Feasibility of creating a high-resolution 3D diffusion tensor imaging based atlas of the human brainstem: a case study at 11.7 T

Multimodal MRI reveals brainstem connections that sustain wakefulness in human consciousness

Consciousness is composed of arousal (i.e., wakefulness) and awareness. Substantial progress has been made in mapping the cortical networks that underlie awareness in the human brain, but knowledge about the subcortical networks that sustain arousal in humans is incomplete. Here, we aimed to map the connectivity of a proposed subcortical arousal network that sustains wakefulness in the human brain, analogous to the cortical default mode network (DMN) that has been shown to contribute to awareness. We integrated data from ex vivo diffusion magnetic resonance imaging (MRI) of three human brains, obtained at autopsy from neurologically normal individuals, with immunohistochemical staining of subcortical brain sections. We identified nodes of the proposed default ascending arousal network (dAAN) in the brainstem, hypothalamus, thalamus, and basal forebrain. Deterministic and probabilistic tractography analyses of the ex vivo diffusion MRI data revealed projection, association, and commissural pathways linking dAAN nodes with one another and with DMN nodes. Complementary analyses of in vivo 7-tesla resting-state functional MRI data from the Human Connectome Project identified the dopaminergic ventral tegmental area in the midbrain as a widely connected hub node at the nexus of the subcortical arousal and cortical awareness networks. Our network-based autopsy methods and connectivity data provide a putative neuroanatomic architecture for the integration of arousal and awareness in human consciousness.

ProbaStem, a pipeline towards the first high-resolution probabilistic atlas of the whole human brainstem

The brainstem plays an essential role in many vital functions, such as autonomic control, consciousness and sleep, motricity, somatic afferent function, and cognition. Its involvement in several neurological diseases and the definition of brainstem targets for deep brain stimulation (DBS) explain the need for brainstem atlases describing its structural organization and connectivity from several modalities, from histology to ultrahigh field ex vivo MRI. Nonetheless, these atlases are often limited to a subpart of the brainstem or only include a single subject, the brainstem variability being considered low. This paper proposes a pipeline to create a high-resolution multisubject probabilistic atlas of the whole human brainstem based on four ultrahigh field ex vivo MRI datasets. The variability of the brainstem structures appears higher than usually considered, both for the volume and position of the central gray matter structures of the brainstem. This justifies the creation of atlases that capture the anatomical variability across subjects. The one we present here only included four specimens, but can easily be incremented due to its highly flexible design.

MRI-Visible Anatomy of the Brainstem

Human brainstem internal anatomy is intricate, complex, and essential to normal brain function. The brainstem is affected by stroke, multiple sclerosis, and most neurodegenerative diseases-a 1-mm focus of pathologic condition can have profound clinical consequences. Unfortunately, detailed internal brainstem anatomy is difficult to see with conventional MRI sequences. We review normal brainstem anatomy visualized on widely available clinical 3-T MRI scanners using fast gray matter acquisition T1 inversion recovery, probabilistic diffusion tractography, neuromelanin, and susceptibility-weighted imaging. Better anatomic localization using these recent innovations improves our ability to diagnose, localize, and treat brainstem diseases. We aim to provide an accessible review of the most clinically relevant brainstem neuroanatomy.

Post mortem mapping of connectional anatomy for the validation of diffusion MRI

Diffusion MRI (dMRI) is a unique tool for the study of brain circuitry, as it allows us to image both the macroscopic trajectories and the microstructural properties of axon bundles in vivo. The Human Connectome Project ushered in an era of impressive advances in dMRI acquisition and analysis. As a result of these efforts, the quality of dMRI data that could be acquired in vivo improved substantially, and large collections of such data became widely available. Despite this progress, the main limitation of dMRI remains: it does not image axons directly, but only provides indirect measurements based on the diffusion of water molecules. Thus, it must be validated by methods that allow direct visualization of axons but that can only be performed in post mortem brain tissue. In this review, we discuss methods for validating the various features of connectional anatomy that are extracted from dMRI, both at the macro-scale (trajectories of axon bundles), and at micro-scale (axonal orientations and other microstructural properties). We present a range of validation tools, including anatomic tracer studies, Klingler's dissection, myelin stains, label-free optical imaging techniques, and others. We provide an overview of the basic principles of each technique, its limitations, and what it has taught us so far about the accuracy of different dMRI acquisition and analysis approaches.

Brainstem Diffusion Tensor Tractography and Clinical Applications in Pain

The brainstem is one of the most vulnerable brain structures in many neurological conditions, such as pain, sleep problems, autonomic dysfunctions, and neurodegenerative disorders. Diffusion tensor imaging and tractography provide structural details and quantitative measures of brainstem fiber pathways. Until recently, diffusion tensor tractographic studies have mainly focused on whole-brain MRI acquisition. Due to the brainstem's spatial localization, size, and tissue characteristics, and limits of imaging techniques, brainstem diffusion MRI poses particular challenges in tractography. We provide a brief overview on recent advances in diffusion tensor tractography in revealing human pathways connecting the brainstem to the subcortical regions (e.g., basal ganglia, mesolimbic, basal forebrain), and cortical regions. Each of these pathways contains different distributions of fiber tracts from known neurotransmitter-specific nuclei in the brainstem. We compare the brainstem tractographic approaches in literature and our in-lab developed automated brainstem tractography in terms of atlas building, technical advantages, and neuroanatomical implications on neurotransmitter systems. Lastly, we summarize recent investigations of using brainstem tractography as a promising tool in association with pain.

Tractography of the Stria Terminalis in the Human Brain

The aim of this study was to investigate the trajectory of the stria terminalis and develop a protocol for mapping the stria terminalis using multi-shell diffusion images based tractography. The stria terminalis was reconstructed by combining one region of interest at the amygdala with another region of interest at the bed nucleus of stria terminalis. In addition, one region of avoidance was placed on the fornix at the interventricular foramen and another was set at the anterior perforated substance. The fiber-tracking protocol was tested in a Human Connectome Project-842 template, 35 healthy subjects from Massachusetts General Hospital, and 20 healthy subjects from the Human Connectome Project using generalized q-sampling imaging based tractography. The stria terminalis was reconstructed in the Human Connectome Project-842 template, 35 Massachusetts General Hospital healthy subjects, and 20 Human Connectome Project healthy subjects with our protocol. The stria terminalis originated from the amygdala and travelled parallel to the fornix. Then, the stria terminalis followed a C-shaped trajectory around the inferior, posterior, and dorsal surfaces of the thalamus before projecting to the bed nucleus of stria terminalis between the thalamus and caudate nucleus. There were no significant differences in the quantitative anisotropy and fractional anisotropy values between the left and right stria terminalis. The stria terminalis was accurately visualized across subjects using multi-shell diffusion images through generalized q-sampling imaging based tractography. This method could be an important tool for the reconstruction and evaluation of the stria terminalis in various neurological disorders. One Sentence Summary The visualizetion of the stria terminalis through the multi-shell diffusion images using generalized q-sampling imaging based tractography.

Mapping the subcortical connectivity of the human default mode network

The default mode network (DMN) mediates self-awareness and introspection, core components of human consciousness. Therapies to restore consciousness in patients with severe brain injuries have historically targeted subcortical sites in the brainstem, thalamus, hypothalamus, basal forebrain, and basal ganglia, with the goal of reactivating cortical DMN nodes. However, the subcortical connectivity of the DMN has not been fully mapped, and optimal subcortical targets for therapeutic neuromodulation of consciousness have not been identified. In this work, we created a comprehensive map of DMN subcortical connectivity by combining high-resolution functional and structural datasets with advanced signal processing methods. We analyzed 7 Tesla resting-state functional MRI (rs-fMRI) data from 168 healthy volunteers acquired in the Human Connectome Project. The rs-fMRI blood-oxygen-level-dependent (BOLD) data were temporally synchronized across subjects using the BrainSync algorithm. Cortical and subcortical DMN nodes were jointly analyzed and identified at the group level by applying a novel Nadam-Accelerated SCAlable and Robust (NASCAR) tensor decomposition method to the synchronized dataset. The subcortical connectivity map was then overlaid on a 7 Tesla 100 µm ex vivo MRI dataset for neuroanatomic analysis using automated segmentation of nuclei within the brainstem, thalamus, hypothalamus, basal forebrain, and basal ganglia. We further compared the NASCAR subcortical connectivity map with its counterpart generated from canonical seed-based correlation analyses. The NASCAR method revealed that BOLD signal in the central lateral nucleus of the thalamus and ventral tegmental area of the midbrain is strongly correlated with that of the DMN. In an exploratory analysis, additional subcortical sites in the median and dorsal raphe, lateral hypothalamus, and caudate nuclei were correlated with the cortical DMN. We also found that the putamen and globus pallidus are negatively correlated (i.e., anti-correlated) with the DMN, providing rs-fMRI evidence for the mesocircuit hypothesis of human consciousness, whereby a striatopallidal feedback system modulates anterior forebrain function via disinhibition of the central thalamus. Seed-based analyses yielded similar subcortical DMN connectivity, but the NASCAR result showed stronger contrast and better spatial alignment with dopamine immunostaining data. The DMN subcortical connectivity map identified here advances understanding of the subcortical regions that contribute to human consciousness and can be used to inform the selection of therapeutic targets in clinical trials for patients with disorders of consciousness.

Tractography of the ansa lenticularis in the human brain

The aim of this study was to make a thorough investigation of the trajectory of the ansa lenticularis (AL) and its subcomponents using high-resolution fiber-tracking tractography. The subcomponents of the AL were reconstructed from one region of interest (ROI) in the area of the globus pallidus combined with another ROI in the red nucleus, substantia nigra, subthalamic nucleus, or thalamus. This fiber-tracking protocol was tested in an HCP-1065 template, 35 healthy subjects from Massachusetts General Hospital (MGH), and 20 healthy subjects from the human connectome project (HCP) using generalized q-sampling imaging (GQI)-based tractography. Quantitative anisotropy and fractional anisotropy were also computed for the AL subcomponents. The subcomponents of the AL could be reconstructed in the HCP-1065 template, 35 MGH healthy subjects, and 20 HCP healthy subjects. The AL descends from the globus pallidus and joins the ansa peduncularis for a short distance, subdividing later into fibers that continue separately to the red nucleus, substantia nigra, subthalamic nucleus, and thalamus. The study demonstrated the trajectory of the ansa lenticularis and its subcomponents using GQI-based tractography, improving our understanding of the anatomical connectivity between the globus pallidus and the thalamo-subthalamic region in the human brain. One Sentence Summary The investigation of the ansa lenticularis and its subcomponents using high-resolution diffusion images based tractography.

A high-resolution interactive atlas of the human brainstem using magnetic resonance imaging

Conventional atlases of the human brainstem are limited by the inflexible, sparsely-sampled, two-dimensional nature of histology, or the low spatial resolution of conventional magnetic resonance imaging (MRI). Postmortem high-resolution MRI circumvents the challenges associated with both modalities. A single human brainstem specimen extending from the rostral diencephalon through the caudal medulla was prepared for imaging after the brain was removed from a 65-year-old male within 24 h of death. The specimen was formalin-fixed for two weeks, then rehydrated and placed in a custom-made MRI compatible tube and immersed in liquid fluorocarbon. MRI was performed in a 7-Tesla scanner with 120 unique diffusion directions. Acquisition time for anatomic and diffusion images were 14 h and 208 h, respectively. Segmentation was performed manually. Deterministic fiber tractography was done using strategically chosen regions of interest and avoidance, with manual editing using expert knowledge of human neuroanatomy. Anatomic and diffusion images were rendered with isotropic resolutions of 50 μm and 200 μm, respectively. Ninety different structures were segmented and labeled, and 11 different fiber bundles were rendered with tractography. The complete atlas is available online for interactive use at https://www.civmvoxport.vm.duke.edu/voxbase/login.php?return_url=%2Fvoxbase%2F. This atlas presents multiple contrasting datasets and selected tract reconstruction with unprecedented resolution for MR imaging of the human brainstem. There are immediate applications in neuroanatomical education, with the potential to serve future applications for neuroanatomical research and enhanced neurosurgical planning through "safe" zones of entry into the human brainstem.

Structural and resting state functional connectivity beyond the cortex

Mapping the structural and functional connectivity of the central nervous system has become a key area within neuroimaging research. While detailed network structures across the entire brain have been probed using animal models, non-invasive neuroimaging in humans has thus far been dominated by cortical investigations. Beyond the cortex, subcortical nuclei have traditionally been less accessible due to their smaller size and greater distance from radio frequency coils. However, major neuroimaging developments now provide improved signal and the resolution required to study these structures. Here, we present an overview of the connectivity between the amygdala, brainstem, cerebellum, spinal cord and the rest of the brain. While limitations to their imaging and analyses remain, we also provide some recommendations and considerations for mapping brain connectivity beyond the cortex.

WIKIBrainStem: An online atlas to manually segment the human brainstem at the mesoscopic scale from ultrahigh field MRI

The brainstem is one of the most densely packed areas of the central nervous system in terms of gray, but also white, matter structures and, therefore, is a highly functional hub. It has mainly been studied by the means of histological techniques, which requires several hundreds of slices with a loss of the 3D coherence of the whole specimen. Access to the inner structure of the brainstem is possible using Magnetic Resonance Imaging (MRI), but this method has a limited spatial resolution and contrast in vivo. Here, we scanned an ex vivo specimen using an ultra-high field (11.7T) preclinical MRI scanner providing data at a mesoscopic scale for anatomical T2-weighted (100 µm and 185 µm isotropic) and diffusion-weighted imaging (300 µm isotropic). We then proposed a hierarchical segmentation of the inner gray matter of the brainstem and defined a set of rules for each segmented anatomical class. These rules were gathered in a freely accessible web-based application, WIKIBrainStem (https://fibratlas.univ-tours.fr/brainstems/index.html), for 99 structures, from which 13 were subdivided into 29 substructures. This segmentation is, to date, the most detailed one developed from ex vivo MRI of the brainstem. This should be regarded as a tool that will be complemented by future results of alternative methods, such as Optical Coherence Tomography, Polarized Light Imaging or histology… This is a mandatory step prior to segmenting multiple specimens, which will be used to create a probabilistic automated segmentation method of ex vivo, but also in vivo, brainstem and may be used for targeting anatomical structures of interest in managing some degenerative or psychiatric disorders.

Visualization of cerebellar peduncles using diffusion tensor imaging

The cerebellum communicates with the cerebral cortex via the superior, middle, and inferior cerebellar peduncles (CPs). To preserve the structure and function of the brainstem and cerebellum, which is compressed in various pathological conditions, it is important to delineate the spatial interrelationship of the CPs for presurgical planning and intraoperative guidance. Diffusion tensor tractography (DTT) is a technique capable of depicting the major fiber bundles in CPs. However, routine use of this technology for brainstem visualization remains challenging due to the anatomical smallness and complexity of the brainstem and susceptibility-induced image distortions. Here, we attempt to visualize CPs using high-resolution DTT in a commercial equipment for the application of this technique in normal clinical settings. DTT and fast imaging employing steady-state acquisition-cycled phases (FIESTA) of the whole brainstem were performed. We rendered the DTT fiber bundle using a region-of-interest-based fiber tracking method onto the structural image generated in FIESTA by automatic image coregistration. Fibers of the CPs were clearly visualized by DTT. The DTT-FIESTA overlaid image revealed the cross-sectional and three-dimensional anatomy of the pyramidal tract and the ascending sensory fibers, in addition to the CPs. This could indicate a geometrical relationship of these fibers in the brainstem. The CPs could be visualized clearly using DTT within clinically acceptable scanning times. This method of visualizing the exact pathway of fiber bundles and cranial nerves in the skull base helps in the planning of surgical approaches.

Opportunities of connectomic neuromodulation

The process of altering neural activity - neuromodulation - has long been used to treat patients with brain disorders and answer scientific questions. Deep brain stimulation in particular has provided clinical benefit to over 150,000 patients. However, our understanding of how neuromodulation impacts the brain is evolving. Instead of focusing on the local impact at the stimulation site itself, we are considering the remote impact on brain regions connected to the stimulation site. Brain connectivity information derived from advanced magnetic resonance imaging data can be used to identify these connections and better understand clinical and behavioral effects of neuromodulation. In this article, we review studies combining neuromodulation and brain connectomics, highlighting opportunities where this approach may prove particularly valuable. We focus on deep brain stimulation, but show that the same principles can be applied to other forms of neuromodulation, such as transcranial magnetic stimulation and MRI-guided focused ultrasound. We outline future perspectives and provide testable hypotheses for future work.

3D Exploration of the Brainstem in 50-Micron Resolution MRI

The brainstem, a structure of vital importance in mammals, is currently becoming a principal focus in cognitive, affective, and clinical neuroscience. Midbrain, pontine and medullary structures serve as the conduit for signals between the forebrain and spinal cord, are the epicenter of cranial nerve-circuits and systems, and subserve such integrative functions as consciousness, emotional processing, pain, and motivation. In this study, we parcellated the nuclear masses and the principal fiber pathways that were visible in a high-resolution T2-weighted MRI dataset of 50-micron isotropic voxels of a postmortem human brainstem. Based on this analysis, we generated a detailed map of the human brainstem. To assess the validity of our maps, we compared our observations with histological maps of traditional human brainstem atlases. Given the unique capability of MRI-based morphometric analysis in generating and preserving the morphology of 3D objects from individual 2D sections, we reconstructed the motor, sensory and integrative neural systems of the brainstem and rendered them in 3D representations. We anticipate the utilization of these maps by the neuroimaging community for applications in basic neuroscience as well as in neurology, psychiatry, and neurosurgery, due to their versatile computational nature in 2D and 3D representations in a publicly available capacity.

The ansa peduncularis in the human brain: A tractography and fiber dissection study

INTRODUCTION

The ansa peduncularis is a composite of white matter fiber bundles closely packed together that sweeps around the cerebral peduncle. The exact components of the ansa peduncularis and their anatomical trajectories are still not established firmly in the literature.

OBJECTIVE

The aim of this study was to examine the topographical anatomy of the ansa peduncularis and its subcomponents using the fiber dissection and tractography techniques.

METHODS

Ten formalin-fixed brains were prepared according to Klingler's method and dissected by the fiber dissection technique from the lateral, medial and inferior surfaces. The ansa peduncularis was also traced using high definition fiber tracking (HDFT) from the MRI data of twenty healthy adults and a 1021-subject template from the Human Connectome Project.

RESULTS

The ventral amygdalofugal pathway system includes white matter fiber bundles with a topographically close relation as they sweep around the cerebral peduncle and contribute to form the ansa peduncularis: amygdaloseptal fibers connect the amygdala and anterior temporal cortex to the septal region and amygdalohypothalamic fibers project from the amygdala to the hypothalamus. Additionally, from the amygdala and anterior temporal cortex, amygdalothalamic fibers project to the medial thalamic region. The ansa lenticularis, which connects the globus pallidus to the thalamus, was not shown in our study.

CONCLUSION

The study demonstrated the trajectory of the ansa peduncularis and its subcomponents, based on fiber dissection and tractography, improving our understanding of human brain anatomical connectivity.

Mapping tracts in the human subthalamic area by 11.7T ex vivo diffusion tensor imaging

The cortico-basal ganglia-thalamo-cortical feedback loops that consist of distinct white matter pathways are important for understanding in vivo imaging studies of functional and anatomical connectivity, and for localizing subthalamic white matter structures in surgical approaches for movement disorders, such as Parkinson's disease. Connectomic analysis in animals has identified fiber connections between the basal ganglia and thalamus, which pass through the fields of Forel, where other fiber pathways related to motor, sensory, and cognitive functions co-exist. We now report these pathways in the human brain on ex vivo mesoscopic (250 μm) diffusion tensor imaging and on tractography. The locations of the tracts were identified relative to the adjacent gray matter structures, such as the internal and external segments of the globus pallidus; the zona incerta; the subthalamic nucleus; the substantia nigra pars reticulata and compacta; and the thalamus. The connectome atlas of the human subthalamic region may serve as a resource for imaging studies and for neurosurgical planning.

Direct In Vivo MRI Discrimination of Brain Stem Nuclei and Pathways

BACKGROUND AND PURPOSE

The brain stem is a complex configuration of small nuclei and pathways for motor, sensory, and autonomic control that are essential for life, yet internal brain stem anatomy is difficult to characterize in living subjects. We hypothesized that the 3D fast gray matter acquisition T1 inversion recovery sequence, which uses a short inversion time to suppress signal from white matter, could improve contrast resolution of brain stem pathways and nuclei with 3T MR imaging.

MATERIALS AND METHODS

After preliminary optimization for contrast resolution, the fast gray matter acquisition T1 inversion recovery sequence was performed in 10 healthy subjects (5 women; mean age, 28.8 ± 4.8 years) with the following parameters: TR/TE/TI = 3000/2.55/410 ms, flip angle = 4°, isotropic resolution = 0.8 mm, with 4 averages (acquired separately and averaged outside k-space to reduce motion; total scan time = 58 minutes). One subject returned for an additional 5-average study that was combined with a previous session to create a highest quality atlas for anatomic assignments. A 1-mm isotropic resolution, 12-minute version, proved successful in a patient with a prior infarct.

RESULTS

The fast gray matter acquisition T1 inversion recovery sequence generated excellent contrast resolution of small brain stem pathways in all 3 planes for all 10 subjects. Several nuclei could be resolved directly by image contrast alone or indirectly located due to bordering visualized structures (eg, locus coeruleus and pedunculopontine nucleus).

CONCLUSIONS

The fast gray matter acquisition T1 inversion recovery sequence has the potential to provide imaging correlates to clinical conditions that affect the brain stem, improve neurosurgical navigation, validate diffusion tractography of the brain stem, and generate a 3D atlas for automatic parcellation of specific brain stem structures.

Inner SPACE: 400-Micron Isotropic Resolution MRI of the Human Brain

Objectives

Clinically relevant neuroanatomy is challenging to teach, learn and remember since many functionally important structures are visualized best using histology stains from serial 2D planar sections of the brain. In clinical patients, the locations of specific structures then must be inferred from spatial position and surface anatomy. A 3D MRI dataset of neuroanatomy has several advantages including simultaneous multi-planar visualization in the same brain, direct end-user manipulation of the data and image contrast identical to clinical MRI. We created 3D MRI datasets of the postmortem brain with high spatial and contrast resolution for simultaneous multi-planar visualization of complex neuroanatomy.

Materials and Methods

Whole human brains (N = 6) were immersion-fixed in 4% formaldehyde for 4 weeks, then washed continuously in water for 48 h. The brains were imaged on a clinical 3-T MRI scanner with a 64-channel head and neck coil using a 3D T2-weighted sequence with 400-micron isotropic resolution (voxel = 0.064 mm³; time = 7 h). Besides resolution, this sequence has multiple adjustments to improve contrast compared to a clinical protocol, including 93% reduced turbo factor and 77% reduced effective echo time.

Results

This MRI microscopy protocol provided excellent contrast resolution of small nuclei and internal myelinated pathways within the basal ganglia, thalamus, brainstem, and cerebellum. Contrast was sufficient to visualize the presence and variation of horizontal layers in the cerebral cortex. 3D isotropic resolution datasets facilitated simultaneous multi-planar visualization and efficient production of specific tailored oblique image orientations to improve understanding of complex neuroanatomy.

Conclusion

We created an unlabeled high-resolution digital 3D MRI dataset of neuroanatomy as an online resource for readers to download, manipulate, annotate and use for clinical practice, research, and teaching that is complementary to traditional histology-based atlases. Digital MRI contrast is quantifiable, reproducible across brains and could help validate novel MRI strategies for in vivo structure visualization.

7 Tesla MRI of the ex vivo human brain at 100 micron resolution

We present an ultra-high resolution MRI dataset of an ex vivo human brain specimen. The brain specimen was donated by a 58-year-old woman who had no history of neurological disease and died of non-neurological causes. After fixation in 10% formalin, the specimen was imaged on a 7 Tesla MRI scanner at 100 µm isotropic resolution using a custom-built 31-channel receive array coil. Single-echo multi-flip Fast Low-Angle SHot (FLASH) data were acquired over 100 hours of scan time (25 hours per flip angle), allowing derivation of synthesized FLASH volumes. This dataset provides an unprecedented view of the three-dimensional neuroanatomy of the human brain. To optimize the utility of this resource, we warped the dataset into standard stereotactic space. We now distribute the dataset in both native space and stereotactic space to the academic community via multiple platforms. We envision that this dataset will have a broad range of investigational, educational, and clinical applications that will advance understanding of human brain anatomy in health and disease.

Brainstem neuroimaging of nociception and pain circuitries

The brainstem is known to be an important brain area for nociception and pain processing, and both relaying and coordinating signaling between the cerebrum, cerebellum, and spinal cord. Although preclinical models of pain have characterized the many roles that brainstem nuclei play in nociceptive processing, the degree to which these circuitries extend to humans is not as well known. Unfortunately, the brainstem is also a very challenging region to evaluate in humans with neuroimaging. The challenges for human brainstem imaging arise from the location of this elongated brain structure, proximity to cardiorespiratory noise sources, and the size of its constituent nuclei. These challenges can require dedicated approaches to brainstem imaging, which should be adopted when study hypotheses are focused on brainstem processing of nociception or modulation of pain perception. In fact, our review will highlight many pain neuroimaging studies that have reported some brainstem involvement in nociceptive processing and chronic pain pathology. However, we note that with recent advances in neuroimaging leading to improved spatial and temporal resolution, more studies are needed that take advantage of data collection and analysis methods focused on the challenges of brainstem neuroimaging.

Ex vivo diffusion MRI of the human brain: Technical challenges and recent advances

This review discusses ex vivo diffusion magnetic resonance imaging (dMRI) as an important research tool for neuroanatomical investigations and the validation of in vivo dMRI techniques, with a focus on the human brain. We review the challenges posed by the properties of post-mortem tissue, and discuss state-of-the-art tissue preparation methods and recent advances in pulse sequences and acquisition techniques to tackle these. We then review recent ex vivo dMRI studies of the human brain, highlighting the validation of white matter orientation estimates and the atlasing and mapping of large subcortical structures. We also give particular emphasis to the delineation of layered gray matter structure with ex vivo dMRI, as this application illustrates the strength of its mesoscale resolution over large fields of view. We end with a discussion and outlook on future and potential directions of the field.

Surgical outcome of motor deficits and neurological status in brainstem cavernous malformations based on preoperative diffusion tensor imaging: a prospective randomized clinical trial

OBJECTIVE: Surgical management of brainstem lesions is challenging due to the highly compact, eloquent anatomy of the brainstem. This study aimed to evaluate the safety and efficacy of preoperative diffusion tensor imaging (DTI) and diffusion tensor tractography (DTT) in brainstem cavernous malformations (CMs). METHODS: A prospective randomized controlled clinical trial was performed by using stratified blocked randomization. The primary eligibility criterion of the study was being a surgical candidate for brainstem CMs (with informed consent). The study enrolled 23 patients who underwent preoperative DTI/DTT and 24 patients who did not (the control group). The pre- and postoperative muscle strength of both limbs and modified Rankin Scale (mRS) scores were evaluated. Muscle strength of any limb at 12 months after surgery at the clinic visit was the primary outcome; worsened muscle strength was considered to be a poor outcome. Outcome assessors were blinded to patient management. This study reports the preliminary results of the interim analysis. RESULTS: The cohort included 47 patients (22 women) with a mean age of 35.7 years. The clinical baselines between these 2 groups were not significantly different. In the DTI/DTT group, the corticospinal tract was affected in 17 patients (73.9%): it was displaced, deformed/partially interrupted, or completely interrupted in 6, 7, and 4 patients, respectively. The surgical approach and brainstem entry point were adjusted in 3 patients (13.0%) based on DTI/DTT data. The surgical morbidity of the DTI/DTT group (7/23, 30.4%) was significantly lower than that of the control group (19/24, 79.2%, p = 0.001). At 12 months, the mean mRS score (1.1, p = 0.034) and percentage of patients with worsened motor deficits (4.3%, p = 0.006) were significantly lower in the DTI/DTT group than in the control group (1.7% and 37.5%). Multivariate logistic regression identified the absence of preoperative DTI/DTT (OR 0.06, 95% CI 0.01-0.73, p = 0.028) and use of the 2-point method (OR 4.15, 95% CI 1.38-12.49, p = 0.011) as independent adverse factors for a worsened motor deficit. The multivariate model found a significant correlation between poor mRS score and both an increased preoperative mRS score (t = 3.559, p = 0.001) and absence of preoperative DTI/DTT (t = -2.747, p = 0.009). CONCLUSIONS: DTI/DTT noninvasively allowed for visualization of the anatomical relationship between vital tracts and pathologies as well as facilitated the brainstem surgical approach and entry-point decision making. The technique was valuable for complex neurosurgical planning to reduce morbidity. Nonetheless, DTI/DTT data should be interpreted cautiously.■ CLASSIFICATION OF EVIDENCE Type of question: therapeutic; study design: randomized controlled trial; evidence: class I. Clinical trial registration no.: NCT01758211 (ClinicalTrials.gov).

Microstructural imaging of the human brain with a 'super-scanner': 10 key advantages of ultra-strong gradients for diffusion MRI

The key component of a microstructural diffusion MRI 'super-scanner' is a dedicated high-strength gradient system that enables stronger diffusion weightings per unit time compared to conventional gradient designs. This can, in turn, drastically shorten the time needed for diffusion encoding, increase the signal-to-noise ratio, and facilitate measurements at shorter diffusion times. This review, written from the perspective of the UK National Facility for In Vivo MR Imaging of Human Tissue Microstructure, an initiative to establish a shared 300 mT/m-gradient facility amongst the microstructural imaging community, describes ten advantages of ultra-strong gradients for microstructural imaging. Specifically, we will discuss how the increase of the accessible measurement space compared to a lower-gradient systems (in terms of Δ, b-value, and TE) can accelerate developments in the areas of 1) axon diameter distribution mapping; 2) microstructural parameter estimation; 3) mapping micro-vs macroscopic anisotropy features with gradient waveforms beyond a single pair of pulsed-gradients; 4) multi-contrast experiments, e.g. diffusion-relaxometry; 5) tractography and high-resolution imaging in vivo and 6) post mortem; 7) diffusion-weighted spectroscopy of metabolites other than water; 8) tumour characterisation; 9) functional diffusion MRI; and 10) quality enhancement of images acquired on lower-gradient systems. We finally discuss practical barriers in the use of ultra-strong gradients, and provide an outlook on the next generation of 'super-scanners'.

Connectivity-based segmentation of the brainstem by probabilistic tractography

Diffusion magnetic resonance imaging is a non-invasive tool increasingly used for the investigation of brain connectivity in vivo. In this paper we propose a method that allows segmentation of the brainstem to four subregions (frontopontine, motor, sensory and reticular) based on connections to supratentorial structures, thereby eliminating the need for using anatomical landmarks within the brainstem for the identification of these subregions. The feasibility of connectivity-based brainstem segmentation was investigated in a group of healthy subjects (n = 20). Multifiber probabilistic tractography was performed using the FMRIB Software Library, and connections between a pontomesencephalic seed mask and four supratentorial target regions (anterior and posterior limbs of the internal capsule, sensory and medial thalamus) were used to determine connectivity maps of the brainstem. Results were compared with a neuroanatomy atlas and histological sections, confirming good anatomic correspondence. The four subregions detected by the connectivity-based segmentation showed good intersubject reproducibility. The presented method may be a potential tool to investigate brainstem connectivity in diseases that distort normal anatomy, and quantitative analyses of the diffusion-related parameters may provide additional information on the involvement of brainstem pathways in certain disease states (e.g., traumatic brain injury, demyelinating disorders, brainstem tumors). The potential clinical applicability of the method is demonstrated in two cases of severe traumatic brain injury.

Visualizing the Human Subcortex Using Ultra-high Field Magnetic Resonance Imaging

With the recent increased availability of ultra-high field (UHF) magnetic resonance imaging (MRI), substantial progress has been made in visualizing the human brain, which can now be done in extraordinary detail. This review provides an extensive overview of the use of UHF MRI in visualizing the human subcortex for both healthy and patient populations. The high inter-subject variability in size and location of subcortical structures limits the usability of atlases in the midbrain. Fortunately, the combined results of this review indicate that a large number of subcortical areas can be visualized in individual space using UHF MRI. Current limitations and potential solutions of UHF MRI for visualizing the subcortex are also discussed.

A probabilistic atlas of human brainstem pathways based on connectome imaging data

The brainstem is a critical structure that regulates vital autonomic functions, houses the cranial nerves and their nuclei, relays motor and sensory information between the brain and spinal cord, and modulates cognition, mood, and emotions. As a primary relay center, the fiber pathways of the brainstem include efferent and afferent connections among the cerebral cortex, spinal cord, and cerebellum. While diffusion MRI has been successfully applied to map various brain pathways, its application for the in vivo imaging of the brainstem pathways has been limited due to inadequate resolution and large susceptibility-induced distortion artifacts. With the release of high-resolution data from the Human Connectome Project (HCP), there is increasing interest in mapping human brainstem pathways. Previous works relying on HCP data to study brainstem pathways, however, did not consider the prevalence (>80%) of large distortions in the brainstem even after the application of correction procedures from the HCP-Pipeline. They were also limited in the lack of adequate consideration of subject variability in either fiber pathways or region of interests (ROIs) used for bundle reconstruction. To overcome these limitations, we develop in this work a probabilistic atlas of 23 major brainstem bundles using high-quality HCP data passing rigorous quality control. For the large-scale data from the 500-Subject release of HCP, we conducted extensive quality controls to exclude subjects with severe distortions in the brainstem area. After that, we developed a systematic protocol to manually delineate 1300 ROIs on 20 HCP subjects (10 males; 10 females) for the reconstruction of fiber bundles using tractography techniques. Finally, we leveraged our novel connectome modeling techniques including high order fiber orientation distribution (FOD) reconstruction from multi-shell diffusion imaging and topography-preserving tract filtering algorithms to successfully reconstruct the 23 fiber bundles for each subject, which were then used to calculate the probabilistic atlases in the MNI152 space for public release. In our experimental results, we demonstrate that our method yielded anatomically faithful reconstruction of the brainstem pathways and achieved improved performance in comparison with an existing atlas of cerebellar peduncles based on HCP data. These atlases have been publicly released on NITRIC (https://www.nitrc.org/projects/brainstem_atlas/) and can be readily used by brain imaging researchers interested in studying brainstem pathways.

Probing the neuroanatomy of the cerebellum using tractography

Diffusion tensor imaging (DTI) is a noninvasive neuroimaging tool assessing the organization of white-matter tracts and brain microstructure in vivo. The technique takes into account the three-dimensional (3D) direction of diffusion of water in space, the brownian movements of water being constrained by the brain microstructure. The main direction of diffusion in the brain is extracted to obtain the principal direction of axonal projection within a given voxel. Overall, the diffusion tensor is a mathematic analysis of the magnitude/directionality (anisotropy) of the movement of water molecules in 3D space. Tracts running in the white matter are subsequently reconstructed graphically with fiber tractography. Tractography can be applied to myelinated and unmyelinated fibers or axonopathy. Decreased fractional anisotropy in white-matter tracts occurs in cases of injury with disorganized or disrupted myelin sheaths. Furthermore, high angular resolution methods enable detection of fiber crossings or convergence. DTI is a modern tool which complements conventional magnetic resonance techniques and is particularly relevant to assess the organization of cerebellar tracts. Indeed, both the afferent and efferent pathways of the cerebellar circuitry passing through the inferior, middle, and superior cerebellar peduncles can be visualized in vivo, including in children. The microanatomy of the cerebellar cortex and cerebellar nuclei is also emerging as a future assessment. Applications in the field of cerebellar disorders are multiple, ranging from developmental disorders to adult-onset cerebellar ataxias.

The functional anatomy of the cerebrocerebellar circuit: A review and new concepts

The cerebrocerebellar circuit is a feedback circuit that bidirectionally connects the neocortex and the cerebellum. According to the classic view, the cerebrocerebellar circuit is specifically involved in the functional regulation of the motor areas of the neocortex. In recent years, studies carried out in experimental animals by morphological and physiological methods, and in humans by magnetic resonance imaging, have indicated that the cerebrocerebellar circuit is also involved in the functional regulation of the nonmotor areas of the neocortex, including the prefrontal, associative, sensory and limbic areas. Moreover, a second type of cerebrocerebellar circuit, bidirectionally connecting the hypothalamus and the cerebellum, has been detected, being specifically involved in the regulation of the hypothalamic functions. This review analyzes the morphological features of the centers and pathways of the cerebrocerebellar circuits, paying particular attention to their organization in different channels, which separately connect the cerebellum with the motor areas and nonmotor areas of the neocortex, and with the hypothalamus. Actually, a considerable amount of new data have led, and are leading, to profound changes on the views on the anatomy, physiology, and pathophysiology of the cerebrocerebellar circuits, so much they may be now considered to be essential for the functional regulation of many neocortex areas, perhaps all, as well as of the hypothalamus and of the limbic system. Accordingly, clinical studies have pointed out an involvement of the cerebrocerebellar circuits in the pathophysiology of an increasing number of neuropsychiatric disorders.

Depressive disorder may be associated with raphe nuclei lesions in patients with brainstem infarction

BACKGROUND

Depression is a common symptom after stroke, but its neural substrates remain unclear. The ascending serotonergic system originates from the raphe nuclei in the brainstem. We hypothesized that depressive disorder due to brainstem infarction is associated with damage to the raphe nuclei.

METHODS

We prospectively enrolled 19 patients who had the first-ever acute isolated brainstem infarction in an observational cross-sectional study. All patients were evaluated by using the Montgomery Åsberg Depression Rating Scale (MADRS), the clinician-rated version of Apathy Evaluation Scale (AES-C) and Mini-Mental State Examination (MMSE). Depressive disorder was diagnosed according to DSM-5 and MADRS score of 12 or greater. Diffusion tensor imaging and proton density-weighted images were used to identify damage in the raphe nuclei. Accordingly, patients were classified into either the raphe-nuclei-damaged or intact group. Prevalence of depressive disorder and the MADRS, AES-C, and MMSE scores were compared between the two groups.

RESULTS

Depressive disorder was more frequent in the damaged group (n=6) than in the intact group (n=13) (83% vs. 15%; P=0.01). MADRS scores were higher in the damaged group than in the intact group (mean±1 SD, 17.5±7.9 vs. 7.0±4.4; P=0.002), whereas the AES-C and MMSE scores did not differ between groups.

LIMITATIONS

We did not assess the damage to the ascending projection fibers from the raphe nuclei.

CONCLUSIONS

Our results suggest that damage to the raphe nuclei underlies depressive disorder due to brainstem infarction, possibly via serotonergic denervation.

Challenges and opportunities for brainstem neuroimaging with ultrahigh field MRI

The human brainstem plays a central role in connecting the cerebrum, the cerebellum and the spinal cord to one another, hosting relay nuclei for afferent and efferent signaling, and providing source nuclei for several neuromodulatory systems that impact central nervous system function. While the investigation of the brainstem with functional or structural magnetic resonance imaging has been hampered for years due to this brain structure's physiological and anatomical characteristics, the field has seen significant advances in recent years thanks to the broader adoption of ultrahigh-field (UHF) MRI scanning. In the present review, we focus on the advantages offered by UHF in the context of brainstem imaging, as well as the challenges posed by the investigation of this complex brain structure in terms of data acquisition and analysis. We also illustrate how UHF MRI can shed new light on the neuroanatomy and neurophysiology underlying different brainstem-based circuitries, such as the central autonomic network and neurotransmitter/neuromodulator systems, discuss existing and foreseeable clinical applications to better understand diseases such as chronic pain and Parkinson's disease, and explore promising future directions for further improvements in brainstem imaging using UHF MRI techniques.

Evaluation of the Differences of Myocardial Fibers between Acute and Chronic Myocardial Infarction: Application of Diffusion Tensor Magnetic Resonance Imaging in a Rhesus Monkey Model

Objective

To understand microstructural changes after myocardial infarction (MI), we evaluated myocardial fibers of rhesus monkeys during acute or chronic MI, and identified the differences of myocardial fibers between acute and chronic MI.

Materials and Methods

Six fixed hearts of rhesus monkeys with left anterior descending coronary artery ligation for 1 hour or 84 days were scanned by diffusion tensor magnetic resonance imaging (MRI) to measure apparent diffusion coefficient (ADC), fractional anisotropy (FA) and helix angle (HA).

Results

Comparing with acute MI monkeys (FA: 0.59 ± 0.02; ADC: 5.0 ± 0.6 × 10^-4 mm²/s; HA: 94.5 ± 4.4°), chronic MI monkeys showed remarkably decreased FA value (0.26 ± 0.03), increased ADC value (7.8 ± 0.8 × 10^-4mm²/s), decreased HA transmural range (49.5 ± 4.6°) and serious defects on endocardium in infarcted regions. The HA in infarcted regions shifted to more components of negative left-handed helix in chronic MI monkeys (-38.3 ± 5.0°–11.2 ± 4.3°) than in acute MI monkeys (-41.4 ± 5.1°–53.1 ± 3.7°), but the HA in remote regions shifted to more components of positive right-handed helix in chronic MI monkeys (-43.8 ± 2.7°–66.5 ± 4.9°) than in acute MI monkeys (-59.5 ± 3.4°–64.9 ± 4.3°).

Conclusion

Diffusion tensor MRI method helps to quantify differences of mechanical microstructure and water diffusion of myocardial fibers between acute and chronic MI monkey's models.

Ultra-High Field MRI Post Mortem Structural Connectivity of the Human Subthalamic Nucleus, Substantia Nigra, and Globus Pallidus

Introduction: The subthalamic nucleus, substantia nigra, and globus pallidus, three nuclei of the human basal ganglia, play an important role in motor, associative, and limbic processing. The network of the basal ganglia is generally characterized by a direct, indirect, and hyperdirect pathway. This study aims to investigate the mesoscopic nature of these connections between the subthalamic nucleus, substantia nigra, and globus pallidus and their surrounding structures.

Methods: A human post mortem brain specimen including the substantia nigra, subthalamic nucleus, and globus pallidus was scanned on a 7 T MRI scanner. High resolution diffusion weighted images were used to reconstruct the fibers intersecting the substantia nigra, subthalamic nucleus, and globus pallidus. The course and density of these tracks was analyzed.

Results: Most of the commonly established projections of the subthalamic nucleus, substantia nigra, and globus pallidus were successfully reconstructed. However, some of the reconstructed fiber tracks such as the connections of the substantia nigra pars compacta to the other included nuclei and the connections with the anterior commissure have not been shown previously. In addition, the quantitative tractography approach showed a typical degree of connectivity previously not documented. An example is the relatively larger projections of the subthalamic nucleus to the substantia nigra pars reticulata when compared to the projections to the globus pallidus internus.

Discussion: This study shows that ultra-high field post mortem tractography allows for detailed 3D reconstruction of the projections of deep brain structures in humans. Although the results should be interpreted carefully, the newly identified connections contribute to our understanding of the basal ganglia.

B0 -orientation dependent magnetic susceptibility-induced white matter contrast in the human brainstem at 11.7T

PURPOSE

To investigate B0 -field-orientation dependent white matter contrast in the human brainstem based on R2 * and frequency difference (Δf) mapping from gradient echo (GRE) imaging at 11.7T.

METHODS

Multi-echo GRE data were acquired from two fixed human brainstem specimens at multiple orientations with respect to the static B0 field. The B0 -orientation dependent modulation curves of R2 * and Δf measurements between short and long echo time regimes were used to reconstruct maps of three-dimensional (3D) white matter orientation vectors. The results were compared with maps from diffusion MRI, susceptibility tensor imaging, and histological staining of the same specimens.

RESULTS

R2 * and Δf maps demonstrated distinct and significant contrast modulation between the corticospinal tract (CST) and transverse pontine fibers (TPF) dependent on B0 orientation. Interleaved fiber orientations of the CST and TPF could be sensitively resolved based on field-orientation-dependent fitting of the R2 * and Δf measurements. The fitted 3D orientation vector maps and peak-to-peak amplitude of R2 * and Δf modulation exhibited close correspondence to primary eigenvector and anisotropy maps derived from diffusion MRI. The amplitude of B0 -orientation dependent R2 * modulation was significantly (P < 0.005) higher in the CST compared with TPF, while fractional anisotropies were comparable.

CONCLUSION

The findings of this study demonstrate the potential of B0 -orientation dependent susceptibility-induced R2 * and Δf contrasts to probe tract-specific orientation and microstructure in white matter. Magn Reson Med 75:2455-2463, 2016. © 2016 Wiley Periodicals, Inc.

Correlating Function and Imaging Measures of the Medial Longitudinal Fasciculus

Objective

To test the validity of diffusion tensor imaging (DTI) measures of tissue injury by examining such measures in a white matter structure with well-defined function, the medial longitudinal fasciculus (MLF). Injury to the MLF underlies internuclear ophthalmoparesis (INO).

Methods

40 MS patients with chronic INO and 15 healthy controls were examined under an IRB-approved protocol. Tissue integrity of the MLF was characterized by DTI parameters: longitudinal diffusivity (LD), transverse diffusivity (TD), mean diffusivity (MD) and fractional anisotropy (FA). Severity of INO was quantified by infrared oculography to measure versional disconjugacy index (VDI).

Results

LD was significantly lower in patients than in controls in the medulla-pons region of the MLF (p < 0.03). FA was also lower in patients in the same region (p < 0.0004). LD of the medulla-pons region correlated with VDI (R = -0.28, p < 0.05) as did FA in the midbrain section (R = 0.31, p < 0.02).

Conclusions

This study demonstrates that DTI measures of brain tissue injury can detect injury to a functionally relevant white matter pathway, and that such measures correlate with clinically accepted evaluation indices for INO. The results validate DTI as a useful imaging measure of tissue integrity.

Evaluate the early changes of myocardial fibers in rhesus monkey during sub-acute stage of myocardial infarction using diffusion tensor magnetic resonance imaging

PURPOSE

The deterioration of cardiac mechanical function starts from the micro-alterations in the myocardial fibers after myocardial infarction (MI) due to the heart beats derived from the systole and diastole of the myocardial fibers. So, we want to evaluate quantitatively the early changes of myocardial fibers in rhesus monkey during sub-acute MI stage.

MATERIALS AND METHODS

Three fixed hearts with infarction after left anterior descending coronary artery ligation for 7days and eight age-matched intact controls were scanned by ex-vivo diffusion tensor magnetic resonance imaging (DT-MRI) to measure apparent diffusion coefficient (ADC), fractional anisotropy (FA) and helix angle (HA).

RESULTS

In comparison with healthy controls, FA and transmural range of HA in MI regions showed a significant reduction whereas ADC showed a significant increment (p<0.01). The double-helix myocardial fibers shifted further to left-handed helix around the infarcted and adjacent myocardium but shifted further to right-handed helix in remote myocardium.

CONCLUSION

HA is sensitive to evaluate quantitatively the early changes of myocardial fibers in sub-acute MI rhesus monkeys. The myocardial fibers in normal monkeys are similar to those in normal humans, suggesting that early changes of myocardial fibers in sub-acute MI monkeys can contribute to more accurately understand those in patients suffering sub-acute MI.

In vivo mapping of macroscopic neuronal projections in the mouse hippocampus using high-resolution diffusion MRI

Recent developments in diffusion magnetic resonance imaging (MRI) make it a promising tool for non-invasive mapping of the spatial organization of axonal and dendritic networks in gray matter regions of the brain. Given the complex cellular environments, in which these networks reside, evidence on the capability of diffusion MRI-based tractography to study these networks is still lacking. In this study, we used a localized diffusion MRI approach to acquire high spatial and angular resolution images of the live mouse hippocampus. The diffusion MRI and tractography results were compared with histology and the Allen mouse brain connectivity atlas using a multi-step image registration pipeline. The results demonstrated that in vivo diffusion MRI data at 0.1mm isotropic resolution revealed the organization of axonal and dendritic networks in the hippocampus and the tractography results shared remarkable similarity with the viral tracer data in term of their spatial projection patterns. Quantitative analysis showed significant correlations between tractography- and tracer-based projection density measurements in the mouse hippocampus. These findings suggest that high-resolution diffusion MRI and tractography can reveal macroscopic neuronal projections in the mouse hippocampus and are important for future development of advanced tractography methods.

Toward an In Vivo Neuroimaging Template of Human Brainstem Nuclei of the Ascending Arousal, Autonomic, and Motor Systems

Brainstem nuclei (Bn) in humans play a crucial role in vital functions, such as arousal, autonomic homeostasis, sensory and motor relay, nociception, sleep, and cranial nerve function, and they have been implicated in a vast array of brain pathologies. However, an in vivo delineation of most human Bn has been elusive because of limited sensitivity and contrast for detecting these small regions using standard neuroimaging methods. To precisely identify several human Bn in vivo, we employed a 7 Tesla scanner equipped with multi-channel receive-coil array, which provided high magnetic resonance imaging sensitivity, and a multi-contrast (diffusion fractional anisotropy and T2-weighted) echo-planar-imaging approach, which provided complementary contrasts for Bn anatomy with matched geometric distortions and resolution. Through a combined examination of 1.3 mm(3) multi-contrast anatomical images acquired in healthy human adults, we semi-automatically generated in vivo probabilistic Bn labels of the ascending arousal (median and dorsal raphe), autonomic (raphe magnus, periaqueductal gray), and motor (inferior olivary nuclei, two subregions of the substantia nigra compatible with pars compacta and pars reticulata, two subregions of the red nucleus, and, in the diencephalon, two subregions of the subthalamic nucleus) systems. These labels constitute a first step toward the development of an in vivo neuroimaging template of Bn in standard space to facilitate future clinical and research investigations of human brainstem function and pathology. Proof-of-concept clinical use of this template is demonstrated in a minimally conscious patient with traumatic brainstem hemorrhages precisely localized to the raphe Bn involved in arousal.

Subject-specific computational modeling of DBS in the PPTg area

Deep brain stimulation (DBS) in the pedunculopontine tegmental nucleus (PPTg) has been proposed to alleviate medically intractable gait difficulties associated with Parkinson's disease. Clinical trials have shown somewhat variable outcomes, stemming in part from surgical targeting variability, modulating fiber pathways implicated in side effects, and a general lack of mechanistic understanding of DBS in this brain region. Subject-specific computational models of DBS are a promising tool to investigate the underlying therapy and side effects. In this study, a parkinsonian rhesus macaque was implanted unilaterally with an 8-contact DBS lead in the PPTg region. Fiber tracts adjacent to PPTg, including the oculomotor nerve, central tegmental tract, and superior cerebellar peduncle, were reconstructed from a combination of pre-implant 7T MRI, post-implant CT, and post-mortem histology. These structures were populated with axon models and coupled with a finite element model simulating the voltage distribution in the surrounding neural tissue during stimulation. This study introduces two empirical approaches to evaluate model parameters. First, incremental monopolar cathodic stimulation (20 Hz, 90 μs pulse width) was evaluated for each electrode, during which a right eyelid flutter was observed at the proximal four contacts (−1.0 to −1.4 mA). These current amplitudes followed closely with model predicted activation of the oculomotor nerve when assuming an anisotropic conduction medium. Second, PET imaging was collected OFF-DBS and twice during DBS (two different contacts), which supported the model predicted activation of the central tegmental tract and superior cerebellar peduncle. Together, subject-specific models provide a framework to more precisely predict pathways modulated by DBS.

Postmortem diffusion MRI of the human brainstem and thalamus for deep brain stimulator electrode localization

Deep brain stimulation (DBS) is an established surgical therapy for medically refractory tremor disorders including essential tremor (ET) and is currently under investigation for use in a variety of other neurologic and psychiatric disorders. There is growing evidence that the anti-tremor effects of DBS for ET are directly related to modulation of the dentatorubrothalamic tract (DRT), a white matter pathway that connects the cerebellum, red nucleus, and ventral intermediate nucleus of the thalamus. Emerging white matter targets for DBS, like the DRT, will require improved three-dimensional (3D) reference maps of deep brain anatomy and structural connectivity for accurate electrode targeting. High-resolution diffusion MRI of postmortem brain specimens can provide detailed volumetric images of important deep brain nuclei and 3D reconstructions of white matter pathways with probabilistic tractography techniques. We present a high spatial and angular resolution diffusion MRI template of the postmortem human brainstem and thalamus with 3D reconstructions of the nuclei and white matter tracts involved in ET circuitry. We demonstrate registration of these data to in vivo, clinical images from patients receiving DBS therapy, and correlate electrode proximity to tractography of the DRT with improvement of ET symptoms.

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.

Diffusion tensor imaging of the auditory nerve in patients with long-term single-sided deafness

A cochlear implant (CI) can restore hearing in patients with profound sensorineural hearing loss by direct electrical stimulation of the auditory nerve. Therefore, the viability of the auditory nerve is vitally important in successful hearing recovery. However, the nerve typically degenerates following cochlear hair cell loss, and the amount of degeneration may considerably differ between the two ears, also in patients with bilateral deafness. A measure that reflects the nerve's condition would help to assess the best of both nerves and decide accordingly which ear should be implanted for optimal benefit from a CI. Diffusion tensor MRI (DTI) may provide such a measure, by allowing noninvasive investigations of the nerve's microstructure. In this pilot study, we show the first use of DTI to image the auditory nerve in five normal-hearing subjects and five patients with long-term profound single-sided sensorineural hearing loss. A specialized acquisition protocol was designed for a 3 T MRI scanner to image the small nerve bundle. The nerve was reconstructed using fiber tractography and DTI metrics - which reflect the nerve's microstructural properties - were computed per tract. Comparing DTI metrics from the deaf-sided with the healthy-sided nerves in patients showed no significant differences. There was a small but significant reduction in fractional anisotropy in both auditory nerves in patients compared with normal-hearing controls. These results are the first evidence of possible changes in the microstructure of the bilateral auditory nerves as a result of single-sided deafness. Our results also indicate that it is too early to assess the degenerative status of the auditory nerve of a subject-specific basis.

Spatial mapping of structural and connectional imaging data for the developing human brain with diffusion tensor imaging

During human brain development from fetal stage to adulthood, the white matter (WM) tracts undergo dramatic changes. Diffusion tensor imaging (DTI), a widely used magnetic resonance imaging (MRI) modality, offers insight into the dynamic changes of WM fibers as these fibers can be noninvasively traced and three-dimensionally (3D) reconstructed with DTI tractography. The DTI and conventional T1 weighted MRI images also provide sufficient cortical anatomical details for mapping the cortical regions of interests (ROIs). In this paper, we described basic concepts and methods of DTI techniques that can be used to trace major WM tracts noninvasively from fetal brain of 14 postconceptional weeks (pcw) to adult brain. We applied these techniques to acquire DTI data and trace, reconstruct and visualize major WM tracts during development. After categorizing major WM fiber bundles into five unique functional tract groups, namely limbic, brain stem, projection, commissural and association tracts, we revealed formation and maturation of these 3D reconstructed WM tracts of the developing human brain. The structural and connectional imaging data offered by DTI provides the anatomical backbone of transcriptional atlas of the developing human brain.

Mapping track density changes in nigrostriatal and extranigral pathways in Parkinson's disease

In Parkinson's disease (PD) the demonstration of neuropathological disturbances in nigrostriatal and extranigral brain pathways using magnetic resonance imaging remains a challenge. Here, we applied a novel diffusion-weighted imaging approach-track density imaging (TDI). Twenty-seven non-demented Parkinson's patients (mean disease duration: 5 years, mean score on the Hoehn & Yahr scale=1.5) were compared with 26 elderly controls matched for age, sex, and education level. Track density images were created by sampling each subject's spatially normalized fiber tracks in 1mm isotropic intervals and counting the fibers that passed through each voxel. Whole-brain voxel-based analysis was performed and significance was assessed with permutation testing. Statistically significant increases in track density were found in the Parkinson's patients, relative to controls. Clusters were distributed in disease-relevant areas including motor, cognitive, and limbic networks. From the lower medulla to the diencephalon and striatum, clusters encompassed the known location of the locus coeruleus and pedunculopontine nucleus in the pons, and from the substantia nigra up to medial aspects of the posterior putamen, bilaterally. The results identified in brainstem and nigrostriatal pathways show a large overlap with the known distribution of neuropathological changes in non-demented PD patients. Our results also support an early involvement of limbic and cognitive networks in Parkinson's disease.

Diffeomorphometry and geodesic positioning systems for human anatomy

The Computational Anatomy project has largely been a study of large deformations within a Riemannian framework as an efficient point of view for generating metrics between anatomical configurations. This approach turns D'Arcy Thompson's comparative morphology of human biological shape and form into a metrizable space. Since the metric is constructed based on the geodesic length of the flows of diffeomorphisms connecting the forms, we call it diffeomorphometry. Just as importantly, since the flows describe algebraic group action on anatomical submanifolds and associated functional measurements, they become the basis for positioning information, which we term geodesic positioning. As well the geodesic connections provide Riemannian coordinates for locating forms in the anatomical orbit, which we call geodesic coordinates. These three components taken together - the metric, geodesic positioning of information, and geodesic coordinates - we term the geodesic positioning system. We illustrate via several examples in human and biological coordinate systems and machine learning of the statistical representation of shape and form.

Localized diffusion magnetic resonance micro-imaging of the live mouse brain

High-resolution diffusion MRI (dMRI) is useful for resolving complex microstructures in the mouse brain, but technically challenging for in vivo studies due to the long scan time. In this study, selective excitation and a three-dimensional fast imaging sequence were used to achieve in vivo high-resolution dMRI of the mouse brain at 11.7Tesla. By reducing the field of view using spatially selective radio frequency pulses, we were able to focus on targeted brain structures and acquire high angular resolution diffusion imaging (HARDI) data at an isotropic resolution of 0.1mm and 30 diffusion encoding directions in approximately 1h. We investigated the complex tissue microstructures of the mouse hippocampus, cerebellum, and several cortical areas using this localized dMRI approach, and compared the results with histological sections stained with several axonal and dendritic markers. In the mouse visual cortex, the results showed predominately radially arranged structures in an outer layer and tangentially arranged structures in an inner layer, similar to observations from postmortem human brain specimens.

Multi-fiber tractography visualizations for diffusion MRI data

In recent years, several new diffusion MRI approaches have been proposed to explore microstructural properties of the white matter, such as Q-ball imaging and spherical deconvolution-based techniques to estimate the orientation distribution function. These methods can describe the estimated diffusion profile with a higher accuracy than the more conventional second-rank diffusion tensor imaging technique. Despite many important advances, there are still inconsistent findings between different models that investigate the "crossing fibers" issue. Due to the high information content and the complex nature of the data, it becomes virtually impossible to interpret and compare results in a consistent manner. In this work, we present novel fiber tractography visualization approaches that provide a more complete picture of the microstructural architecture of fiber pathways: multi-fiber hyperstreamlines and streamribbons. By visualizing, for instance, the estimated fiber orientation distribution along the reconstructed tract in a continuous way, information of the local fiber architecture is combined with the global anatomical information derived from tractography. Facilitating the interpretation of diffusion MRI data, this approach can be useful for comparing different diffusion reconstruction techniques and may improve our understanding of the intricate white matter network.

The Human Connectome Project and beyond: initial applications of 300 mT/m gradients

The engineering of a 3 T human MRI scanner equipped with 300 mT/m gradients - the strongest gradients ever built for an in vivo human MRI scanner - was a major component of the NIH Blueprint Human Connectome Project (HCP). This effort was motivated by the HCP's goal of mapping, as completely as possible, the macroscopic structural connections of the in vivo healthy, adult human brain using diffusion tractography. Yet, the 300 mT/m gradient system is well suited to many additional types of diffusion measurements. Here, we present three initial applications of the 300 mT/m gradients that fall outside the immediate scope of the HCP. These include: 1) diffusion tractography to study the anatomy of consciousness and the mechanisms of brain recovery following traumatic coma; 2) q-space measurements of axon diameter distributions in the in vivo human brain and 3) postmortem diffusion tractography as an adjunct to standard histopathological analysis. We show that the improved sensitivity and diffusion-resolution provided by the gradients are rapidly enabling human applications of techniques that were previously possible only for in vitro and animal models on small-bore scanners, thereby creating novel opportunities to map the microstructure of the human brain in health and disease.