Brain white and gray matter anatomy of MRI segmentation based on tissue evaluation

Different approaches to gray and white matter measurements in magnetic resonance imaging (MRI) have been studied. For clinical use, the estimated values must be reliable and accurate when, unfortunately, many techniques fail on these criteria in an unrestricted clinical environment. A recent method for tissue clusterization in MRI analysis has the advantage of great simplicity, and it takes the account of partial volume effects. In this study, we will evaluate the intensity of MR sequences known as T1-weighted images in an axial sliced section. Intensity group clustering algorithms are proposed to achieve further diagnosis for brain MRI, which has been hardly studied. Subjective study has been suggested to evaluate the clustering group intensity in order to obtain the best diagnosis as well as better detection for the suspected cases. This technique makes use of image tissue biases of intensity value pixels to provide 2 regions of interest as techniques. Moreover, the original mathematic solution could still be used with a specific set of modern sequences. There are many advantages to generalize the solution, which give far more scope for application and greater accuracy.     

Characterization of central nervous system structures by magnetic resonance diffusion anisotropy

Diffusion-weighted magnetic resonance imaging (MRI) provides information about tissue water diffusion. Diffusion anisotropy, which can be measured with diffusion tensor MRI, is a quantitative measure of the directional dependence of the diffusion restriction that is introduced by biological structures such as nerve fibers. Diffusion tensor MRI data was obtained in the brain, brain stem, and cervical spinal cord. For each region, scans were performed in four normal volunteers. Fractional anisotropy (FA), an index of diffusion anisotropy, was measured within regions of interest located in the corpus callosum, capsula interna, thalamus, caudate nucleus, putamen, brain cortex, pyramidal tract of the medulla, accessory olivary nucleus, dorsal olivary nucleus, inferior olivary nucleus, spinal white and gray matter. The highest FA value was measured in the corpus callosum (81 +/- 3%). The values of the other areas decreased in the following order: pyramidal tract in the medulla (72 +/- 1%), spinal white matter (65 +/- 4%), capsula interna (62 +/- 3%), accessory olivary nucleus (36 +/- 2%), spinal gray matter (35 +/- 5%), dorsal olivary nucleus in the medulla (29 +/- 2%), thalamus (28 +/- 2%), inferior olivary nucleus (15 +/- 2%), putamen (13 +/- 2%), caudate nucleus (13 +/- 2%), and brain cortex (9 +/- 1%). Our results indicate that the underlying fiber architecture, fiber density, and uniformity of nerve fiber direction affect anisotropy values of the various structures. Characterization of various central nervous system structures with diffusion anisotropy is possible and may be useful to monitor degenerative diseases in the central nervous system.     

High-resolution magnetic resonance imaging tracks changes in organ and tissue mass in obese and aging rats

Magnetic resonance imaging (MRI) has the ability to discriminate between various soft tissues in vivo. Whole body, specific organ, total adipose tissue (TAT), intra-abdominal adipose tissue (IAAT), and skeletal muscle (SM) weights determined by MRI were compared with weights determined by dissection and chemical analysis in two studies with male Sprague-Dawley rats. A 4.2-T MRI machine acquired high-resolution, in vivo, longitudinal whole body images of rats as they developed obesity or aged. Weights of the whole body and specific tissues were determined using computer image analysis software, including semiautomatic segmentation algorithms for volume calculations. High correlations were found for body weight (r = 0.98), TAT (r = 0.99), and IAAT (r = 0.98) between MRI and dissection and chemical analyses. MRI estimated the weight of the brain, kidneys, and spleen with high accuracy (r > 0.9), but overestimated IAAT, SM, and liver volumes. No differences were detected in organ weights using MRI and dissection measurements. Longitudinal MRI measurements made during the development of obesity and aging accurately represented changes in organ and tissue mass.     

Standardized method for the harvest of nonhuman primate tissue optimized for multiple modes of analyses

Appropriate animal models are critical to conduct translational studies of human disorders without variables that can confound clinical studies. Such analytic methods as patch-clamp electrophysiological and voltammetric recordings of neurons in brain slices require living brain tissue. In order to obtain viable tissue from nonhuman primate brains, tissue collection methods must be designed to preserve cardiovascular and respiratory functions for as long as possible. This paper describes a method of necropsy that has been used in three species of monkeys that satisfies this requirement. At necropsy, animals were maintained under a deep surgical plane of anesthesia while a craniotomy was conducted to expose the brain. Following the craniotomy, animals were perfused with ice-cold, oxygenated artificial cerebrospinal fluid to displace blood and to reduce the temperature of the entire brain. The brain was removed within minutes of death and specific brain regions were immediately dissected for subsequent in vitro electrophysiology or voltammetry experiments. This necropsy method also provided for the collection of tissue blocks containing all brain regions that were immediately frozen and stored for subsequent genomic, proteomic, autoradiographic and histological studies. An added benefit from the design of this necropsy method is that all major peripheral tissues were also collected and are now being utilized in a wide range of genomic, biochemical and histological assays. This necropsy method has resulted in the establishment and growth of a nonhuman primate alcohol tissue bank designed to distribute central nervous system and peripheral tissues to the larger scientific community.     

On the unimportance of constitutive models in computing brain deformation for image-guided surgery

Imaging modalities that can be used intra-operatively do not provide sufficient details to confidently locate the abnormalities and critical healthy areas that have been identified from high-resolution pre-operative scans. However, as we have shown in our previous work, high quality pre-operative images can be warped to the intra-operative position of the brain. This can be achieved by computing deformations within the brain using a biomechanical model. In this paper, using a previously developed patient-specific model of brain undergoing craniotomy-induced shift, we conduct a parametric analysis to investigate in detail the influences of constitutive models of the brain tissue. We conclude that the choice of the brain tissue constitutive model, when used with an appropriate finite deformation solution, does not affect the accuracy of computed displacements, and therefore a simple linear elastic model for the brain tissue is sufficient.     

Robust Volume Assessment of Brain Tissues for 3-Dimensional Fourier Transformation MRI via a Novel Multispectral Technique

A new TRIO algorithm method integrating three different algorithms is proposed to perform brain MRI segmentation in the native coordinate space, with no need of transformation to a standard coordinate space or the probability maps for segmentation. The method is a simple voxel-based algorithm, derived from multispectral remote sensing techniques, and only requires minimal operator input to depict GM, WM, and CSF tissue clusters to complete classification of a 3D high-resolution multislice-multispectral MRI data. Results showed very high accuracy and reproducibility in classification of GM, WM, and CSF in multislice-multispectral synthetic MRI data. The similarity indexes, expressing overlap between classification results and the ground truth, were 0.951, 0.962, and 0.956 for GM, WM, and CSF classifications in the image data with 3% noise level and 0% non-uniformity intensity. The method particularly allows for classification of CSF with 0.994, 0.961 and 0.996 of accuracy, sensitivity and specificity in images data with 3% noise level and 0% non-uniformity intensity, which had seldom performed well in previous studies. As for clinical MRI data, the quantitative data of brain tissue volumes aligned closely with the brain morphometrics in three different study groups of young adults, elderly volunteers, and dementia patients. The results also showed very low rates of the intra- and extra-operator variability in measurements of the absolute volumes and volume fractions of cerebral GM, WM, and CSF in three different study groups. The mean coefficients of variation of GM, WM, and CSF volume measurements were in the range of 0.03% to 0.30% of intra-operator measurements and 0.06% to 0.45% of inter-operator measurements. In conclusion, the TRIO algorithm exhibits a remarkable ability in robust classification of multislice-multispectral brain MR images, which would be potentially applicable for clinical brain volumetric analysis and explicitly promising in cross-sectional and longitudinal studies of different subject groups.     

Regional distribution of in vitro release of thyrotropin releasing hormone in rat brain

To increase our knowledge of the TRH functions in brain and the processes of TRH compartmentalization and release, we studied the in vitro release of endogenous TRH in different brain areas. We also determined the correlation between TRH levels and release under both basal and stimulated conditions. TRH concentration was measured in tissues and media by specific radioimmunoassay. TRH-like material detected in olfactory bulb and hypothalamic incubates (basal or K+ stimulated) were shown to be chromatographically identical to synthetic TRH. Different brain regions showed high variability in the basal release of TRH (1-20% of tissue content). This suggests the existence of different pools. The response to depolarizing stimulus (56 mM K+) was significant only in the following regions: median eminence, total hypothalamus, preoptic area, nucleus accumbens-lateral septum, amygdala, mesencephalon, medulla oblongata and the cervical region of the spinal cord. These regions have been shown to contain a high number of receptors, a high concentration of TRH nerve endings and are susceptible to TRH effects. These results support the hypothesis that TRH functions as neuromodulator in these areas.     

Regional brain serotonin synthesis is increased in the olfactory bulbectomy rat model of depression: an autoradiographic study

Serotonin synthesis rates were evaluated using alpha-[14C]methyl-l-tryptophan (alpha-MTrp) autoradiographic methods in olfactory bulbectomized (OBX) rats. They were significantly (p < 0.05) increased in the frontal (50%) and parietal (40%) cortices, superior olive (over 30%), and the substantia nigra (30%) in the OBX rats as compared to the sham operated animals. There were also increases in 5-hydroxytryptamine (5-HT) synthesis in some limbic areas: the cingulate (32%), the medial forebrain bundle (58%), the hippocampus (13-25%) and the thalamus (22-40%). The largest increase in 5-HT synthesis after OBX was observed in the sensory-motor cortex (67%). 5-HT synthesis rates were significantly decreased in the dorsal and medial raphe nuclei, but there was no significant change the ventral tegmental area and the locus coeruleus following OBX. These results indicate that olfactory bulbectomy causes an imbalance in 5-HT synthesis in some projection areas by disproportionally increasing 5-HT synthesis rates in specific brain regions and making more 5-HT available for neurotransmission. This imbalance in 5-HT synthesis and the subsequent elevation of tissue 5-HT may be responsible for the creation of non-physiological circuitry which may, in part, be reflected in the symptoms resembling human depression.     

A Novel Procedure for Rapid Imaging of Adult Mouse Brains with MicroCT Using Iodine-Based Contrast

High-resolution Magnetic Resonance Imaging (MRI) has been the primary modality for obtaining 3D cross-sectional anatomical information in animals for soft tissue, particularly brain. However, costs associated with MRI can be considerably high for large phenotypic screens for gross differences in the structure of the brain due to pathology and/or experimental manipulations. MicroCT (mCT), especially benchtop mCT, is becoming a common laboratory equipment with throughput rates equal or faster than any form of high-resolution MRI at lower costs. Here we explore adapting previously developed contrast based mCT to image adult mouse brains in-situ. We show that 2% weight per volume (w/v) iodine-potassium iodide solution can be successfully used to image adult mouse brains within 48 hours post-mortem when a structural support matrix is used. We demonstrate that hydrogel can be effectively used as a perfusant which limits the tissue shrinkage due to iodine.     

Estradiol acts in the medial preoptic area, arcuate nucleus, and dorsal raphe nucleus to reduce food intake in ovariectomized rats

Estradiol (E2) exerts an inhibitory effect on food intake in a variety of species. While compelling evidence indicates that central, rather than peripheral, estrogen receptors (ERs) mediate this effect, the exact brain regions involved have yet to be conclusively identified. In order to identify brain regions that are sufficient for E2's anorectic effect, food intake was monitored for 48 h following acute, unilateral, microinfusions of vehicle and two doses (0.25 and 2.5 μg) of a water-soluble form of E2 in multiple brain regions within the hypothalamus and midbrain of ovariectomized rats. Dose-related decreases in 24-h food intake were observed following E2 administration in the medial preoptic area (MPOA), arcuate nucleus (ARC), and dorsal raphe nucleus (DRN). Within the former two brain areas, the larger dose of E2 also decreased 4-h food intake. Food intake was not influenced, however, by similar E2 administration in the paraventricular nucleus, lateral hypothalamus, or ventromedial nucleus. These data suggest that E2-responsive neurons within the MPOA, ARC, and DRN participate in the estrogenic control of food intake and provide specific brain areas for future investigations of the cellular mechanism underlying estradiol's anorexigenic effect.     

Whole Animal Perfusion Fixation for Rodents

The goal of fixation is to rapidly and uniformly preserve tissue in a life-like state. While placing tissue directly in fixative works well for small pieces of tissue, larger specimens like the intact brain pose a problem for immersion fixation because the fixative does not reach all regions of the tissue at the same rate ^5,7. Often, changes in response to hypoxia begin before the tissue can be preserved ¹². The advantage of directly perfusing fixative through the circulatory system is that the chemical can quickly reach every corner of the organism using the natural vascular network. In order to utilize the circulatory system most effectively, care must be taken to match physiological pressures ³. It is important to note that physiological pressures are dependent on the species used. Techniques for perfusion fixation vary depending on the tissue to be fixed and how the tissue will be processed following fixation. In this video, we describe a low-cost, rapid, controlled and uniform fixation procedure using 4% paraformaldehyde perfused via the vascular system: through the heart of the rat to obtain the best possible preservation of the brain for immunohistochemistry. The main advantage of this technique (vs. gravity-fed systems) is that the circulatory system is utilized most effectively.     

Diffusion MRI: a new strategy for assessment of cancer therapeutic efficacy

The use of anatomical imaging in clinical oncology practice traditionally relies on comparison of patient scans acquired before and following completion of therapeutic intervention. Therapeutic success is typically determined from inspection of gross anatomical images to assess changes in tumor size. Imaging could provide significant additional insight into therapeutic impact if a specific parameter or combination of parameters could be identified which reflect tissue changes at the cellular or physiologic level. This would provide an early indicator or treatment response/outcome in an individual patient before completion of therapy. Moreover, response of a tumor to therapeutic intervention may be heterogeneous. The use of imaging could assist in delineating therapeutic-induced spatial heterogeneity within a tumor mass by providing information related to specific regions that are resistant or responsive to treatment. Largely untapped potential resides in exploratory methods such as diffusion MRI, which is a nonvolumetric intravoxel measure of tumor response based upon water molecular mobility. Alterations in water mobility reflect changes in tissue structure at the cellular level. While the clinical utility of diffusion MRI for oncologic practice is still under active investigation, this overview on the use of diffusion MRI for the evaluation of brain tumors will serve to introduce how this approach may be applied in the future for the management of patients with solid tumors.     

Cortical cerebral atrophy in patients with Parkinson’s disease: New opportunities for in vivo diagnostics

The Parkinson’s disease (PD) pathology is not limited to degeneration of the nigrostriatal dopaminergic system, but also includes the wide lesion of various regions of cerebral cortex. In our study we aimed to identify differences in the brain cortical thickness in patients with early and advanced PD using MRI morphometry. Sixty-seven patients with Hoehn–Yahr stages 2 and 3 were examined. All patients underwent MRI with subsequent post-processing and estimation of cortical thickness values in different brain regions. Significant differences in the visual and cingulate cortex, fusiform gyri, frontopolar zone of a dominant hemisphere, and Brodmann’s areas 1, 2, 3, and 4 of a non-dominant hemisphere were obtained. These data show relationship between the non-motor manifestations of PD and degeneration of certain cortical regions of the brain.     

Chronic murine toxoplasmosis is defined by subtle changes in neuronal connectivity

Recent studies correlate chronic Toxoplasma gondii (T. gondii) infection with behavioral changes in rodents; additionally, seropositivity in humans is reported to be associated with behavioral and neuropsychiatric diseases. In this study we investigated whether the described behavioral changes in a murine model of chronic toxoplasmosis are associated with changes in synaptic plasticity and brain neuronal circuitry. In mice chronically infected with T. gondii, magnetic resonance imaging (MRI) data analysis displayed the presence of heterogeneous lesions scattered throughout all brain areas. However, a higher density of lesions was observed within specific regions such as the somatosensory cortex (SSC). Further histopathological examination of these brain areas indicated the presence of activated resident glia and recruited immune cells accompanied by limited alterations of neuronal viability. In vivo diffusion-tensor MRI analysis of neuronal fiber density within the infected regions revealed connectivity abnormalities in the SSC. Altered fiber density was confirmed by morphological analysis of individual, pyramidal and granule neurons, showing a reduction in dendritic arbor and spine density within the SSC, as well as in the hippocampus. Evaluation of synapse efficacy revealed diminished levels of two key synaptic proteins, PSD95 and synaptophysin, within the same brain areas, indicating deficits in functionality of the synaptic neurotransmission in infected mice. Our results demonstrate that persistent T. gondii infection in a murine model results in synaptic deficits within brain structures leading to disturbances in the morphology of noninfected neurons and modified brain connectivity, suggesting a potential explanation for the behavioral and neuropsychiatric alterations.KEY WORDS: Parasites, Behavioral manipulation, Neuronal connectivity     

Ultrastructure and energy-dispersive x-ray microanalysis of cartilage after rapid freezing, low temperature freeze drying, and embedding in Spurr's resin

In order to undertake meaningful high-resolution x-ray microanalysis of tissues, methods should be used that minimize the introduction of artefacts produced by loss or translocation of ions. The most ideal method is rapid freezing but the subsequent sectioning of frozen tissues is technically difficult. An alternative method is to freeze dry the tissues at a low temperature, and then embed them in resin. This facilitates the rapid production of reproducible thin sections. With freeze-dried, embedded hypertrophic cartilage, the morphology was similar to that seen using aqueous fixatives even when no additional electron density is introduced by the use of osmium vapor. Energy-dispersive analysis of specific areas show that little or no loss or migration of ions occurs from structures such as mitochondria. Mitochondrial granules consisting of calcium and phosphorus precipitates were not observed except where the cells were damaged as a result of the freezing process. This may suggest that these granules only appear when tissue is damaged because of inadequate preservation.     

Appearance matters: neural correlates of food choice and packaging aesthetics

Neuro-imaging holds great potential for predicting choice behavior from brain responses. In this study we used both traditional mass-univariate and state-of-the-art multivariate pattern analysis to establish which brain regions respond to preferred packages and to what extent neural activation patterns can predict realistic low-involvement consumer choices. More specifically, this was assessed in the context of package-induced binary food choices. Mass-univariate analyses showed that several regions, among which the bilateral striatum, were more strongly activated in response to preferred food packages. Food choices could be predicted with an accuracy of up to 61.2% by activation patterns in brain regions previously found to be involved in healthy food choices (superior frontal gyrus) and visual processing (middle occipital gyrus). In conclusion, this study shows that mass-univariate analysis can detect small package-induced differences in product preference and that MVPA can successfully predict realistic low-involvement consumer choices from functional MRI data.     

A Magnetic Resonance Image Based Atlas of the Rabbit Brain for Automatic Parcellation

Rabbit brain has been used in several works for the analysis of neurodevelopment. However, there are not specific digital rabbit brain atlases that allow an automatic identification of brain regions, which is a crucial step for various neuroimage analyses, and, instead, manual delineation of areas of interest must be performed in order to evaluate a specific structure. For this reason, we propose an atlas of the rabbit brain based on magnetic resonance imaging, including both structural and diffusion weighted, that can be used for the automatic parcellation of the rabbit brain. Ten individual atlases, as well as an average template and probabilistic maps of the anatomical regions were built. In addition, an example of automatic segmentation based on this atlas is described.     

Assessment of factors that confound MRI and neuropathological correlation of human postmortem brain tissue

In spite of considerable technical advance in MRI techniques, the optical resolution of these methods are still limited. Consequently, the delineation of cytoarchitectonic fields based on probabilistic maps and brain volume changes, as well as small-scale changes seen in MRI scans need to be verified by neuronanatomical/neuropathological diagnostic tools. To attend the current interdisciplinary needs of the scientific community, brain banks have to broaden their scope in order to provide high quality tissue suitable for neuroimaging- neuropathology/anatomy correlation studies. The Brain Bank of the Brazilian Aging Brain Research Group (BBBABSG) of the University of Sao Paulo Medical School (USPMS) collaborates with researchers interested in neuroimaging-neuropathological correlation studies providing brains submitted to postmortem MRI in-situ. In this paper we describe and discuss the parameters established by the BBBABSG to select and to handle brains for fine-scale neuroimaging-neuropathological correlation studies, and to exclude inappropriate/unsuitable autopsy brains. We tried to assess the impact of the postmortem time and storage of the corpse on the quality of the MRI scans and to establish fixation protocols that are the most appropriate to these correlation studies. After investigation of a total of 36 brains, postmortem interval and low body temperature proved to be the main factors determining the quality of routine MRI protocols. Perfusion fixation of the brains after autopsy by mannitol 20% followed by formalin 20% was the best method for preserving the original brain shape and volume, and for allowing further routine and immunohistochemical staining. Taken to together, these parameters offer a methodological progress in screening and processing of human postmortem tissue in order to guarantee high quality material for unbiased correlation studies and to avoid expenditures by post-imaging analyses and histological processing of brain tissue.     

Dynamic Adjustment of Stimuli in Real Time Functional Magnetic Resonance Imaging

The conventional fMRI image analysis approach to associating stimuli to brain activation is performed by carrying out a massive number of parallel univariate regression analyses. fMRI blood-oxygen-level dependent (BOLD) signal, the basis of these analyses, is known for its low signal-noise-ratio and high spatial and temporal signal correlation. In order to ensure accurate localization of brain activity, stimulus administration in an fMRI session is often lengthy and repetitive. Real-time fMRI BOLD signal analysis is carried out as the signal is observed. This method allows for dynamic, real-time adjustment of stimuli through sequential experimental designs. We have developed a voxel-wise sequential probability ratio test (SPRT) approach for dynamically determining localization, as well as decision rules for stopping stimulus administration. SPRT methods and general linear model (GLM) approaches are combined to identify brain regions that are activated by specific elements of stimuli. Stimulus administration is dynamically stopped when sufficient statistical evidence is collected to determine activation status across regions of interest, following predetermined statistical error thresholds. Simulation experiments and an example based on real fMRI data show that scan volumes can be substantially reduced when compared with pre-determined, fixed designs while achieving similar or better accuracy in detecting activated voxels. Moreover, the proposed approach is also able to accurately detect differentially activated areas, and other comparisons between task-related GLM parameters that can be formulated in a hypothesis-testing framework. Finally, we give a demonstration of SPRT being employed in conjunction with a halving algorithm to dynamically adjust stimuli.