense regions apparently associated with intracellular paramagnetic iron proteins, and an enlarged myometrium exhibiting adenomyosis foci.     

Water entry for the black locust (<Emphasis Type="Italic">Robinia pseudoacacia</Emphasis> L.) seeds observed by dedicated micro-magnetic resonance imaging

Water entry at germination for black locust (Robinia pseudoacacia L.) seeds which are known as hard seeds with impermeable seed coat to water, was examined using micro-magnetic resonance imaging (MRI). The MRI apparatus equipped with a low-field (1 T; Tesla) permanent magnet was used, which is open access, easy maintenance, operable and transportable. The excellent point of the apparatus is that T ₁-enhancement of water signals absorbed in dry seeds against steeping free water is stronger than the apparatuses with high-field superconducting magnets, which enabled clear detection of water entry. Water hardly penetrated into the seeds for more than 8 h but approximately 60 % of seeds germinated by incubating on wet filter papers for several days. Hot water treatments above 75 °C for 3 min effectively induced water gap; scarification was 70 % at 100 °C and 75 °C, declined to 15 % at 50 °C and decreased further at room temperature. Water entered into the scarified seeds exclusively through the lens, spread along the dorsal side of the seeds and reached the hypocotyl, whereas water migrated slowly through hilum side to radicle within 3 h.     

Human ocular dominance columns as revealed by high-field functional magnetic resonance imaging.

We mapped ocular dominance columns (ODCs) in normal human subjects using high-field (4 T) functional magnetic resonance imaging (fMRI) with a segmented echo planar imaging technique and an in-plane resolution of 0.47 x 0.47 mm(2). The differential responses to left or right eye stimulation could be reliably resolved in anatomically well-defined sections of V1. The orientation and width ( approximately 1 mm) of mapped ODC stripes conformed to those previously revealed in postmortem brains stained with cytochrome oxidase. In addition, we showed that mapped ODC patterns could be largely reproduced in different experiments conducted within the same experimental session or over different sessions. Our results demonstrate that high-field fMRI can be used for studying the functions of human brains at columnar spatial resolution.     

Magnetic resonance-guided, real-time targeted delivery and imaging of magnetocapsules immunoprotecting pancreatic islet cells

In type I diabetes mellitus, islet transplantation provides a moment-to-moment fine regulation of insulin. Success rates vary widely, however, necessitating suitable methods to monitor islet delivery, engraftment and survival. Here magnetic resonance-trackable magnetocapsules have been used simultaneously to immunoprotect pancreatic beta-cells and to monitor, non-invasively in real-time, hepatic delivery and engraftment by magnetic resonance imaging (MRI). Magnetocapsules were detected as single capsules with an altered magnetic resonance appearance on capsule rupture. Magnetocapsules were functional in vivo because mouse beta-cells restored normal glycemia in streptozotocin-induced diabetic mice and human islets induced sustained C-peptide levels in swine. In this large-animal model, magnetocapsules could be precisely targeted for infusion by using magnetic resonance fluoroscopy, whereas MRI facilitated monitoring of liver engraftment over time. These findings are directly applicable to ongoing improvements in islet cell transplantation for human diabetes, particularly because our magnetocapsules comprise clinically applicable materials.     

Validation of ultrasound estimates of visceral fat in black South African adolescents

Accurate quantification of visceral adipose tissue (VAT) is needed to understand ethnic variations and their implications for metabolic disease risk. The use of reference methods such as computed tomography (CT) and magnetic resonance imaging (MRI) is limited in large epidemiological studies. Surrogate measures such as anthropometry and dual-energy X-ray absorptiometry (DXA) do not differentiate between VAT and subcutaneous abdominal adipose tissue (SCAT). Ultrasound provides a validated estimate of VAT and SCAT in white populations. This study aimed to validate the use of ultrasound-based assessment of VAT in black South African adolescents. One hundred healthy adolescents (boys = 48, girls = 52) aged 18-19 years participating in the birth to twenty cohort study had VAT and SCAT measured by single slice MRI at L4. These MRI "criterion measures" were related to ultrasound VAT and SCAT thickness, anthropometry (BMI, waist and hip circumferences), and DXA android region fat. Ultrasound VAT thickness showed the strongest correlations with MRI VAT (Spearman's correlation coefficients: r = 0.72 and r = 0.64; in boys and girls, respectively), and substantially improved the estimation of MRI VAT compared to anthropometry and DXA alone; in regression models the addition of ultrasound VAT thickness to models containing BMI, waist, and DXA android fat improved the explained variance in VAT from 39% to 60% in boys, and from 31% to 52% in girls. In conclusion, ultrasound substantially increased the precision of estimating VAT beyond anthropometry and DXA alone. Black South African adolescents have relatively little VAT compared to elderly whites, and we therefore provide new ultrasound-based prediction equations for VAT specific to this group.