Comparison of SNR and CNR for in vivo mouse brain imaging at 3 and 7 T using well matched scanner configurations

Mouse Brain MRI: Including In Vivo, Ex Vivo, and fcMRI for the Study of Microcephaly

With its sensitivity to soft tissue, MRI is a powerful tool for the study of the neuroanatomical manifestations of a variety of conditions, such as microcephaly-related morbidities that are not easily visualized by other imaging techniques, such as CT. In addition to structural imaging, more recently, researchers have found changes in brain function in a wide range of neurological conditions-highlighting the utility of MRI for the study of microcephaly.In this methods chapter, basic mouse preparation and the acquisition of data for in vivo anatomical MRI will be discussed. Additionally, we will provide our protocol for the perfusion and fixation of brain tissue with gadolinium contrast agent. Following that, the process of optimization of system parameters will be shown for anatomical imaging of in vivo and ex vivo brain tissue. Lastly, the chapter will detail a protocol for fcMRI along with a discussion of considerations specific to functional imaging.

Multiple-mouse magnetic resonance imaging with cryogenic radiofrequency probes for evaluation of brain development

Multiple-mouse magnetic resonance imaging (MRI) increases scan throughput by imaging several mice simultaneously in the same magnet bore, enabling multiple images to be obtained in the same time as a single scan. This increase in throughput enables larger studies than otherwise feasible and is particularly advantageous in longitudinal study designs where frequent imaging time points result in high demand for MRI resources. Cryogenically-cooled radiofrequency probes (CryoProbes) have been demonstrated to have significant signal-to-noise ratio benefits over comparable room temperature coils for in vivo mouse imaging. In this work, we demonstrate implementation of a multiple-mouse MRI system using CryoProbes, achieved by mounting four such coils in a 30-cm, 7-Tesla magnet bore. The approach is demonstrated for longitudinal quantification of brain structure from infancy to early adulthood in a mouse model of Sanfilippo syndrome (mucopolysaccharidosis type III), generated by knockout of the Hgsnat gene. We find that Hgsnat^-/- mice have regionally increased growth rates compared to Hgsnat^+/+ mice in a number of brain regions, notably including the ventricles, amygdala and superior colliculus. A strong sex dependence was also noted, with the lateral ventricle volume growing at an accelerated rate in males, but several structures in the brain parenchyma growing faster in females. This approach is broadly applicable to other mouse models of human disease and the increased throughput may be particularly beneficial in studying mouse models of neurodevelopmental disorders.

Divergence-Free Constrained Phase Unwrapping and Denoising for 4D Flow MRI Using Weighted Least-Squares

A novel divergence-free constrained phase unwrapping method was proposed and evaluated for 4D flow MRI. The unwrapped phase field was obtained by integrating the phase variations estimated from the wrapped phase data using weighted least-squares. The divergence-free constraint for incompressible blood flow was incorporated to regulate and denoise the resulting phase field. The proposed method was tested on synthetic phase data of left ventricular flow and in vitro 4D flow measurement of Poiseuille flow. The method was additionally applied to in vivo 4D flow measurements in the thoracic aorta from 30 human subjects. The performance of the proposed method was compared to the state-of-the-art 4D single-step Laplacian algorithm. The synthetic phase data were completely unwrapped by the proposed method for all the cases with velocity encoding (venc) as low as 20% of the maximum velocity and signal-to-noise ratio as low as 5. The in vitro Poiseuille flow data were completely unwrapped with a 60% increase in the velocity-to-noise ratio. For the in-vivo aortic datasets with venc ratio less than 0.4, the proposed method significantly improved the success rate by as much as 40% and reduced the velocity error levels by a factor of 10 compared to the state-of-the-art method. The divergence-free constrained method exhibits reliability and robustness on phase unwrapping and shows improved accuracy of velocity and hemodynamic quantities by unwrapping the low-venc 4D flow MRI data.

T2-weighted turbo spin-echo magnetic resonance imaging of canine brain anatomy at 1.5T, 3T, and 7T field strengths

Post-mortem T2 weighted images of canine heads were acquired at 1.5T, 3T, and 7T. This study aimed to (1) identify anatomical structures of the canine brain using an ultra-high-field magnetic resonance imaging (MRI) (7T) to help to facilitate their localization on high field MRI images (3T and 1.5T), where these structures may appear less well defined and delineated and (2) evaluate the visibility of canine brain anatomical structures on 1.5T, 3T, and 7T MRI images for optimizing clinical utility. Our hypothesis was that the provided subjective image quality comparison at different field strengths may offer a general baseline for canine brain anatomy and may help clinicians evaluate MRI options better. Six canine heads were examined with 1.5T, 3T, and 7T MRI scanners. T2-weighted images were acquired in three orthogonal planes at each field strength using a turbo spin-echo sequence. Fifty neuroanatomic structures were identified and evaluated on the 7T MR images; subsequently, those were found on the 3T and 45 out of the 50 structures were detected on the 1.5T imaging. The structures that were not able to be identified on the 1.5T imaging included the septum pellucidum, oculomotor nucleus, substantia nigra, claustrum, and thalamic nucleus griseus. Images acquired at 7T were subjective of higher spatial and contrast resolution. However, the ultra-high-field images were prone to artifacts at the interface between tissues of different magnetic properties. In conclusion, 3T MR imaging appears to be the best comprise for evaluating canine brain anatomy on MRI with fewer imaging artifacts.

Cardiac MRI Assessment of Mouse Myocardial Infarction and Regeneration

Small animal models are indispensable for cardiac regeneration research. Studies in mouse and rat models have provided important insights into the etiology and mechanisms of cardiovascular diseases and accelerated the development of therapeutic strategies. It is vitally important to be able to evaluate the therapeutic efficacy and have reliable surrogate markers for therapeutic development for cardiac regeneration research. Magnetic resonance imaging (MRI), a versatile and noninvasive imaging modality with excellent penetration depth, tissue coverage, and soft-tissue contrast, is becoming a more important tool in both clinical settings and research arenas. Cardiac MRI (CMR) is versatile, noninvasive, and capable of measuring many different aspects of cardiac functions, and, thus, is ideally suited to evaluate therapeutic efficacy for cardiac regeneration. CMR applications include assessment of cardiac anatomy, regional wall motion, myocardial perfusion, myocardial viability, cardiac function assessment, assessment of myocardial infarction, and myocardial injury. Myocardial infarction models in mice are commonly used model systems for cardiac regeneration research. In this chapter, we discuss various CMR applications to evaluate cardiac functions and inflammation after myocardial infarction.

Comparison of image quality in brain MRI with and without MR compatible incubator and predictive value of brain MRI at expected delivery date in preterm babies

Objectives MR compatible incubators (MRcI) offer the examination of preterm and critically ill infants in controlled environment. The aim of the study was to compare objective and subjective image quality as well as diagnostic value of MRI brain examinations with and without using the MRcI. Thus, predictive value of brain MRI at expected delivery date in general was investigated. Methods This retrospective study included MRI brain examinations conducted at patients' corrected age ≤6 months and presence of four standard sequences (PD TSE transversal, T2 TSE transversal, T2 TSE sagittal and T1 SE transversal). Signal-to-Noise Ratio (SNR) and Contrast-to-Noise Ratio (CNR) was calculated. Subjective image quality was estimated using a 5-point Likert scale. Findings of MRI were compared with those of previous transfontanellar ultrasound because of additional diagnostic information. Severe brain abnormality scaled by score of Kidokoro was related to results of Munich Functional Developmental Diagnostics (MFDD) within first year. Results One hundred MRI brain examinations (76 with MRcI, 24 without MRcI) were performed in 79 patients. Using the MRcI SNR and CNR were significantly higher in PD- and in T2-weighted sequences (p<0.05). TSE PD transversal demonstrated a higher risk of non-diagnostic quality using MRcI (OR 5.23; 95%-CI 1.86-14.72). MRcI revealed additional diagnostic information (OR 5.69; 95%-CI 1.15-28.24). Severe brain abnormality was associated with walking deficits (r=0.570; p=0.021). Conclusions The MRcI increased objective image quality and revealed additional diagnostic information to transfontanellar ultrasound. Nevertheless, prediction of infants' future development remains limited.

A Multicenter Preclinical MRI Study: Definition of Rat Brain Relaxometry Reference Maps

Similarly to human population imaging, there are several well-founded motivations for animal population imaging, the most notable being the improvement of the validity of statistical results by pooling a sufficient number of animal data provided by different imaging centers. In this paper, we demonstrate the feasibility of such a multicenter animal study, sharing raw data from forty rats and processing pipelines between four imaging centers. As specific use case, we focused on T1 and T2 mapping of the healthy rat brain at 7T. We quantitatively report about the variability observed across two MR data providers and evaluate the influence of image processing steps on the final maps, using three fitting algorithms from three centers. Finally, to derive relaxation times from different brain areas, two multi-atlas segmentation pipelines from different centers were performed on two different platforms. Differences between the two data providers were 2.21% for T1 and 9.52% for T2. Differences between processing pipelines were 1.04% for T1 and 3.33% for T2. These maps, obtained in healthy conditions, may be used in the future as reference when exploring alterations in animal models of pathology.

Assessment of signal-to-noise ratio and contrast-to-noise ratio in 3 T magnetic resonance imaging in the presence of zirconium, titanium, and titanium-zirconium alloy implants

OBJECTIVE

We quantitatively compared the signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) in T1 weighted imaging (WI) and T2 WI sequences in 3 Tesla (T) magnetic resonance imaging (MRI) using zirconium, titanium (grades 4 and 5), and titanium-zirconium alloy implants to evaluate the effect of implant type and imaging sequence.

STUDY DESIGN

MRI was acquired using a 3 T magnet with a 16-channel head coil. Implants of each type were mounted in gel and scanned in axial, coronal, and sagittal planes using fast spin echo sequences in T1 WI (TR = 600, TE = 12 milliseconds) and T2 WI (TR = 3000, TE = 80 milliseconds) sequences. Data were transferred to Synapse 3-D software, and images were measured twice by an oral and maxillofacial radiologist blinded to the type of implants.

RESULTS

Zirconium implants resulted in the lowest SNR and CNR values (P < .05). No significant differences were identified between titanium (grades 4 and 5) and titanium-zirconium implants. The T2 WI sequence had a significantly higher SNR and CNR than T1 WI. There was no difference in intraobserver agreement between T1 WI and T2 WI.

CONCLUSIONS

CNR and SNR at 3 T MRI are dependent on implant type and imaging sequence. Titanium (grades 4 and 5) and titanium-zirconium implants and the T2 WI sequence produced higher SNR and CNR values.

Deep residual network for off-resonance artifact correction with application to pediatric body MRA with 3D cones

PURPOSE

To enable rapid imaging with a scan time-efficient 3D cones trajectory with a deep-learning off-resonance artifact correction technique.

METHODS

A residual convolutional neural network to correct off-resonance artifacts (Off-ResNet) was trained with a prospective study of pediatric MRA exams. Each exam acquired a short readout scan (1.18 ms ± 0.38) and a long readout scan (3.35 ms ± 0.74) at 3 T. Short readout scans, with longer scan times but negligible off-resonance blurring, were used as reference images and augmented with additional off-resonance for supervised training examples. Long readout scans, with greater off-resonance artifacts but shorter scan time, were corrected by autofocus and Off-ResNet and compared with short readout scans by normalized RMS error, structural similarity index, and peak SNR. Scans were also compared by scoring on 8 anatomical features by two radiologists, using analysis of variance with post hoc Tukey's test and two one-sided t-tests. Reader agreement was determined with intraclass correlation.

RESULTS

The total scan time for long readout scans was on average 59.3% shorter than short readout scans. Images from Off-ResNet had superior normalized RMS error, structural similarity index, and peak SNR compared with uncorrected images across ±1 kHz off-resonance (P < .01). The proposed method had superior normalized RMS error over -677 Hz to +1 kHz and superior structural similarity index and peak SNR over ±1 kHz compared with autofocus (P < .01). Radiologic scoring demonstrated that long readout scans corrected with Off-ResNet were noninferior to short readout scans (P < .05).

CONCLUSION

The proposed method can correct off-resonance artifacts from rapid long-readout 3D cones scans to a noninferior image quality compared with diagnostically standard short readout scans.

Optimization of molecularly targeted MRI in the brain: empirical comparison of sequences and particles

BACKGROUND

Molecular MRI is an evolving field of research with strong translational potential. Selection of the appropriate MRI sequence, field strength and contrast agent depend largely on the application. The primary aims of the current study were to: 1) assess the sensitivity of different MRI sequences for detection of iron oxide particles in mouse brain; 2) determine the effect of magnetic field strength on detection of iron oxide particles in vivo; and 3) compare the sensitivity of targeted microparticles of iron oxide (MPIO) or ultra-small superparamagnetic iron oxide (USPIO) for detection of vascular cell adhesion molecule-1 (VCAM-1) in vivo.

METHODS

Mice were injected intrastriatally with interleukin 1β to induce VCAM-1 expression on the cerebral vasculature. Subsequently, animals were injected intravenously with either VCAM-MPIO or VCAM-USPIO and imaged 1 or 13 hours post-injection, respectively. MRI was performed at 4.7, 7.0, or 9.4 T, using three different T2*-weighted sequences: single gradient echo 3D (GE3D), multi-gradient echo 3D (MGE3D) and balanced steady-state free precession 3D (bSSFP3D).

RESULTS

MGE3D yielded the highest signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) for the detection of iron oxide particles. All sequences showed a significant increase in SNR and CNR from 4.7 to 7.0 T, but no further improvement at 9.4 T. However, whilst targeted MPIO enabled sensitive detection of VCAM-1 expression on the cerebral vasculature, the long half-life (16.5 h vs 1.2 min) and lower relaxivity per particle (1.29×10-14 vs 1.18×10-9 Hz L/particle) of USPIO vs. MPIO rendered them impractical for molecular MRI.

CONCLUSION

These findings demonstrate clear advantages of MPIO compared to USPIO for molecularly-targeted MRI, and indicate that the MGE3D sequence is optimal for MPIO detection. Moreover, higher field strengths (7.0/9.4 T) showed enhanced sensitivity over lower field strengths (4.7 T). With the development of biodegradable MPIO, these agents hold promise for clinical translation.

Development and validation of a new MRI simulation technique that can reliably estimate optimal in vivo scanning parameters in a glioblastoma murine model

BACKGROUND

Magnetic Resonance Imaging (MRI) relies on optimal scanning parameters to achieve maximal signal-to-noise ratio (SNR) and high contrast-to-noise ratio (CNR) between tissues resulting in high quality images. The optimization of such parameters is often laborious, time consuming, and user-dependent, making harmonization of imaging parameters a difficult task. In this report, we aim to develop and validate a computer simulation technique that can reliably provide "optimal in vivo scanning parameters" ready to be used for in vivo evaluation of disease models.

METHODS

A glioblastoma murine model was investigated using several MRI imaging methods. Such MRI methods underwent a simulated and an in vivo scanning parameter optimization in pre- and post-contrast conditions that involved the investigation of tumor, brain parenchyma and cerebrospinal fluid (CSF) CNR values in addition to the time relaxation values of the related tissues. The CNR tissues information were analyzed and the derived scanning parameters compared in order to validate the simulated methodology as a reliable technique for "optimal in vivo scanning parameters" estimation.

RESULTS

The CNRs and the related scanning parameters were better correlated when spin-echo-based sequences were used rather than the gradient-echo-based sequences due to augmented inhomogeneity artifacts affecting the latter methods. "Optimal in vivo scanning parameters" were generated successfully by the simulations after initial scanning parameter adjustments that conformed to some of the parameters derived from the in vivo experiment.

CONCLUSION

Scanning parameter optimization using the computer simulation was shown to be a valid surrogate to the in vivo approach in a glioblastoma murine model yielding in a better delineation and differentiation of the tumor from the contralateral hemisphere. In addition to drastically reducing the time invested in choosing optimal scanning parameters when compared to an in vivo approach, this simulation program could also be used to harmonize MRI acquisition parameters across scanners from different vendors.

MRI in the Study of Animal Models of Neurodegenerative Diseases

Magnetic Resonance Imaging (MRI) is an important tool to study various animal models of degenerative diseases. This chapter describes routine protocols of T ₁-, T ₂-, and T ₂*-weighted and diffusion-weighted MRI for rodent brain and spinal cord. These protocols can be used to measure atrophy, axonal and myelin injury and changes in white matter connectivity.

Biomolecular MRI reporters: Evolution of new mechanisms

Magnetic resonance imaging (MRI) is a powerful technique for observing the function of specific cells and molecules inside living organisms. However, compared to optical microscopy, in which fluorescent protein reporters are available to visualize hundreds of cellular functions ranging from gene expression and chemical signaling to biomechanics, to date relatively few such reporters are available for MRI. Efforts to develop MRI-detectable biomolecules have mainly focused on proteins transporting paramagnetic metals for T1 and T2 relaxation enhancement or containing large numbers of exchangeable protons for chemical exchange saturation transfer. While these pioneering developments established several key uses of biomolecular MRI, such as imaging of gene expression and functional biosensing, they also revealed that low molecular sensitivity poses a major challenge for broader adoption in biology and medicine. Recently, new classes of biomolecular reporters have been developed based on alternative contrast mechanisms, including enhancement of spin diffusivity, interactions with hyperpolarized nuclei, and modulation of blood flow. These novel reporters promise to improve sensitivity and enable new forms of multiplexed and functional imaging.

Post-mortem magnetic resonance microscopy (MRM) of the murine brain at 7 Tesla results in a gain of resolution as compared to in vivo MRM

Small-animal MRI with high field strength allows imaging of the living animal. However, spatial resolution in in vivo brain imaging is limited by the scanning time. Measurements of fixated mouse brains allow longer measurement time, but fixation procedures are time consuming, since the process of fixation may take several weeks. We here present a quick and simple post-mortem approach without fixation that allows high-resolution MRI even at 7 Tesla (T2-weighted MRI). This method was compared to in vivo scans with optimized spatial resolution for the investigation of anesthetized mice (T1-weighted MRI) as well as to ex situ scans of fixed brains (T1- and T2-weighted scans) by using standard MRI-sequences, along with anatomic descriptions of areas observable in the MRI, analysis of tissue shrinkage and post-processing procedures (intensity inhomogeneity correction, PCNN3D brain extract, SPMMouse segmentation, and volumetric measurement). Post-mortem imaging quality was sufficient to determine small brain substructures on the morphological level, provided fast possibilities for volumetric acquisition and for automatized processing without manual correction. Moreover, since no fixation was used, tissue shrinkage due to fixation does not occur as it is, e.g., the case by using ex vivo brains that have been kept in fixatives for several days. Thus, the introduced method is well suited for comparative investigations, since it allows determining small structural alterations in the murine brain at a reasonable high resolution even by MRI performed at 7 Tesla.

A new method of reconstructing the human laryngeal architecture using micro-MRI

OBJECTIVES/HYPOTHESIS

A realistic three-dimentional (3D) model of the larynx could be of value for the understanding of normal laryngeal motion and for studying pathological changes as well as in modeling potential therapy outcomes. The objective of this research was to present a new method of creating a computer model of the human larynx using data obtained through micro-magnetic resonance imaging (MRI) scanning.

STUDY DESIGN

Prospective study.

METHODS

A 7-T micro-MRI scanner was used to scan an excised larynx obtained postmortem from a 68-year-old woman. MRI data was manually segmented and compiled into 3D images using Mimics12.1 reconstruction software. Measurements of the reconstructed structures were also calculated using Mimics12.1.

RESULTS

The 3D laryngeal model contained the thyroid, cricoid, and arytenoid cartilages. Nearly all of the intrinsic muscles could be segmented. Although the cricoarytenoid joint could be visualized, the features of the cricothyroid joint were not clear. Muscle and cartilage volumes and surface areas were calculated from the 3D model.

CONCLUSIONS

The combination of MRI and 3D reconstruction generates promising results in the hopes of creating a highly realistic and detailed model of the human larynx.

Diffusion tensor imaging correlates with cytopathology in a rat model of neonatal hydrocephalus

Background

Diffusion tensor imaging (DTI) is a non-invasive MRI technique that has been used to quantify CNS abnormalities in various pathologic conditions. This study was designed to quantify the anisotropic diffusion properties in the brain of neonatal rats with hydrocephalus (HCP) and to investigate association between DTI measurements and cytopathology.

Methods

DTI data were acquired between postnatal day 7 (P7) and P12 in 12 rats with HCP induced at P2 and in 15 age-matched controls. Animals were euthanized at P11 or P22/P23 and brains were processed with immunohistochemistry for glial fibrillary acidic protein (GFAP), ionized calcium-binding adaptor molecule (Iba-1), and luxol fast blue (LFB) to assess astrocytosis, microglial reactivity and degree of myelination, respectively.

Results

Hydrocephalic rats were consistently found to have an abnormally low (at corrected p-level of <0.05) fractional anisotropy (FA) value and an abnormally high mean diffusivity (MD) value in the cerebral cortex (CX), the corpus callosum (CC), and the internal capsule (IC). Immunohistochemical analysis demonstrated trends of increasing astrocyte and microglial reactivity in HCP rats at P11 that reached statistical significance at P22/P23. A trend toward reduced myelination in the HCP rats was also found at P22/P23. Correlation analysis at P11 for the CC demonstrated statistically significant correlations (or trends) between the DTI measurement (the decreased FA and increased MD values) and the GFAP or Iba-1 rankings. The immunohistochemical rankings in the IC at P22/P23 were also significantly correlated or demonstrated a trend with both FA and MD values.

Conclusions

This study demonstrates the feasibility of employing DTI on the brain in experimental hydrocephalus in neonatal rats and reveals impairments in multiple regions of interest in both grey and white matter. A strong correlation was found between the immunohistochemical results and the changes in anisotropic diffusion properties.

Multishot PROPELLER for high-field preclinical MRI

With the development of numerous mouse models of cancer, there is a tremendous need for an appropriate imaging technique to study the disease evolution. High-field T(2)-weighted imaging using PROPELLER (Periodically Rotated Overlapping ParallEL Lines with Enhanced Reconstruction) MRI meets this need. The two-shot PROPELLER technique presented here provides (a) high spatial resolution, (b) high contrast resolution, and (c) rapid and noninvasive imaging, which enables high-throughput, longitudinal studies in free-breathing mice. Unique data collection and reconstruction makes this method robust against motion artifacts. The two-shot modification introduced here retains more high-frequency information and provides higher signal-to-noise ratio than conventional single-shot PROPELLER, making this sequence feasible at high fields, where signal loss is rapid. Results are shown in a liver metastases model to demonstrate the utility of this technique in one of the more challenging regions of the mouse, which is the abdomen.