Magnetic resonance imaging as a tool for in vivo and ex vivo anatomical phenotyping in experimental genetic models

In vivo symmetric multi-contrast MRI brain templates and atlas for spontaneously hypertensive rats

Spontaneously hypertensive rats (SHRs) are a valuable animal model of essential hypertension. The increasing use of SHRs in neuroimaging has generated an urgent demand for a template set that provides a reference for advanced data analysis. Structural T2-weighted magnetic resonance imaging (MRI), diffusion tensor imaging (DTI) and functional MRI scans that were used to build the template set were obtained from 8 SHRs longitudinally scanned in vivo at 10, 24 and 52 weeks of age. These symmetric multi-contrast templates were constructed by iterative registration and averaging. The cortical atlas was derived from the Tohoku atlas, and the subcortical regions were manually delineated based on the templates. A set of SHR brain images named the Hebei Medical University rat brain template set (HRT) comprised 3D symmetric T2WI, raw T2-weighted signal with no added diffusion weighting (B0), fractional anisotropy (FA), mean diffusivity (MD) and blood oxygen level-dependent (BOLD) templates; tissue probability maps (TPMs) of gray matter (GM), white matter (WM) and cerebrospinal fluid (CSF); and a whole-brain atlas with 163 labels. We quantitatively validated the template and characterized the longitudinal changes in brain morphology in different brain tissues as SHRs aged. To our knowledge, the HRT is the first MRI template set for SHRs. We believe that the HRT can serve as a beneficial tool for precise analysis of the SHR brain using structural and functional MRI, which can promote neuroimaging studies on essential hypertension.

Ratlas-LH: An MRI template of the Lister hooded rat brain with stereotaxic coordinates for neurosurgical implantations

There is currently no brain atlas available to specifically determine stereotaxic coordinates for neurosurgery in Lister hooded rats despite the popularity of this strain for behavioural neuroscience studies in the United Kingdom and elsewhere. We have created a dataset, which we refer to as ‘Ratlas-LH’ (for Lister hooded). Ratlas-LH combines in vivo magnetic resonance images of the brain of young adult male Lister hooded rats with ex vivo micro-computed tomography images of the ex vivo skull, as well as a set of delineations of brain regions, adapted from the Waxholm Space Atlas of the Sprague Dawley Rat Brain. Ratlas-LH was produced with an isotropic resolution of 0.15 mm. It has been labelled in such a way as to provide a stereotaxic coordinate system for the determination of distances relative to the skull landmark of bregma. We have demonstrated that the atlas can be used to determine stereotaxic coordinates to accurately target brain regions in the Lister hooded rat brain. Ratlas-LH is freely available to facilitate neurosurgical procedures in the Lister hooded rat.

MRI study of cerebral blood flow, vascular reactivity, and vascular coupling in systemic hypertension

Chronic hypertension alters cerebrovascular function, which can lead to neurovascular pathologies and increased susceptibility to neurological disorders. The purpose of this study was to utilize in vivo MRI methods with corroborating immunohistology to evaluate neurovascular dysfunction due to progressive chronic hypertension. The spontaneously hypertensive rat (SHR) model at different stages of hypertension was studied to evaluate: i) basal cerebral blood flow (CBF), ii) cerebrovascular reactivity (CVR) assessed by CBF and blood-oxygenation level dependent (BOLD) signal changes to hypercapnia, iii) neurovascular coupling from CBF and BOLD changes to forepaw stimulation, and iv) damage of neurovascular unit (NVU) components (microvascular, astrocyte and neuron densities). Comparisons were made with age-matched normotensive Wistar Kyoto (WKY) rats. In 10-week SHR (mild hypertension), basal CBF was higher (p < 0.05), CVR trended higher, and neurovascular coupling response was higher (p < 0.05), compared to normotensive rats. In 40-week SHR (severe hypertension), basal CBF, CVR, and neurovascular coupling response were reversed to similar or below normotensive rats, and were significantly different from 10-week SHR (p < 0.05). Immunohistological analysis found significantly reduced microvascular density, increased astrocytes, and reduced neuronal density in SHR at 40 weeks (p < 0.05) but not at 10 weeks (p > 0.05) in comparison to age-matched controls. In conclusion, we observed a bi-phasic basal CBF, CVR and neurovascular coupling response from early to late hypertension using in vivo MRI, with significant changes prior to changes in the NVU components from histology. MRI provides clinically relevant data that might be useful to characterize neurovascular pathogenesis on the brain in hypertension.

Brain Morphometry and Longitudinal Relaxation Time of Spontaneously Hypertensive Rats (SHRs) in Early and Intermediate Stages of Hypertension Investigated by 3D VFA-SPGR MRI

Cerebral small vessel disease(s) (SVD) results from pathological changes of the small blood vessels in the brain and is common in older people. The diagnostic features by which SVD manifests in brain includes white matter hyperintensities, lacunes, dilated perivascular spaces, microbleeds, and atrophy. In the present study, we use in vivo magnetic resonance imaging (MRI) to characterize brain morphometry and longitudinal relaxation time (T1) of spontaneously hypertensive rats (SHRs) to study the contribution of chronic hypertension to SVD relevant pathology. Male SHR and Wistar-Kyoto (WKY) rats underwent 3D variable flip angle spoiled gradient echo brain MRI at 9.4 T at early (seven weeks old) and established (19 weeks old) stages of hypertension. The derived proton density weighted and T1 images were utilized for morphometry and to characterize T1 properties in gray matter (GM), white matter (WM) and cerebrospinal fluid (CSF). Custom tissue probability maps were constructed for accurate computerized whole brain tissue segmentations and voxel-wise analyses. Characteristic morphological differences between the two strains included enlarged ventricles, smaller corpus callosum (CC) volumes and general 'thinning' of CC in SHR compared to WKY rats at both age groups. While we did not observe parenchymal T1 differences, the T1 of CSF was elevated in SHR compared to controls. Collectively these findings indicate that SHRs develop WM atrophy which is a clinically robust MRI biomarker associated with WM degeneration.

Enhanced Cortical Thickness Measurements for Rodent Brains via Lagrangian-based RK4 Streamline Computation

The cortical thickness of the mammalian brain is an important morphological characteristic that can be used to investigate and observe the brain's developmental changes that might be caused by biologically toxic substances such as ethanol or cocaine. Although various cortical thickness analysis methods have been proposed that are applicable for human brain and have developed into well-validated open-source software packages, cortical thickness analysis methods for rodent brains have not yet become as robust and accurate as those designed for human brains. Based on a previously proposed cortical thickness measurement pipeline for rodent brain analysis,¹ we present an enhanced cortical thickness pipeline in terms of accuracy and anatomical consistency. First, we propose a Lagrangian-based computational approach in the thickness measurement step in order to minimize local truncation error using the fourth-order Runge-Kutta method. Second, by constructing a line object for each streamline of the thickness measurement, we can visualize the way the thickness is measured and achieve sub-voxel accuracy by performing geometric post-processing. Last, with emphasis on the importance of an anatomically consistent partial differential equation (PDE) boundary map, we propose an automatic PDE boundary map generation algorithm that is specific to rodent brain anatomy, which does not require manual labeling. The results show that the proposed cortical thickness pipeline can produce statistically significant regions that are not observed in the the previous cortical thickness analysis pipeline.

Mapping registration sensitivity in MR mouse brain images

Nonlinear registration algorithms provide a way to estimate structural (brain) differences based on magnetic resonance images. Their ability to align images of different individuals and across modalities has been well-researched, but the bounds of their sensitivity with respect to the recovery of salient morphological differences between groups are unclear. Here we develop a novel approach to simulate deformations on MR brain images to evaluate the ability of two registration algorithms to extract structural differences corresponding to biologically plausible atrophy and expansion. We show that at a neuroanatomical level registration accuracy is influenced by the size and compactness of structures, but do so differently depending on how much change is simulated. The size of structures has a small influence on the recovered accuracy. There is a trend for larger structures to be recovered more accurately, which becomes only significant as the amount of simulated change is large. More compact structures can be recovered more accurately regardless of the amount of simulated change. Both tested algorithms underestimate the full extent of the simulated atrophy and expansion. Finally we show that when multiple comparisons are corrected for at a voxelwise level, a very low rate of false positives is obtained. More interesting is that true positive rates average around 40%, indicating that the simulated changes are not fully recovered. Simulation experiments were run using two fundamentally different registration algorithms and we identified the same results, suggesting that our findings are generalizable across different classes of nonlinear registration algorithms.

A segmentation protocol and MRI atlas of the C57BL/6J mouse neocortex

The neocortex is the largest component of the mammalian cerebral cortex. It integrates sensory inputs with experiences and memory to produce sophisticated responses to an organism's internal and external environment. While areal patterning of the mouse neocortex has been mapped using histological techniques, the neocortex has not been comprehensively segmented in magnetic resonance images. This study presents a method for systematic segmentation of the C57BL/6J mouse neocortex. We created a minimum deformation atlas, which was hierarchically segmented into 74 neocortical and cortical-related regions, making it the most detailed atlas of the mouse neocortex currently available. In addition, we provide mean volumes and relative intensities for each structure as well as a nomenclature comparison between the two most cited histological atlases of the mouse brain. This MR atlas is available for download, and it should enable researchers to perform automated segmentation in genetic models of cortical disorders.

Smoothness-guided 3-D reconstruction of 2-D histological images

This paper tackles two problems: (1) the reconstruction of 3-D volumes from 2-D post-mortem slices (e.g., histology, autoradiography, immunohistochemistry) in the absence of external reference, and (2) the quantitative evaluation of the 3-D reconstruction. We note that the quality of a reconstructed volume is usually assessed by considering the smoothness of some reconstructed structures of interest (e.g., the gray-white matter surfaces in brain images). Here we propose to use smoothness as a means to drive the reconstruction process itself. From a pair-wise rigid reconstruction of the 2-D slices, we first extract the boundaries of structures of interest. Those are then smoothed with a min-max curvature flow confined to the 2-D planes in which the slices lie. Finally, for each slice, we estimate a linear or flexible transformation from the sparse displacement field computed from the flow, which we apply to the original 2-D slices to obtain a smooth volume. In addition, we present a co-occurrence matrix-based technique to quantify the smoothness of reconstructed volumes. We discuss and validate the application of both our reconstruction approach and the smoothness measure on synthetic examples as well as real histological data.

Cortical thickness measured from MRI in the YAC128 mouse model of Huntington's disease

A recent study found differences in localised regions of the cortex between the YAC128 mouse model of Huntington's Disease (HD) and wild-type mice. There are, however, few tools to automatically examine shape differences in the cortices of mice. This paper describes an algorithm for automatically measuring cortical thickness across the entire cortex from MRI of fixed mouse brain specimens. An analysis of the variance of the method showed that, on average, a 50 microm (0.05 mm) localised difference in cortical thickness can be measured using MR scans. Applying these methods to 8-month-old YAC128 mouse model mice representing an early stage of HD, we found an increase in cortical thickness in the sensorimotor cortex, and also revealed regions wherein decreasing striatal volume correlated with increasing cortical thickness, indicating a potential compensatory response.