Creation of Computerized 3D MRI-Integrated Atlases of the Human Basal Ganglia and Thalamus

In Vivo Super-Resolution Track-Density Imaging for Thalamic Nuclei Identification

The development of novel techniques for the in vivo, non-invasive visualization and identification of thalamic nuclei has represented a major challenge for human neuroimaging research in the last decades. Thalamic nuclei have important implications in various key aspects of brain physiology and many of them show selective alterations in various neurologic and psychiatric disorders. In addition, both surgical stimulation and ablation of specific thalamic nuclei have been proven to be useful for the treatment of different neuropsychiatric diseases. The present work aimed at describing a novel protocol for histologically guided delineation of thalamic nuclei based on short-tracks track-density imaging (stTDI), which is an advanced imaging technique exploiting high angular resolution diffusion tractography to obtain super-resolved white matter maps. We demonstrated that this approach can identify up to 13 distinct thalamic nuclei bilaterally with very high inter-subject (ICC: 0.996, 95% CI: 0.993-0.998) and inter-rater (ICC:0.981; 95% CI:0.963-0.989) reliability, and that both subject-based and group-level thalamic parcellation show a fair share of similarity to a recent standard-space histological thalamic atlas. Finally, we showed that stTDI-derived thalamic maps can be successfully employed to study structural and functional connectivity of the thalamus and may have potential implications both for basic and translational research, as well as for presurgical planning purposes.

Evolution of Human Brain Atlases in Terms of Content, Applications, Functionality, and Availability

Human brain atlases have been evolving tremendously, propelled recently by brain big projects, and driven by sophisticated imaging techniques, advanced brain mapping methods, vast data, analytical strategies, and powerful computing. We overview here this evolution in four categories: content, applications, functionality, and availability, in contrast to other works limited mostly to content. Four atlas generations are distinguished: early cortical maps, print stereotactic atlases, early digital atlases, and advanced brain atlas platforms, and 5 avenues in electronic atlases spanning the last two generations. Content-wise, new electronic atlases are categorized into eight groups considering their scope, parcellation, modality, plurality, scale, ethnicity, abnormality, and a mixture of them. Atlas content developments in these groups are heading in 23 various directions. Application-wise, we overview atlases in neuroeducation, research, and clinics, including stereotactic and functional neurosurgery, neuroradiology, neurology, and stroke. Functionality-wise, tools and functionalities are addressed for atlas creation, navigation, individualization, enabling operations, and application-specific. Availability is discussed in media and platforms, ranging from mobile solutions to leading-edge supercomputers, with three accessibility levels. The major application-wise shift has been from research to clinical practice, particularly in stereotactic and functional neurosurgery, although clinical applications are still lagging behind the atlas content progress. Atlas functionality also has been relatively neglected until recently, as the management of brain data explosion requires powerful tools. We suggest that the future human brain atlas-related research and development activities shall be founded on and benefit from a standard framework containing the core virtual brain model cum the brain atlas platform general architecture.

An ancestor of the stereotactic atlases: the Tabulae Anatomicae of Bartolomeo Eustachio

The authors report the history of the Tabulae Anatomicae of Bartolomeo Eustachio (ca. 1510-1574). In the tables, the anatomical illustrations were drawn inside a numerical frame, with pairs of numbers on the y- and x-axes to identify single anatomical details in the reference table. The measures and the references could be calculated using the graduated margins divided by 5 units for each the x-axis and y-axis. The Tabulae Anatomicae can be considered a precursor to modern anatomical reference systems that are the basis of studies on cerebral localization mainly used for stereotactic procedures.

A probabilistic atlas of the human thalamic nuclei combining ex vivo MRI and histology

The human thalamus is a brain structure that comprises numerous, highly specific nuclei. Since these nuclei are known to have different functions and to be connected to different areas of the cerebral cortex, it is of great interest for the neuroimaging community to study their volume, shape and connectivity in vivo with MRI. In this study, we present a probabilistic atlas of the thalamic nuclei built using ex vivo brain MRI scans and histological data, as well as the application of the atlas to in vivo MRI segmentation. The atlas was built using manual delineation of 26 thalamic nuclei on the serial histology of 12 whole thalami from six autopsy samples, combined with manual segmentations of the whole thalamus and surrounding structures (caudate, putamen, hippocampus, etc.) made on in vivo brain MR data from 39 subjects. The 3D structure of the histological data and corresponding manual segmentations was recovered using the ex vivo MRI as reference frame, and stacks of blockface photographs acquired during the sectioning as intermediate target. The atlas, which was encoded as an adaptive tetrahedral mesh, shows a good agreement with previous histological studies of the thalamus in terms of volumes of representative nuclei. When applied to segmentation of in vivo scans using Bayesian inference, the atlas shows excellent test-retest reliability, robustness to changes in input MRI contrast, and ability to detect differential thalamic effects in subjects with Alzheimer's disease. The probabilistic atlas and companion segmentation tool are publicly available as part of the neuroimaging package FreeSurfer.

Warping an atlas derived from serial histology to 5 high-resolution MRIs

Previous work from our group demonstrated the use of multiple input atlases to a modified multi-atlas framework (MAGeT-Brain) to improve subject-based segmentation accuracy. Currently, segmentation of the striatum, globus pallidus and thalamus are generated from a single high-resolution and -contrast MRI atlas derived from annotated serial histological sections. Here, we warp this atlas to five high-resolution MRI templates to create five de novo atlases. The overall goal of this work is to use these newly warped atlases as input to MAGeT-Brain in an effort to consolidate and improve the workflow presented in previous manuscripts from our group, allowing for simultaneous multi-structure segmentation. The work presented details the methodology used for the creation of the atlases using a technique previously proposed, where atlas labels are modified to mimic the intensity and contrast profile of MRI to facilitate atlas-to-template nonlinear transformation estimation. Dice's Kappa metric was used to demonstrate high quality registration and segmentation accuracy of the atlases. The final atlases are available at https://github.com/CobraLab/atlases/tree/master/5-atlas-subcortical.

Topographic anatomy of the subthalamic nucleus localized by high-resolution human brain atlas superimposing digital images of cross-sectioned surfaces and histological images of microscopic sections from frozen cadaveric brains

Despite the recent advent of neuro-radiographic techniques, creating a 'perfect' human brain atlas providing precise and consistent images with minimal distortion is practically difficult. In this study, we created a new human brain atlas from cadaveric brains with serial sections of 50 μm thickness covering the entire basal ganglia. Human cerebral hemispheres were obtained from 10 donated cadavers and fixed in 10% formalin solution, cut in a block measuring 50 mm × 30 mm × 50 mm around the midpoint of the anterior and posterior commissures and frozen at -40 °C. Each block was cut into 50-μm-thick sections on the freezing microtome and the cross-sectioned surface was photographed. Simultaneously, every 10th slice from one sagittal hemisphere was sampled and stained using the Kluver-Barrera method. Prepared slides were photographed under light microscopy, and data from digital images of the cross-sectioned surface (DICSS) and digital images from microscopic sections (DIMS) were processed. Gray areas on DICSS largely represented areas of dense cellularity, and around subthalamic nucleus (STN), the zona incerta and field of Forel were clearly distinguishable on the anterosuperior side, as was the substantia nigra on the caudal side. DICSS successfully delineated the anatomical structure identical to the STN and surrounding contiguous nuclei. This new brain atlas will allow elucidation of anatomy that cannot be clearly disclosed from modern radiographic imaging or is very difficult to analyze with spatially inconsistent histological sections, and will contribute to further progress in anatomical studies of the human basal ganglia.

7T MRI subthalamic nucleus atlas for use with 3T MRI

Deep brain stimulation (DBS) of the subthalamic nucleus (STN) reduces motor symptoms in most patients with Parkinson disease (PD), yet may produce untoward effects. Investigation of DBS effects requires accurate localization of the STN, which can be difficult to identify on magnetic resonance images collected with clinically available 3T scanners. The goal of this study is to develop a high-quality STN atlas that can be applied to standard 3T images. We created a high-definition STN atlas derived from seven older participants imaged at 7T. This atlas was nonlinearly registered to a standard template representing 56 patients with PD imaged at 3T. This process required development of methodology for nonlinear multimodal image registration. We demonstrate mm-scale STN localization accuracy by comparison of our 3T atlas with a publicly available 7T atlas. We also demonstrate less agreement with an earlier histological atlas. STN localization error in the 56 patients imaged at 3T was less than 1 mm on average. Our methodology enables accurate STN localization in individuals imaged at 3T. The STN atlas and underlying 3T average template in MNI space are freely available to the research community. The image registration methodology developed in the course of this work may be generally applicable to other datasets.

A Novel Method for Constructing Histological Section Datasets of the Basal Ganglia in Digitized Human Brain

To investigate the construction of the histological section datasets in the basal ganglia of digitized human brain to provide a reference for the meso-level histological data acquisition. A fresh adult brain from a cadaver with no neurological disease was selected, and tissue blocks of the basal ganglia in the right hemisphere was extracted using the visualization method, followed by pretreatments including gradient dehydrating, gelatin-embedding and setting of calibration points. And then the tissue blocks was cryosectioned into 60-μm-thick coronal sections and the sectional images were captured simultaneously by a digital camera at a fixed position. Two series of sections (one section out of ten) were Nissl-stained with Toluidine blue and immunostained with the calbindin D-28K, respectively. Stained sections were digitized by a high resolution scanner. After alignment and registration, contours of nuclei and different nucleic function divisions in the digital images of stained sections were identified, and then were segmented and labeled using software exploited by ourselves. Datasets of one set of registrated serial sectional images and two sets of registrated histochemically stained images in basal ganglia area were obtained, which provide a histological reference for the neurosurgery and diagnostic imaging. a systematic method of cutting, slicing, staining, data acquisition and image registration of large tissue blocks was established, providing a reference for histological data acquisition on the digital human. Anat Rec, 300:1011-1021, 2017. © 2016 Wiley Periodicals, Inc.

Assessment of Age-Related Morphometric Changes of Subcortical Structures in Healthy People Using Ultra-High Field 7 Tesla Magnetic Resonance Imaging

Objective: To assess the age-related morphometric changes of subcortical structures in healthy people.

Materials and Methods: Ultra-high field 7 tesla magnetic resonance (MR) imaging in humans was used to visualize the subcortical structures of healthy young, middle-aged and elderly participants. Using the magnetization-prepared two rapid acquisition gradient echo (MP2RAGE) sequence, we assessed the visibility of the margins of the thalamus and white matter in the thalamus, as well as the anterior commissure (AC) and posterior commissure (PC) length, the maximal height of the thalamus, the half width of the third ventricle and the distance between the AC and the center of the mammillothalamic tract (MTT) at the level of the AC-PC plane. All quantitative data were statistically evaluated.

Results: The AC-PC length did not differ significantly among the three groups. The maximal height of the thalamus decreased with age (r_s(53) = −0.719, p < 0.001). The half width of the third ventricle (r_s(53) = 0.705, p < 0.001) and the distance between the AC and the center of the MTT (r_s(53) = 0.485, p < 0.001) increased with age. The distance between the AC and the center of the MTT of the young and the elderly participants differed significantly (p = 0.007).

Conclusion: The AC-PC length is not a good candidate for proportional correction during atlas-to-patient registration. The maximal height of the thalamus and the half width of the third ventricle correlated strongly with age, and the MTT position in relation to the AC shifted posteriorly as age increased. These age-related morphometric changes of subcortical structures should be considered in targeting for functional neurosurgery.

Multimodal 7T Imaging of Thalamic Nuclei for Preclinical Deep Brain Stimulation Applications

Precise neurosurgical targeting of electrode arrays within the brain is essential to the successful treatment of a range of brain disorders with deep brain stimulation (DBS) therapy. Here, we describe a set of computational tools to generate in vivo, subject-specific atlases of individual thalamic nuclei thus improving the ability to visualize thalamic targets for preclinical DBS applications on a subject-specific basis. A sequential nonlinear atlas warping technique and a Bayesian estimation technique for probabilistic crossing fiber tractography were applied to high field (7T) susceptibility-weighted and diffusion-weighted imaging, respectively, in seven rhesus macaques. Image contrast, including contrast within thalamus from the susceptibility-weighted images, informed the atlas warping process and guided the seed point placement for fiber tractography. The susceptibility-weighted imaging resulted in relative hyperintensity of the intralaminar nuclei and relative hypointensity in the medial dorsal nucleus, pulvinar, and the medial/ventral border of the ventral posterior nuclei, providing context to demarcate borders of the ventral nuclei of thalamus, which are often targeted for DBS applications. Additionally, ascending fiber tractography of the medial lemniscus, superior cerebellar peduncle, and pallidofugal pathways into thalamus provided structural demarcation of the ventral nuclei of thalamus. The thalamic substructure boundaries were validated through in vivo electrophysiological recordings and post-mortem blockface tissue sectioning. Together, these imaging tools for visualizing and segmenting thalamus have the potential to improve the neurosurgical targeting of DBS implants and enhance the selection of stimulation settings through more accurate computational models of DBS.

Functional Connectivity of Vim Nucleus in Tremor- and Akinetic-/Rigid-Dominant Parkinson's Disease

AIMS

The aim of this study was to investigate the involvement of the ventral intermediate nucleus of thalamus (Vim) in the tremor- and akinetic-/rigid-related networks in Parkinson's disease (PD).

METHODS

Tremor-dominant (TD) and akinetic-/rigid-dominant (ARD) PD patients were recruited and scanned by resting-state functional MRI. Functional connectivity from the Vim nucleus was analyzed.

RESULTS

In the TD patients, the Vim nucleus exhibited increased connectivity with the cerebellum/dentate nucleus, primary motor cortex (M1), supplementary motor area (SMA), premotor cortex, thalamus, globus pallidus, putamen, and parietal cortex compared with the controls, while the connections between the Vim nucleus and M1 and cerebellum/dentate nucleus had positive correlations with the tremor scores. In the ARD patients, the Vim nucleus only showed enhanced connectivity with the globus pallidus and limbic lobe compared with the controls, and no connectivity showed correlation against the akinetic-rigidity scores. TD patients had increased connectivity with the Vim nucleus in the cerebellum, M1, SMA, thalamus, globus pallidus, putamen, and parietal cortex compared with ARD patients.

CONCLUSIONS

This study demonstrates that the Vim nucleus has an important role in the tremor-related network, but not in the akinetic-/rigid-related network. Our finding is helpful to explain the selective effect of Vim deep brain stimulation in PD.

A New Approach for Deep Gray Matter Analysis Using Partial-Volume Estimation

Introduction

The existence of partial volume effects in brain MR images makes it challenging to understand physio-pathological alterations underlying signal changes due to pathology across groups of healthy subjects and patients. In this study, we implement a new approach to disentangle gray and white matter alterations in the thalamus and the basal ganglia. The proposed method was applied to a cohort of early multiple sclerosis (MS) patients and healthy subjects to evaluate tissue-specific alterations related to diffuse inflammatory or neurodegenerative processes.

Method

Forty-three relapsing-remitting MS patients and nineteen healthy controls underwent 3T MRI including: (i) fluid-attenuated inversion recovery, double inversion recovery, magnetization-prepared gradient echo for lesion count, and (ii) T1 relaxometry. We applied a partial volume estimation algorithm to T1 relaxometry maps to gray and white matter local concentrations as well as T1 values characteristic of gray and white matter in the thalamus and the basal ganglia. Statistical tests were performed to compare groups in terms of both global T1 values, tissue characteristic T1 values, and tissue concentrations.

Results

Significant increases in global T1 values were observed in the thalamus (p = 0.038) and the putamen (p = 0.026) in RRMS patients compared to HC. In the Thalamus, the T1 increase was associated with a significant increase in gray matter characteristic T1 (p = 0.0016) with no significant effect in white matter.

Conclusion

The presented methodology provides additional information to standard MR signal averaging approaches that holds promise to identify the presence and nature of diffuse pathology in neuro-inflammatory and neurodegenerative diseases.

In Vivo 7T MRI of the Non-Human Primate Brainstem

Structural brain imaging provides a critical framework for performing stereotactic and intraoperative MRI-guided surgical procedures, with procedural efficacy often dependent upon visualization of the target with which to operate. Here, we describe tools for in vivo, subject-specific visualization and demarcation of regions within the brainstem. High-field 7T susceptibility-weighted imaging and diffusion-weighted imaging of the brain were collected using a customized head coil from eight rhesus macaques. Fiber tracts including the superior cerebellar peduncle, medial lemniscus, and lateral lemniscus were identified using high-resolution probabilistic diffusion tractography, which resulted in three-dimensional fiber tract reconstructions that were comparable to those extracted from sequential application of a two-dimensional nonlinear brain atlas warping algorithm. In the susceptibility-weighted imaging, white matter tracts within the brainstem were also identified as hypointense regions, and the degree of hypointensity was age-dependent. This combination of imaging modalities also enabled identifying the location and extent of several brainstem nuclei, including the periaqueductal gray, pedunculopontine nucleus, and inferior colliculus. These clinically-relevant high-field imaging approaches have potential to enable more accurate and comprehensive subject-specific visualization of the brainstem and to ultimately improve patient-specific neurosurgical targeting procedures, including deep brain stimulation lead implantation.

An MRI atlas of the mouse basal ganglia

The basal ganglia are a group of subpallial nuclei that play an important role in motor, emotional, and cognitive functions. Morphological changes and disrupted afferent/efferent connections in the basal ganglia have been associated with a variety of neurological disorders including psychiatric and movement disorders. While high-resolution magnetic resonance imaging has been used to characterize changes in brain structure in mouse models of these disorders, no systematic method for segmentation of the C57BL/6 J mouse basal ganglia exists. In this study we have used high-resolution MR images of ex vivo C57BL/6 J mouse brain to create a detailed protocol for segmenting the basal ganglia. We created a three-dimensional minimum deformation atlas, which includes the segmentation of 35 striatal, pallidal, and basal ganglia-related structures. In addition, we provide mean volumes, mean T2 contrast intensities and mean FA and ADC values for each structure. This MR atlas is available for download, and enables researchers to perform automated segmentation in genetic models of basal ganglia disorders.

Probabilistic MRI brain anatomical atlases based on 1,000 Chinese subjects

Brain atlases are designed to provide a standard reference coordinate system of the brain for neuroscience research. Existing human brain atlases are widely used to provide anatomical references and information regarding structural characteristics of the brain. The majority of them, however, are derived from one paticipant or small samples of the Western population. This poses a limitation for scientific studies on Eastern subjects. In this study, 10 new Chinese brain atlases for different ages and genders were constructed using MR anatomical images based on HAMMER (Hierarchical Attribute Matching Mechanism for Elastic Registration). A total of 1,000 Chinese volunteers ranging from 18 to 70 years old participated in this study. These population-specific brain atlases represent the basic structural characteristics of the Chinese population. They may be utilized for basic neuroscience studies and clinical diagnosis, including evaluation of neurological and neuropsychiatric disorders, in Chinese patients and those from other Eastern countries.

Magnetic Resonance Imaging (MRI) in Parkinson's Disease

Recent developments in brain imaging methods are on the verge of changing the evaluation of people with Parkinson's disease (PD). This includes an assortment of techniques ranging from diffusion tensor imaging (DTI) to iron-sensitive methods such as T₂^*, as well as adiabatic methods R_1ρ and R_2ρ, resting-state functional MRI, and magnetic resonance spectroscopy (MRS). Using a multi-modality approach that ascertains different aspects of the pathophysiology or pathology of PD, it may be possible to better characterize disease phenotypes as well as provide a surrogate of disease and a potential means to track disease progression.

Multimodal imaging and image analysis techniques for neuromodulation

Functional neurosurgical procedures used to treat the debilitating motor symptoms of Parkinson's disease and that target small subcortical structures have typically relied on semi-qualitative manual approaches that rely upon the establishing qualitative between volumetric imaging data and print atlases. This chapter reviews many new high -precision and -accuracy techniques that can be used for the full automated localization of these targets. These techniques rely on the a priori development of neuroanatomical atlases derived from magnetic resonance imaging data, high-resolution identification of subcortical structures from histology, and spatially localized data bases of intra-operative recordings and successful surgical outcomes. Other novel structural and functional MRI techniques that allow for the direct visualization of thalamic sub nuclei are also reviewed.

A multi-modal approach to computer-assisted deep brain stimulation trajectory planning

PURPOSE

Both frame-based and frameless approaches to deep brain stimulation (DBS) require planning of insertion trajectories that mitigate hemorrhagic risk and loss of neurological function. Currently, this is done by manual inspection of multiple potential electrode trajectories on MR-imaging data. We propose and validate a method for computer-assisted DBS trajectory planning.

METHOD

Our framework integrates multi-modal MRI analysis (T1w, SWI, TOF-MRA) to compute suitable DBS trajectories that optimize the avoidance of specific critical brain structures. A cylinder model is used to process each trajectory and to evaluate complex surgical constraints described via a combination of binary and fuzzy segmented datasets. The framework automatically aggregates the multiple constraints into a unique ranking of recommended low-risk trajectories. Candidate trajectories are represented as a few well-defined cortical entry patches of best-ranked trajectories and presented to the neurosurgeon for final trajectory selection.

RESULTS

The proposed algorithm permits a search space containing over 8,000 possible trajectories to be processed in less than 20 s. A retrospective analysis on 14 DBS cases of patients with severe Parkinson's disease reveals that our framework can improve the simultaneous optimization of many pre-formulated surgical constraints. Furthermore, all automatically computed trajectories were evaluated by two neurosurgeons, were judged suitable for surgery and, in many cases, were judged preferable or equivalent to the manually planned trajectories used during the operation.

CONCLUSIONS

This work provides neurosurgeons with an intuitive and flexible decision-support system that allows objective and patient-specific optimization of DBS lead trajectories, which should improve insertion safety and reduce surgical time.