Development of representative magnetic resonance imaging-based atlases of the canine brain and evaluation of three methods for atlas-based segmentation

Magnetic resonance imaging in canine idiopathic epilepsy: a mini-review

Magnetic resonance imaging (MRI) in an integral part of the diagnostic workup in canines with idiopathic epilepsy (IE). While highly sensitive and specific in identifying structural lesions, conventional MRI is unable to detect changes at the microscopic level. Utilizing more advanced neuroimaging techniques may provide further information on changes at the neuronal level in the brain of canines with IE, thus providing crucial information on the pathogenesis of canine epilepsy. Additionally, earlier detection of these changes may aid clinicians in the development of improved and targeted therapies. Advances in MRI techniques are being developed which can assess metabolic, cellular, architectural, and functional alterations; as well alterations in neuronal tissue mechanical properties, some of which are currently being applied in research on canine IE. This mini-review focuses on novel MRI techniques being utilized to better understand canine epilepsy, which include magnetic resonance spectroscopy, diffusion-weighted imaging, diffusion tensor imaging, perfusion-weighted imaging, voxel based morphometry, and functional MRI; as well as techniques applied in human medicine and their potential use in veterinary species.

Age-Related Brain Atrophy and the Positive Effects of Behavioral Enrichment in Middle-Aged Beagles

Aging dogs serve as a valuable preclinical model for Alzheimer's disease (AD) due to their natural age-related development of β-amyloid (Aβ) plaques, human-like metabolism, and large brains that are ideal for studying structural brain aging trajectories from serial neuroimaging. Here we examined the effects of chronic treatment with the calcineurin inhibitor (CNI) tacrolimus or the nuclear factor of activated T cells (NFAT)-inhibiting compound Q134R on age-related canine brain atrophy from a longitudinal study in middle-aged beagles (36 females, 7 males) undergoing behavioral enrichment. Annual MRI was analyzed using modern, automated techniques for region-of-interest-based and voxel-based volumetric assessments. We found that the frontal lobe showed accelerated atrophy with age, while the caudate nucleus remained relatively stable. Remarkably, the hippocampus increased in volume in all dogs. None of these changes were influenced by tacrolimus or Q134R treatment. Our results suggest that behavioral enrichment can prevent atrophy and increase the volume of the hippocampus but does not prevent aging-associated prefrontal cortex atrophy.

Comparative neurogenetics of dog behavior complements efforts towards human neuropsychiatric genetics

Domestic dogs display a wide array of heritable behaviors that have intermediate genetic complexity thanks to a long history of human-influenced selection. Comparative genetics in dogs could address the scarcity of non-human neurogenetic systems relevant to human neuropsychiatric disorders, which are characterized by mental, emotional, and behavioral symptoms and involve vastly complex genetic and non-genetic risk factors. Our review describes the diverse behavioral "phenome" of domestic dogs, past and ongoing sources of behavioral selection, and the state of canine behavioral genetics. We highlight two naturally disordered behavioral domains that illustrate how dogs may prove useful as a comparative, forward neurogenetic system: canine age-related cognitive dysfunction, which can be examined more rapidly given the attenuated lifespan of dogs, and compulsive disorders, which may have genetic roots in purpose-bred behaviors. Growing community science initiatives aimed at the companion dog population will be well suited to investigating such complex behavioral phenotypes and offer a comparative resource that parallels human genomic initiatives in scale and dimensionality.

Automatic brain extraction and brain tissues segmentation on multi-contrast animal MRI

For many neuroscience applications, brain extraction in MRI images is the first pre-processing step of a quantification pipeline. Once the brain is extracted, further post-processing calculations become faster, more specific and easier to implement and interpret. It is the case, for example, of functional MRI brain studies, or relaxation time mappings and brain tissues classifications to characterise brain pathologies. Existing brain extraction tools are mostly adapted to work on the human anatomy, this gives poor results when applied to animal brain images. We have developed an atlas-based Veterinary Images Brain Extraction (VIBE) algorithm that encompasses a pre-processing step to adapt the atlas to the patient's image, and a subsequent registration step. We show that the brain extraction is achieved with excellent results in terms of Dice and Jaccard metrics. The algorithm is automatic, with no need to adapt the parameters in a broad range of situations: we successfully tested multiple MRI contrasts (T1-weighted, T2-weighted, T2-weighted FLAIR), all the acquisition planes (sagittal, dorsal, transverse), different animal species (dogs and cats) and canine cranial conformations (brachycephalic, mesocephalic, dolichocephalic). VIBE can be successfully extended to other animal species, provided that an atlas for that specific species exists. We show also how brain extraction, as a preliminary step, can help to segment brain tissues with a K-Means clustering algorithm.

Age-related brain atrophy in cats without apparent neurological and behavioral signs using voxel-based morphometry

Introduction

Brain atrophy is observed with aging and may cause cognitive decline or dysfunction. Aging cats may demonstrate behavioral changes related to cognitive dysfunction. In the clinical veterinary field, although the conventional region of interest method by manual or semiauto tracing on magnetic resonance imaging is used to detect atrophy of regional structures, such as the hippocampus, it is difficult to assess atrophy globally. Voxel-based morphometry (VBM) has been developed to detect global and regional abnormalities in humans. The purpose of the present study investigates whether the feline brain volume decreases with aging using VBM analysis.

Materials

A total of 65 cats, aged 17-200 months, without apparent neurological and behavioral signs were included in the statistical analysis.

Results

We observed that the gray matter in the bilateral parietal lobes was decreased significantly with aging. The regions that showed decreased volume included the right postcruciate, cingulate gyrus, rostral suprasylvian/ectosylvian gyri, and the left postcruciate gyrus. No significant reduction in white matter was observed. Together, our results show that age-related brain atrophy can be detected using VBM analysis.

Discussion

The age-related atrophy of the parietal cortex may not cause neurological and behavioral signs in cats. Therefore, veterinarians should consider age when assessing the relation between morphometric and functional abnormalities of the parietal cortex in cats.

Volumetric assessment and longitudinal changes of subcortical structures in formalinized Beagle brains

High field MRI is an advanced technique for diagnostic and research purposes on animal models, such as the Beagle dog. In this context, studies on neuroscience applications, e.g. aging and neuro-pathologies, are currently increasing. This led to a need for reference values, in terms of volumetric assessment, for the structures typically involved. Nowadays, several canine brain MRI atlases have been provided. However, no reports are available regarding the measurements’ reproducibility and little is known about the effect of formalin on MRI segmentation. Here, we assessed the segmentation variability of selected structures among operators (two operators segmented the same data) in a sample of 11 Beagle dogs. Then, we analyzed, for one Beagle dog, the longitudinal volumetric changes of these structures. We considered four conditions: in vivo, post mortem (after euthanasia), ex vivo (brain extracted and studied after 1 month in formalin, and after 12 months). The MRI data were collected with a 3 T scanner. Our findings suggest that the segmentation procedure was overall reproducible since only slight statistical differences were detected. In the post mortem/ ex vivo comparison, most structures showed a higher contrast, thereby leading to greater reproducibility between operators. We observed a net increase in the volume of the studied structures. This could be justified by the intrinsic relaxation time changes observed because of the formalin fixation. This led to an improvement in brain structure visualization and segmentation. To conclude, MRI-based segmentation seems to be a useful and accurate tool that allows longitudinal studies on formalin-fixed brains.

Fuzzy C-Means Clustering Algorithm-Based Magnetic Resonance Imaging Image Segmentation for Analyzing the Effect of Edaravone on the Vascular Endothelial Function in Patients with Acute Cerebral Infarction

This paper aimed to discuss the denoising ability of magnetic resonance imaging (MRI) images based on fuzzy C-means clustering (FCM) algorithm and the influence of Butylphthalide combined with Edaravone treatment on nerve function and vascular endothelial function in patients with acute cerebral infarction (ACI). Based on FCM algorithm, Markov Random Field (MRF) model algorithm was introduced to obtain a novel algorithm (NFCM), which was compared with FCM and MRF algorithm in terms of misclassification rate (MCR) and difference of Kappa index (KI). 90 patients with ACI diagnosed in hospital from December 2018 to December 2019 were selected as subjects, who were divided into combined treatment group (conventional treatment + Edaravone + Butylphthalide) and Edaravone group (conventional treatment + Edaravone) randomly, each consisting of 45 cases. The National Institutes of Health Stroke Scale (NIHSS) score and endothelial function index level such as plasma nitric oxide (NO), human endothelin-1 (ET-1), and vascular endothelial cell growth factor (VEGF) were compared before and after treatment between the two groups. The results showed that the MCR of NFCM was evidently inferior to FCM and MRF, and the KI was notably higher relative to the other two algorithms. After treatment, the NIHSS score of the combined treatment group was (9.09 ± 1.86) points and that of Edaravone group was (14.97 ± 3.44) points, with evident difference between the two groups (P < 0.05). After treatment, the NO of the combined treatment was (54.63 ± 4.85), and that of Edaravone group was (41.54 ± 5.27), which was considerably different (P < 0.01), and the VEGF and ET-1 of combined treatment group were greatly inferior to Edaravone group (P < 0.01). It was revealed that the novel algorithm based on FCM can obtain more favorable quality and segmentation accuracy of MRI images. Moreover, Butylphthalide combined with Edaravone treatment can effectively improve nerve function, vascular endothelial function, and short-term prognosis in ACI, which was safe and worthy of clinical adoption.

Anatomic Interactive Atlas of the Loggerhead Sea Turtle (Caretta caretta) Head

Simple Summary

Because several diseases have been reported affecting the head of sea turtles, accurate anatomic knowledge of this body part is necessary. We provide an open access, anatomic, interactive atlas of the head of the loggerhead sea turtle (Caretta caretta), to facilitate anatomic learning using osteology, gross dissection, and computed tomography (CT) images. Using segmentation and visualization software, relevant anatomic structures were identified and colored in all images, and a computer atlas was developed. This atlas, composed of 55 images, provides an interactive anatomic resource for veterinarians, biologists, researchers, and students involved in loggerhead sea turtle conservation.

Abstract

The head of the sea turtle is susceptible to congenital, developmental, traumatic, and infectious disorders. An accurate interpretation and thorough understanding of the anatomy of this region could be useful for veterinary practice on sea turtles. The purpose of this study was to develop an interactive two-dimensional (2D) atlas viewing software of the head of the loggerhead sea turtle (Caretta caretta) using images obtained via osteology, gross dissections, and computed tomography (CT). The atlas is composed of 10 osteology, 13 gross dissection, 10 sagittal multiplanar reconstructed CT (bone and soft tissue kernels), and 22 transverse CT (bone and soft tissue windows) images. All images were segmented and colored using ITK-SNAP software. The visualization and image assessment were performed using the Unity 3D platform to facilitate the development of interactive content in 2D. This atlas can be useful as an interactive anatomic resource for assessment of the head of loggerhead sea turtles.

Diffusion tensor imaging of the visual pathway in dogs with primary angle-closure glaucoma

OBJECTIVE

To describe measurements of in vivo structures of the visual pathway beyond the retina and optic nerve head associated with canine primary angle-closure glaucoma (PACG).

METHODS

A prospective pilot study was conducted using magnetic resonance diffusion tensor imaging (DTI) to obtain quantitative measures of the optic nerve, chiasm, tract, and lateral geniculate nucleus (LGN) in dogs with and without PACG. 3-Tesla DTI was performed on six affected dogs and five breed, age- and sex-matched controls. DTI indices of the optic nerve, optic chiasm, optic tracts, and LGN were compared between normal, unilateral PACG, and bilateral PACG groups. Intra-class correlation coefficient (ICC) was calculated to assess intra-observer reliability.

RESULTS

Quantitative measurements of the optic nerve, optic tract, optic chiasm, and LGN were obtained in all dogs. There was a trend for reduced fractional anisotropy (FA) associated with disease for all structures assessed. Compared to the same structure in normal dogs, FA, and radial diffusivity (RD) of the optic nerve was consistently higher in the unaffected eye in dogs with unilateral PACG. Intra-observer reliability was excellent for measurements of the optic nerve (ICC: 0.92), good for measurements of the optic tract (ICC: 0.89) and acceptable for measures of the optic chiasm (ICC: 0.71) and lateral geniculate nuclei (ICC: 0.76).

CONCLUSION

Diffusivity and anisotropy measures provide a quantifiable means to evaluate the visual pathway in dogs. DTI has potential to provide in vivo measures of axonal and myelin injury and transsynaptic degeneration in canine PACG.

Stereotactic Cortical Atlas of the Domestic Canine Brain

The domestic canine (canis familiaris) is a growing novel model for human neuroscientific research. Unlike rodents and primates, they demonstrate unique convergent sociocognitive skills with humans, are highly trainable and able to undergo non-invasive experimental procedures without restraint, including fMRI. In addition, the gyrencephalic structure of the canine brain is more similar to that of human than rodent models. The increasing use of dogs for non-invasive neuroscience studies has generating a need for a standard canine cortical atlas that provides common spatial referencing and cortical segmentation for advanced neuroimaging data processing and analysis. In this manuscript we create and make available a detailed MRI-based cortical atlas for the canine brain. This atlas includes a population template generated from 30 neurologically and clinically normal non-brachycephalic dogs, tissue segmentation maps and a cortical atlas generated from Jerzy Kreiner's myeloarchitectonic-based histology atlas. The provided cortical parcellation includes 234 priors from frontal, sensorimotor, parietal, temporal, occipital, cingular and subcortical regions. The atlas was validated using an additional canine cohort with variable cranial conformations. This comprehensive cortical atlas provides a reference standard for canine brain research and will improve and standardize processing and data analysis and interpretation in functional and structural MRI research.

Network analysis of canine brain morphometry links tumour risk to oestrogen deficiency and accelerated brain ageing

Structural ‘brain age’ is a valuable but complex biomarker for several brain disorders. The dog is an unrivalled comparator for neurological disease modeling, however canine brain morphometric diversity creates computational and statistical challenges. Using a data-driven approach, we explored complex interactions between patient metadata, brain morphometry, and neurological disease. Twenty-four morphometric parameters measured from 286 canine brain magnetic resonance imaging scans were combined with clinical parameters to generate 9,438 data points. Network analysis was used to cluster patients according to their brain morphometry profiles. An ‘aged-brain’ profile, defined by a small brain width and volume combined with ventriculomegaly, was revealed in the Boxer breed. Key features of this profile were paralleled in neutered female dogs which, relative to un-neutered females, had an 11-fold greater risk of developing brain tumours. Boxer dog and geriatric dog groups were both enriched for brain tumour diagnoses, despite a lack of geriatric Boxers within the cohort. Our findings suggest that advanced brain ageing enhances brain tumour risk in dogs and may be influenced by oestrogen deficiency—a risk factor for dementia and brain tumours in humans. Morphometric features of brain ageing in dogs, like humans, might better predict neurological disease risk than patient chronological age.

Grey matter volume in healthy and epileptic beagles using voxel-based morphometry - a pilot study

BACKGROUND

One of the most common chronic neurological disorders in dogs is idiopathic epilepsy (IE) diagnosed as epilepsy without structural changes in the brain. In the current study the hypothesis should be proven that subtle grey matter changes occur in epileptic dogs. Therefore, magnetic resonance (MR) images of one dog breed (Beagles) were used to obtain an approximately uniform brain shape. Local differences in grey matter volume (GMV) were compared between 5 healthy Beagles and 10 Beagles with spontaneously recurrent seizures (5 dogs with IE and 5 dogs with structural epilepsy (SE)), using voxel-based morphometry (VBM). T1W images of all dogs were prepared using Amira 6.3.0 for brain extraction, FSL 4.1.8 for registration and SPM12 for realignment. After creation of tissue probability maps of cerebrospinal fluid, grey and white matter from control images to segment all extracted brains, GM templates for each group were constructed to normalize brain images for parametric statistical analysis, which was achieved using SPM12.

RESULTS

Epileptic Beagles (IE and SE Beagles) displayed statistically significant reduced GMV in olfactory bulb, cingulate gyrus, hippocampus and cortex, especially in temporal and occipital lobes. Beagles with IE showed statistically significant decreased GMV in olfactory bulb, cortex of parietal and temporal lobe, hippocampus and cingulate gyrus, Beagles with SE mild statistically significant GMV reduction in temporal lobe (p < 0.05; family- wise error correction).

CONCLUSION

These results suggest that, as reported in epileptic humans, focal reduction in GMV also occurs in epileptic dogs. Furthermore, the current study shows that VBM analysis represents an excellent method to detect GMV differences of the brain between a healthy dog group and dogs with epileptic syndrome, when MR images of one breed are used.

A stereotaxic breed-averaged, symmetric T2w canine brain atlas including detailed morphological and volumetrical data sets

Stereotaxic systems and automatic tissue segmentation routines enable neuronavigation as well as reproducible processing of neuroimage datasets. Such systems have been developed for humans, non-human-primates, sheep, and rodents, but not for dogs. Although dogs share important neurofunctional and -anatomical features with humans, and in spite of their importance in translational neuroscience, little is known about the variability of the canine brain morphology and, possibly related, function. Moreover, we lack templates, tissue probability maps (TPM), and stereotaxic brain labels for implementation in standard software utilities such as Statistical Parametric Mapping (SPM). Hence, objective and reproducible, image-based investigations are currently impeded in dogs. We have created a detailed stereotaxic reference frame for dogs including TPM and tissue labels, enabling inter-individual and cross-study neuroimage analysis. T2w datasets were acquired from 16 neurologically inconspicuous dogs of different breeds by 3T MRI. The datasets were averaged after initial preprocessing using linear and nonlinear registration algorithms as implemented in SPM8. TPM for gray (GM) and white matter (WM) as well as cerebrospinal fluid (CSF) were created. Different cortical, subcortical, medullary, and CSF regions were manually labeled to create a spatial binary atlas being aligned with the template. A proof-of-concept for automatic determination of morphological and volumetrical characteristics was performed using additional canine datasets (n = 64) including a subgroup of laboratory beagles (n = 24). Overall, 21 brain regions were labeled using the segmented tissue classes of the brain template. The proof-of-concept trial revealed excellent suitability of the created tools for image processing and subsequent analysis. There was high intra-breed variability in frontal lobe and hippocampus volumes, and noticeable inter-breed corpus callosum volume variation. The T2w brain template provides important, breed-averaged canine brain anatomy features in a spatial standard coordinate system. TPM allows automatic tissue segmentation using SPM and enables unbiased automatic image processing or morphological characterization in different canine breeds. The reported volumetric and morphometric results may serve as a starting point for further research aimed at in vivo analysis of canine brain anatomy and function.