In vivo fiber tracking in the rat brain on a clinical 3T MRI system using a high strength insert gradient coil

Diffusion Tensor Imaging-Based Studies at the Group-Level Applied to Animal Models of Neurodegenerative Diseases

The understanding of human and non-human microstructural brain alterations in the course of neurodegenerative diseases has substantially improved by the non-invasive magnetic resonance imaging (MRI) technique of diffusion tensor imaging (DTI). Animal models (including disease or knockout models) allow for a variety of experimental manipulations, which are not applicable to humans. Thus, the DTI approach provides a promising tool for cross-species cross-sectional and longitudinal investigations of the neurobiological targets and mechanisms of neurodegeneration. This overview with a systematic review focuses on the principles of DTI analysis as used in studies at the group level in living preclinical models of neurodegeneration. The translational aspect from in-vivo animal models toward (clinical) applications in humans is covered as well as the DTI-based research of the non-human brains' microstructure, the methodological aspects in data processing and analysis, and data interpretation at different abstraction levels. The aim of integrating DTI in multiparametric or multimodal imaging protocols will allow the interrogation of DTI data in terms of directional flow of information and may identify the microstructural underpinnings of neurodegeneration-related patterns.

Development, integration and use of an ultra-high-strength gradient system on a human-size 3 T magnet for small animal MRI

This study aims to integrate an ultra-high-strength gradient coil system on a clinical 3 T magnet and demonstrate its preclinical imaging capabilities. Dedicated phantoms were used to qualitatively and quantitatively assess the performance of the gradient system. Advanced MR imaging sequences, including diffusion tensor imaging (DTI) and quantitative susceptibility mapping (QSM), were implemented and executed on an ex vivo specimen as well as in vivo rats. The DTI and QSM results on the phantom agreed well with those in the literature. Furthermore, studies on ex vivo specimens have demonstrated the applicability of DTI and QSM on our system to probe microstructural changes in a mild traumatic brain injury rat model. The feasibility of in vivo rat DTI was also demonstrated. We showed that the inserted ultra-high-strength gradient coil was successfully integrated on a clinically used magnet. After careful tuning and calibration, we verified the accuracy and quantitative preclinical imaging capability of the integrated system in phantom and in vivo rat brain experiments. This study can be essential to establish dedicated animal MRI platform on clinical MRI scanners and facilitate translational studies at clinical settings.

Small animal, positron emission tomography-magnetic resonance imaging system based on a clinical magnetic resonance imaging scanner: evaluation of basic imaging performance

Development of advanced preclinical imaging techniques has had an important impact on the field of biomedical research, with positron emission tomography (PET) imaging the most mature of these efforts. Developers of preclinical PET scanners have joined the recent multimodality imaging trend by combining PET imaging with other modalities, such as magnetic resonance imaging (MRI). Our group has developed a combined PET-MRI insert for the imaging of animals up to the size of rats in a clinical 3T MRI scanner. The system utilizes a sequential scanner configuration instead of the more common coplanar geometry. The PET component of the system consists of a ring of 12 liquid-cooled, SiPM-based detector modules ( diameter = 15.2    cm ). System performance was evaluated with the NEMA NU 4-2008 protocol. Spatial resolution is ∼ 1.71    mm 5 cm from the center of the field-of-view measured from single-slice rebinned filtered backprojection-reconstructed images. Peak noise equivalent count rate is 17.7 kcps at 8.5 MBq; peak sensitivity is 2.9%. The MRI component of the system is composed of a 12-cm-diameter birdcage transmit/receive coil with a dual-preamplifier interface possessing very low noise preamplifiers. System performance was evaluated using American College of Radiology-based methods. Image homogeneity is 99%; the ghosting ratio is 0.0054. The signal-to-noise ratio is 95 and spatial resolution is ∼ 0.25    mm . There was no discernable cross-modality interference.

Dietary Docosahexaenoic Acid Improves Cognitive Function, Tissue Sparing, and Magnetic Resonance Imaging Indices of Edema and White Matter Injury in the Immature Rat after Traumatic Brain Injury

Traumatic brain injury (TBI) is the leading cause of acquired neurologic disability in children. Specific therapies to treat acute TBI are lacking. Cognitive impairment from TBI may be blunted by decreasing inflammation and oxidative damage after injury. Docosahexaenoic acid (DHA) decreases cognitive impairment, oxidative stress, and white matter injury in adult rats after TBI. Effects of DHA on cognitive outcome, oxidative stress, and white matter injury in the developing rat after experimental TBI are unknown. We hypothesized that DHA would decrease early inflammatory markers and oxidative stress, and improve cognitive, imaging and histologic outcomes in rat pups after controlled cortical impact (CCI). CCI or sham surgery was delivered to 17 d old male rat pups exposed to DHA or standard diet for the duration of the experiments. DHA was introduced into the dam diet the day before CCI to allow timely DHA delivery to the pre-weanling pups. Inflammatory cytokines and nitrates/nitrites were measured in the injured brains at post-injury Day (PID) 1 and PID2. Morris water maze (MWM) testing was performed at PID41-PID47. T2-weighted and diffusion tensor imaging studies were obtained at PID12 and PID28. Tissue sparing was calculated histologically at PID3 and PID50. DHA did not adversely affect rat survival or weight gain. DHA acutely decreased oxidative stress and increased anti-inflammatory interleukin 10 in CCI brains. DHA improved MWM performance and lesion volume late after injury. At PID12, DHA decreased T2-imaging measures of cerebral edema and decreased radial diffusivity, an index of white matter injury. DHA improved short- and long-term neurologic outcomes after CCI in the rat pup. Given its favorable safety profile, DHA is a promising candidate therapy for pediatric TBI. Further studies are needed to explore neuroprotective mechanisms of DHA after developmental TBI.

Dynamic responses of selective brain white matter fiber tracts to binge alcohol and recovery in the rat

To determine the dynamics of white matter vulnerability to excessive alcohol consumption, diffusion tensor imaging (DTI) was used in an animal model of alcohol exposure. Quantitative, in vivo fiber tracking results are presented from rats with DTI conducted at 3 time points: baseline; after 4 days of intragastric alcohol to blood alcohol levels of ~250mg/dL; and after one week of recovery. Binge alcohol followed by a week of sobriety resulted in rapidly reversible decreases in fractional anisotropy (FA), a measure of the coherence of fiber tracts, in callosal genu and fimbria-fornix but not splenium; and increases in mean diffusivity (MD), an index of freely diffusing water in tissue, selective to the fimbria-fornix. These effects were confirmed with tract-based spatial statistics (TBSS). The directionality of changes in DTI metrics reproduce those observed in human alcoholism. That a single exposure to binge alcohol can cause substantial transient changes detectable in DTI metrics demonstrates the potential for rapid neuroplasticity.

The translational role of diffusion tensor image analysis in animal models of developmental pathologies

Diffusion tensor magnetic resonance imaging (DTI) has proven itself a powerful technique for clinical investigation of the neurobiological targets and mechanisms underlying developmental pathologies. The success of DTI in clinical studies has demonstrated its great potential for understanding translational animal models of clinical disorders, and preclinical animal researchers are beginning to embrace this new technology to study developmental pathologies. In animal models, genetics can be effectively controlled, drugs consistently administered, subject compliance ensured, and image acquisition times dramatically increased to reduce between-subject variability and improve image quality. When pairing these strengths with the many positive attributes of DTI, such as the ability to investigate microstructural brain organization and connectivity, it becomes possible to delve deeper into the study of both normal and abnormal development. The purpose of this review is to provide new preclinical investigators with an introductory source of information about the analysis of data resulting from small animal DTI studies to facilitate the translation of these studies to clinical data. In addition to an in-depth review of translational analysis techniques, we present a number of relevant clinical and animal studies using DTI to investigate developmental insults in order to further illustrate techniques and to highlight where small animal DTI could potentially provide a wealth of translational data to inform clinical researchers.

Diffusion tensor imaging of diffuse axonal injury in a rat brain trauma model

Diffusion tensor imaging (DTI) was used to study traumatic brain injury. The impact-acceleration trauma model was used in rats. Here, in addition to diffusivities (mean, axial and radial), fractional anisotropy (FA) was used, in particular, as a parameter to characterize the cerebral tissue early after trauma. DTI was implemented at 7 T using fast spiral k-space sampling and the twice-refocused spin echo radiofrequency sequence for eddy current minimization. The method was carefully validated on different phantom measurements. DTI of a trauma group (n = 5), as well as a sham group (n = 5), was performed at different time points during 6 h following traumatic brain injury. Two cerebral regions, the cortex and corpus callosum, were analyzed carefully. A significant decrease in diffusivity in the trauma group versus the sham group was observed, suggesting the predominance of cellular edema in both cerebral regions. No significant FA change was detected in the cortex. In the corpus callosum of the trauma group, the FA indices were significantly lower. A net discontinuity in fiber reconstructions in the corpus callosum was observed by fiber tracking using DTI. Histological analysis using Hoechst, myelin basic protein and Bielschowsky staining showed fiber disorganization in the corpus callosum in the brains of the trauma group. On the basis of our histology results and the characteristics of the impact-acceleration model responsible for the presence of diffuse axonal injury, the detection of low FA caused by a drastic reduction in axial diffusivity and the presence of fiber disconnections of the DTI track in the corpus callosum were considered to be related to the presence of diffuse axonal injury.

Synergy of image analysis for animal and human neuroimaging supports translational research on drug abuse

The use of structural magnetic resonance imaging (sMRI) and diffusion tensor imaging (DTI) in animal models of neuropathology is of increasing interest to the neuroscience community. In this work, we present our approach to create optimal translational studies that include both animal and human neuroimaging data within the frameworks of a study of post-natal neuro-development in intra-uterine cocaine-exposure. We propose the use of non-invasive neuroimaging to study developmental brain structural and white matter pathway abnormalities via sMRI and DTI, as advanced MR imaging technology is readily available and automated image analysis methodology have recently been transferred from the human to animal imaging setting. For this purpose, we developed a synergistic, parallel approach to imaging and image analysis for the human and the rodent branch of our study. We propose an equivalent design in both the selection of the developmental assessment stage and the neuroimaging setup. This approach brings significant advantages to study neurobiological features of early brain development that are common to animals and humans but also preserve analysis capabilities only possible in animal research. This paper presents the main framework and individual methods for the proposed cross-species study design, as well as preliminary DTI cross-species comparative results in the intra-uterine cocaine-exposure study.

Murine diffusion imaging using snapshot interleaved EPI acquisition at 7T

Diffusion tensor imaging (DTI) is a powerful magnetic resonance imaging tool for quantitative assessment of white matter micro structure. The majority of DTI methods employ Echo Planar Imaging (EPI) because it is insensitive to motion. However, EPI suffers from distortions and signal losses induced by inhomogeneities in magnetic field susceptibility. This is particularly accentuated in murine imaging at very high magnetic fields. The purpose of this study is to demonstrate that a Snapshot Interleaved EPI acquisition block combined with a stimulated echo module for diffusion sensitization can be successfully used to obtain high quality DTI of a mouse brain at 7T. This technique preserves the EPI speed but reduces its susceptibility artifacts and signal losses. Signal to noise ratio is also reduced but remains higher than in the DTI acquisitions based on a fast low angle shot technique. In vivo results using this new approach are presented along with a full description of the methodology.

Tractographic reconstruction protocol optimization in the rat brain in-vivo: towards a normal atlas

The tractographic reconstruction of anatomical and microstructural features provided by Magnetic Resonance (MR) Diffusion Tensor Imaging (DTI) gives essential information of brain damage in several pathological animal models. The optimization of a tractographic protocol is undertaken in normal rats for the future construction of a reference atlas, as prerequisite for preclinical pathological in-vivo studies. High field, preclinical in-vivo DTI faces important difficulties relevant to Signal-to-Noise Ratio (SNR), distortion, high required resolution, movement sensitivity. Given a pixel-size of 0.17 mm and TE/TR = 29/6500 ms, b value and slice thickness were fixed at 700 s/mm(2) and 0.58 mm, respectively, on preventive ex-vivo studies. In-vivo studies led to the choice of 30 diffusion directions, averaged on 16 runs. The final protocol required 51 min scanning and permitted a reliable reconstruction of main rat brain bundles. Tract reconstruction stopping rules required proper setting. In conclusion, the viability of DTI tractography on in-vivo rat studies was shown, towards the construction of a normal reference atlas.

Diffusion tensor echo planar imaging using surface coil transceiver with a semiadiabatic RF pulse sequence at 14.1T

Diffusion magnetic resonance studies of the brain are typically performed using volume coils. Although in human brain this leads to a near optimal filling factor, studies of rodent brain must contend with the fact that only a fraction of the head volume can be ascribed to the brain. The use of surface coil as transceiver increases Signal-to-Noise Ratio (SNR), reduces radiofrequency power requirements and opens the possibility of parallel transmit schemes, likely to allow efficient acquisition schemes, of critical importance for reducing the long scan times implicated in diffusion tensor imaging. This study demonstrates the implementation of a semiadiabatic echo planar imaging sequence (echo time=40 ms, four interleaves) at 14.1T using a quadrature surface coil as transceiver. It resulted in artifact free images with excellent SNR throughout the brain. Diffusion tensor derived parameters obtained within the rat brain were in excellent agreement with reported values.

In vivo diffusion tensor magnetic resonance imaging and fiber tracking of the mouse brain

Until very recently, the study of neural architecture using fixed tissue has been a major scientific focus of neurologists and neuroanatomists. A non-invasive detailed insight into the brain's axonal connectivity in vivo has only become possible since the development of diffusion tensor magnetic resonance imaging (DT-MRI). This unique approach of analyzing axonal projections in the living brain was used in the present study to describe major white matter fiber tracts of the mouse brain and also to identify for the first time non-invasively the rich connectivity between the amygdala and different target regions. To overcome the difficulties associated with high spatially and temporally resolved DT-MRI measurements a 4-shot diffusion weighted spin echo (SE) echo planar imaging (EPI) protocol was adapted to mouse brain imaging at 9.4T. Diffusion tensor was calculated from data sets acquired by using 30 diffusion gradient directions while keeping the acquisition time at 91 min. Two fiber tracking algorithms were employed. A deterministic approach (fiber assignment by continuous tracking - FACT algorithm) allowed us to identify and generate the 3D representations of various neural pathways. A probabilistic approach was further used for the generation of probability maps of connectivity with which it was possible to investigate - in a statistical sense - all possible connecting pathways between selected seed points. We show here applications to determine the connection probability between regions belonging to the visual or limbic systems. This method does not require a priori knowledge about the projections' trajectories and is shown to be efficient even if the investigated pathway is long or three-dimensionally complex. Additionally, high resolution images of rotational invariant parameters of the diffusion tensor, such as fractional anisotropy, volume ratio or main eigenvalues allowed quantitative comparisons in-between regions of interest (ROIs) and showed significant differences between various white matter regions.

Quantitative diffusion tensor deterministic and probabilistic fiber tractography in relapsing-remitting multiple sclerosis

PURPOSE

Our aim was to study the quantitative fiber tractography variations and patterns in patients with relapsing-remitting multiple sclerosis (RRMS) and to assess the correlation between quantitative fiber tractography and Expanded Disability Status Scale (EDSS).

MATERIAL AND METHODS

Twenty-eight patients with RRMS and 28 age-matched healthy volunteers underwent a diffusion tensor MR imaging study. Quantitative deterministic and probabilistic fiber tractography were generated in all subjects. And mean numbers of tracked lines and fiber density were counted. Paired-samples t tests were used to compare tracked lines and fiber density in RRMS patients with those in controls. Bivariate linear regression model was used to determine the relationship between quantitative fiber tractography and EDSS in RRMS.

RESULTS

Both deterministic and probabilistic tractography's tracked lines and fiber density in RRMS patients were less than those in controls (P<.001). Both deterministic and probabilistic tractography's tracked lines and fiber density were found negative correlations with EDSS in RRMS (P<.001). The fiber tract disruptions and reductions in RRMS were directly visualized on fiber tractography.

CONCLUSION

Changes of white matter tracts can be detected by quantitative diffusion tensor fiber tractography, and correlate with clinical impairment in RRMS.

In vivo evidence for alcohol-induced neurochemical changes in rat brain without protracted withdrawal, pronounced thiamine deficiency, or severe liver damage

Magnetic resonance spectroscopy (MRS) studies in human alcoholics report decreases in N-acetylaspartate (NAA) and choline-containing (Cho) compounds. Whether alterations in brain metabolite levels are attributable to alcohol per se or to physiological effects of protracted withdrawal or impaired nutritional or liver status remains unclear. Longitudinal effects of alcohol on brain metabolites measured in basal ganglia with single-voxel MRS were investigated in sibling pairs of wild-type Wistar rats, with one rat per pair exposed to escalating doses of vaporized alcohol, the other to vapor chamber air. MRS was conducted before alcohol exposure and twice during exposure. After 16 weeks of alcohol exposure, rats achieved average blood alcohol levels (BALs) of approximately 293 mg per 100 ml and had higher Cho and a trend for higher glutamine+glutamate (Glx) than controls. After 24 weeks of alcohol exposure, BALs rose to approximately 445 mg per 100 ml, and alcohol-exposed rats had higher Cho, Glx, and glutamate than controls. Thiamine and thiamine monophosphate levels were significantly lower in the alcohol than the control group but did not reach levels low enough to be considered clinically relevant. Histologically, livers of alcohol-exposed rats exhibited greater steatosis and lower glycogenosis than controls, but were not cirrhotic. This study demonstrates a specific pattern of neurobiochemical changes suggesting excessive membrane turnover or inflammation, indicated by high Cho, and alterations to glutamate homeostasis in the rat brain in response to extended vaporized alcohol exposure. Thus, we provide novel in vivo evidence for alcohol exposure as causing changes in brain chemistry in the absence of protracted withdrawal, pronounced thiamine deficiency, or severe liver damage.

Rapid and efficient mapping of regional ventilation in the rat lung using hyperpolarized 3He with Flip Angle Variation for Offset of RF and Relaxation (FAVOR)

A novel imaging method is presented, Flip Angle Variation for Offset of RF and Relaxation (FAVOR), for rapid and efficient measurement of rat lung ventilation using hyperpolarized helium-3 (3He) gas. The FAVOR technique utilizes variable flip angles to remove the cumulative effect of RF pulses and T1 relaxation on the hyperpolarized gas signal and thereby eliminates the need for intervening air wash-out breaths and multiple cycles of 3He wash-in breaths before each image. The former allows an improvement in speed (by a factor of approximately 30) while the latter reduces the cost of each measurement (by a factor of approximately 5). The FAVOR and conventional ventilation methods were performed on six healthy male Brown Norway rats (190-270 g). Lobar measurements of ventilation, r, obtained with the FAVOR method were not significantly different from those obtained with the conventional method for the right middle and caudal and left lobes (P>0.05 by a Wilcoxon matched pairs test). A methacholine challenge test was also administered to an animal and reduction and recovery of r was detected by the FAVOR method. The reduced 3He consumption and the improvement in speed provided by FAVOR suggest that it may allow measurement of ventilation in human subjects not previously possible.

Flow-compensated self-gating

OBJECTIVE

Self-gating (SG) is a method to record cardiac movement during MR imaging. It uses information from an additional short, non-spatially encoded data acquisition. This usually lengthens TE and increases the sensitivity to flow artifacts. A new flow compensation scheme optimized for self-gating sequences is introduced that has very little or no time penalty over self-gating sequences without flow compensation.

MATERIALS AND METHODS

Three variants of a self-gated 2D spoiled gradient echo or fast low angle shot (FLASH) sequence were implemented: without (noFC), with a conventional, serial (cFC), and with a new, time-efficient flow compensation (sFC). In experiments on volunteers and small animals, the sequence variants were compared with regard to the SG signal and the flow artifacts in the images.

RESULTS

Both cFC and sFC reduce flow artifacts in cardiac images. The SG signal of the sFC is more sensitive to physiological motion, so that a cardiac trigger can be extracted more precisely as in cFC. In a typical setting for small animal imaging, sFC technique reduces the echo/repetition time over cFC by about 23%/14%.

CONCLUSION

The time-efficient sFC technique provides flow-compensated images with cardiac triggering in both volunteers and small animals.

Early postnatal development of rat brain: in vivo diffusion tensor imaging

Perinatal hypoxia is a major cause of neurodevelopmental deficits. Neuronal migration patterns are particularly sensitive to perinatal hypoxia/ischemia and are associated with the clinical deficits. The rat model of hypoxia/ischemia at P7 mimics that of perinatal injury in humans. Before assessing the effects of postnatal injury on brain development, it is essential to determine the normal developmental trajectories of various brain structures in individual animals. In vivo longitudinal diffusion tensor imaging (DTI) was performed from postnatal day 0 (P0) to P56 on Wistar rats. The DTI metrics, mean diffusivity (MD), fractional anisotropy (FA), axial (lambdal) and radial (lambdat) diffusivities, were determined for four gray matter and eight white matter structures. The FA of the cortical plate and the body of corpus callosum decreased significantly during the first 3 weeks after birth. The decrease in the cortical plate's FA value was associated mainly with an increase in lambdat. The initial decrease in FA of corpus callosum was associated with a significant decrease in lambdal. The FA of corpus callosum increased during the rest of the observational period, which was mainly associated with a decrease in lambdat. The FA of gray matter structures, hippocampus, caudate putamen, and cortical mantle did not show significant changes between P0 and P56. In contrast, the majority of white matter structures showed significant changes between P0 and P56. These temporal changes in the DTI metrics were related to the neuronal and axonal pruning and myelination that are known to occur in the developing brain.

Magnetic resonance imaging approaches for studying alcoholism using mouse models

Mice are one of the most commonly used animal models of alcoholism, and extensive genetic and behavioral data related to alcohol consumption and its consequences in different strains are available. However, only recently have researchers begun to combine magnetic resonance imaging (MRI) technology with other experimental strategies to study the effects of alcohol in mice. This powerful combination enables structural and functional data of alcohol's effects on the brain of living animals to be obtained. This article reviews the challenges associated with the use of these technologies in mice and discusses the application of these advanced technologies to mouse models of alcoholism.