Functional anatomy of subcortical circuits issuing from or integrating at the human brainstem

Diffusion tensor subspace imaging of double diffusion-encoded MRI delineates small fibers and gray-matter microstructure not visible with single encoding techniques

PURPOSE

Double diffusion encoding (DDE) acquisition strategies promise specificity for small-dimensional structures inaccessible to single diffusion encoding (SDE). For DDE-weighted MRI scans to become relevant for whole brain imaging, signal reconstruction frameworks must accurately report microstructural features of interest-especially microscale anisotropy in complex tissue environments. This study examined the recently developed diffusion tensor subspace imaging (DiTSI) framework and its radial and spherical anisotropy metrics (RA and SA, respectively) in postmortem human brain tissue specimens.

METHODS

MRI microscopy including multishell SDE-weighted and DDE-weighted imaging was performed for healthy brain stem and temporal lobe specimens and for specimens with Alzheimer's disease pathology and neurodegeneration. The DiTSI framework was compared with four other diffusion MRI frameworks, and angular and radial DDE sampling were evaluated.

RESULTS

DDE acquisition and the DiTSI metric maps of SA and RA in temporal lobe and brain-stem specimens were found to be distinct from fractional anisotropy and orientation dispersion index in providing complementary and selective contrast of microscale anisotropy at the gray-matter/white-matter interface in the cortex and in hippocampal layers. DiTSI maps also unmasked small fascicles in the brain stem that were not detectable by SDE techniques and provided selective contrast across the major fiber pathways. Results also revealed prominent reductions of SA and RA in tissue with Alzheimer's disease pathology that were not observed for any other framework.

CONCLUSIONS

New contrasts were evident for DiTSI framework metrics over a range of tissue environments with promise toward providing novel markers of pathology.

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.

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.

The brainstem in multiple sclerosis: MR identification of tracts and nuclei damage

Objective

To evaluate the 3D Fast Gray Acquisition T1 Inversion Recovery (FGATIR) sequence for MRI identification of brainstem tracts and nuclei damage in multiple sclerosis (MS) patients.

Methods

From april to december 2020, 10 healthy volunteers and 50 patients with remitted-relapsing MS (58% female, mean age 36) underwent MR imaging in the Neuro-imaging department of the C.H.N.O. des Quinze-Vingts, Paris, France. MRI was achieved on a 3 T system (MAGNETOM Skyra) using a 64-channel coil. 3D FGATIR sequence was first performed on healthy volunteers to classify macroscopically identifiable brainstem structures. Then, FGATIR was assessed in MS patients to locate brainstem lesions detected with Proton Density/T2w (PD/T2w) sequence.

Results

In healthy volunteers, FGATIR allowed a precise visualization of tracts and nuclei according to their myelin density. Including FGATIR in MR follow-up of MS patients helped to identify structures frequently involved in the inflammatory process. Most damaged tracts were the superior cerebellar peduncle and the transverse fibers of the pons. Most frequently affected nuclei were the vestibular nuclei, the trigeminal tract, the facial nerve and the solitary tract.

Conclusion

Combination of FGATIR and PD/T2w sequences opened prospects to define MS elective injury in brainstem tracts and nuclei, with particular lesion features suggesting variations of the inflammatory process within brainstem structures. In a further study, hypersignal quantification and microstructure information should be evaluated using relaxometry and diffusion tractography. Technical improvements would bring novel parameters to train an artificial neural network for accurate automated labeling of MS lesions within the brainstem.

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.

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.

Retrosigmoid Approach: A Simple and Safe Way to Resect Intrinsic Pontomedullary Lesions

Objectives  The main objective of this article is to describe a simple and safe protocol for the microsurgical management of ventrally located intrinsic pontomedullary lesions based on the retrosigmoid approach, cortectomy performed utilizing safe entry zones of the pons and medulla, and a delicate microsurgical resection. The intraoperative protocol includes redundant procedures that provide security in decision-making during surgery. Design  A prospective series of 11 cases is presented. All patients were studied following the same clinical and imaging workup. A regular retrosigmoid craniotomy surgical approach was utilized. The peritrigeminal area in the pons and the olivary area in the medulla were considered as the safe entry zones. Neuronavigation of the white fiber tracts and electrophysiological monitoring were used as intraoperative aids to locate the lesions, the safe entry zones, and the placement of the cortectomy. Results  Six lesions were pontine, two medullary, and the remaining six pontomedullary. Eight lesions were cavernomas, while the remaining three tumors. Overall, we obtained a postoperative functional improvement in the affected cranial nerves in 90.1% of the patients and a total or partial recovery of long ascending or descending pathway symptoms in 72.3% of the patients. All the patients were satisfied with the procedure and the results. Conclusions  Radical resection of ventral intrinsic pontomedullary lesions displays a high degree of intraoperative reliability, and a good clinical result is possible using simple surgical procedures. The anatomical references are the first element in the decision-making process during surgery.

Brain stem – from general view to computational model based on switchboard rules of operation

Despite great progress in understanding the functions and structures of the central nervous system (CNS) the brain stem remains one of the least understood systems. We know that the brain stem acts as a decision station preparing the organism to act in a specific way, but such functions are rather difficult to model with sufficient precision to replicate experimental data due to the scarcity of data and complexity of large-scale simulations of brain stem structures. The approach proposed in this article retains some ideas of previous models, and provides more precise computational realization that enables qualitative interpretation of the functions played by different network states. Simulations are aimed primarily at the investigation of general switching mechanisms which may be executed in brain stem neural networks, as far as studying how the aforementioned mechanisms depend on basic neural network features: basic ionic channels, accommodation, and the influence of noise.

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.

Brain morphological alteration and cognitive dysfunction in multiple system atrophy

Multiple system atrophy (MSA) is a progressive neurodegenerative disease in adults, manifesting various clinical symptoms including autonomic nerve dysfunction, Parkinson's syndrome, cerebellar ataxia, and pyramidal sign. The clinical diagnosis and classification of MSA are mainly dependent on motion and non-motion symptoms, such as autonomic nerve dysfunction. In addition, an increasing amount of clinical and pathological evidence has shown that about half of the MSA patients exhibit distinct types and levels of cognitive dysfunction. However, cognitive dysfunction has not been included in the current diagnosis criteria of MSA. In most cases, it was even used as an exclusion criterion of MSA. Based on the neuroimaging, neuropathology and neuropsychology, this review summarized the morphological changes of the brain in the patients with MSA, and discussed possible brain regions that could be associated with cognitive impairment. The article may provide a theoretical basis for incorporating cognitive dysfunction into the criteria of MSA diagnosis.

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.

Brain stem modeling at a system level – chances and limitations

The topic of brain stem computational simulation still seems understudied in contemporary scientific literature. Current advances in neuroscience leave the brain stem as one of the least known parts of the human central nervous system. Brain stem lesions are particularly damaging to the most important physiological functions. Advances in brain stem modeling may influence important issues within the core of neurology, neurophysiology, neurosurgery, and neurorehabilitation. Direct results may include both development of knowledge and optimization and objectivization of clinical practice in the aforementioned medical areas. Despite these needs, progress in the area of computational brain stem models seems to be too slow. The aims of this paper are both to recognize the strongest limitations in the area of computational brain stem simulations and to assess the extent to which current opportunities may be exploited. Despite limitations, the emerging view of the brain stem provided by its computational models enables a wide repertoire of functions, including core dynamic behavior.

Human Connectome-Based Tractographic Atlas of the Brainstem Connections and Surgical Approaches

BACKGROUND

The brainstem is one of the most challenging areas for the neurosurgeon because of the limited space between gray matter nuclei and white matter pathways. Diffusion tensor imaging-based tractography has been used to study the brainstem structure, but the angular and spatial resolution could be improved further with advanced diffusion magnetic resonance imaging (MRI).

OBJECTIVE

To construct a high-angular/spatial resolution, wide-population-based, comprehensive tractography atlas that presents an anatomical review of the surgical approaches to the brainstem.

METHODS

We applied advanced diffusion MRI fiber tractography to a population-based atlas constructed with data from a total of 488 subjects from the Human Connectome Project-488. Five formalin-fixed brains were studied for surgical landmarks. Luxol Fast Blue-stained histological sections were used to validate the results of tractography.

RESULTS

We acquired the tractography of the major brainstem pathways and validated them with histological analysis. The pathways included the cerebellar peduncles, corticospinal tract, corticopontine tracts, medial lemniscus, lateral lemniscus, spinothalamic tract, rubrospinal tract, central tegmental tract, medial longitudinal fasciculus, and dorsal longitudinal fasciculus. Then, the reconstructed 3-dimensional brainstem structure was sectioned at the level of classic surgical approaches, namely supracollicular, infracollicular, lateral mesencephalic, perioculomotor, peritrigeminal, anterolateral (to the medulla), and retro-olivary approaches.

CONCLUSION

The advanced diffusion MRI fiber tracking is a powerful tool to explore the brainstem neuroanatomy and to achieve a better understanding of surgical approaches.

ABBREVIATIONS

CN, cranial nerveCPT, corticopontine tractCST, corticospinal tractCTT, central tegmental tractDLF, dorsal longitudinal fasciculusHCP, Human Connectome ProjectML, medial lemniscusMLF, medial longitudinal fasciculusRST, rubrospinal tractSTT, spinothalamic tract.

Clinical Neuropathology image 4-2017: High-resolution 7 Tesla MRI of postmortem brain specimens: improving neuroimaging-neuropathology correlations

No Abstract available.

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.

Pain Perception in Buddhism Perspective

Dhamma, which Lord Buddha has presented to people after his enlightenment, analyzes every phenomenon and objects into their ultimate elements. The explanation of sensory system is also found in a part of Dhamma named Abhidhammapitaka, the Book of the Higher Doctrine in Buddhism. To find out the relationship between explanation of pain in the present neuroscience and the explanation of pain in Abhidhamma, the study was carried out by the use of a comprehensive review. The comparisons were in terms of peripheral stimulation, signal transmission, modulation, perception, suffering, determination and decision making for the responding to pain. We found that details of the explanation on pain mechanism and perception in Abhidhamma could associate well with our present scientific knowledge. Furthermore, more refinement information about the process and its function in particular aspects of pain perception were provided in Abhidhammapitaka.

Three-dimensional microsurgical anatomy and the safe entry zones of the brainstem

BACKGROUND

There have been no studies of the structure and safe surgical entry zones of the brainstem based on fiber dissection studies combined with 3-dimensional (3-D) photography.

OBJECTIVE

To examine the 3-D internal architecture and relationships of the proposed safe entry zones into the midbrain, pons, and medulla.

METHODS

Fifteen formalin and alcohol-fixed human brainstems were dissected by using fiber dissection techniques, ×6 to ×40 magnification, and 3-D photography to define the anatomy and the safe entry zones. The entry zones evaluated were the perioculomotor, lateral mesencephalic sulcus, and supra- and infracollicular areas in the midbrain; the peritrigeminal zone, supra- and infrafacial approaches, acoustic area, and median sulcus above the facial colliculus in the pons; and the anterolateral, postolivary, and dorsal medullary sulci in the medulla.

RESULTS

The safest approach for lesions located below the surface is usually the shortest and most direct route. Previous studies have often focused on surface structures. In this study, the deeper structures that may be at risk in each of the proposed safe entry zones plus the borders of each entry zone were defined. This study includes an examination of the relationships of the cerebellar peduncles, long tracts, intra-axial segments of the cranial nerves, and important nuclei of the brainstem to the proposed safe entry zones.

CONCLUSION

Fiber dissection technique in combination with the 3-D photography is a useful addition to the goal of making entry into the brainstem more accurate and safe.

Anatomic Study of the Central Core of the Cerebrum Correlating 7-T Magnetic Resonance Imaging and Fiber Dissection With the Aid of a Neuronavigation System

BACKGROUND:

Different strategies have been used to study the fiber tract anatomy of the human brain in vivo and ex vivo. Nevertheless, the ideal method to study white matter anatomy has yet to be determined because it should integrate information obtained from multiple sources.

OBJECTIVE:

We developed an anatomic method in cadaveric specimens to study the central core of the cerebrum combining traditional white matter dissection with high-resolution 7-T magnetic resonance imaging (MRI) of the same specimen coregistered using a neuronavigation system.

METHODS:

Ten cerebral hemispheres were prepared using the traditional Klingler technique. Before dissection, a structural ultrahigh magnetic field 7-T MRI study was performed on each hemisphere specifically prepared with surface fiducials for neuronavigation. The dissection was then performed from the medial hemispheric surface using the classic white fiber dissection technique. During each step of the dissection, the correlation between the anatomic findings and the 7-T MRI was evaluated with the neuronavigation system.

RESULTS:

The anatomic study was divided in 2 stages: diencephalic and limbic. The diencephalic stage included epithalamic, thalamic, hypothalamic, and subthalamic components. The limbic stage consisted of extending the dissection to complete the Papez circuit. The detailed information given by the combination of both methods allowed us to identify and validate the position of fibers that may be difficult to appreciate and dissect (ie, the medial forebrain bundle).

CONCLUSION:

The correlation of high-definition 7-T MRI and the white matter dissection technique with neuronavigation significantly improves the understanding of the structural connections in complex areas of the human cerebrum.

White matter fiber tracking directed by interpolating splines and a methodological framework for evaluation

Image-based tractography of white matter (WM) fiber bundles in the brain using diffusion weighted MRI (DW-MRI) has become a useful tool in basic and clinical neuroscience. However, proper tracking is challenging due to the anatomical complexity of fiber pathways, the coarse resolution of clinically applicable whole-brain in vivo imaging techniques, and the difficulties associated with verification. In this study we introduce a new tractography algorithm using splines (denoted Spline). Spline reconstructs smooth fiber trajectories iteratively, in contrast to most other tractography algorithms that create piecewise linear fiber tract segments, followed by spline fitting. Using DW-MRI recordings from eight healthy elderly people participating in a longitudinal study of cognitive aging, we compare our Spline algorithm to two state-of-the-art tracking methods from the TrackVis software suite. The comparison is done quantitatively using diffusion metrics (fractional anisotropy, FA), with both (1) tract averaging, (2) longitudinal linear mixed-effects model fitting, and (3) detailed along-tract analysis. Further validation is done on recordings from a diffusion hardware phantom, mimicking a coronal brain slice, with a known ground truth. Results from the longitudinal aging study showed high sensitivity of Spline tracking to individual aging patterns of mean FA when combined with linear mixed-effects modeling, moderately strong differences in the along-tract analysis of specific tracts, whereas the tract-averaged comparison using simple linear OLS regression revealed less differences between Spline and the two other tractography algorithms. In the brain phantom experiments with a ground truth, we demonstrated improved tracking ability of Spline compared to the two reference tractography algorithms being tested.

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

A three-dimensional stereotaxic atlas of the human brainstem based on high resolution ex vivo diffusion tensor imaging (DTI) is introduced. The atlas consists of high resolution (125-255 μm isotropic) three-dimensional DT images of the formalin-fixed brainstem acquired at 11.7 T. The DTI data revealed microscopic neuroanatomical details, allowing three-dimensional visualization and reconstruction of fiber pathways including the decussation of the pyramidal tract fibers, and interdigitating fascicles of the corticospinal and transverse pontine fibers. Additionally, strong gray-white matter contrasts in the apparent diffusion coefficient (ADC) maps enabled precise delineation of gray matter nuclei in the brainstem, including the cranial nerve and the inferior olivary nuclei. Comparison with myelin-stained histology shows that at the level of resolution achieved in this study, the structural details resolved with DTI contrasts in the brainstem were comparable to anatomical delineation obtained with histological sectioning. Major neural structures delineated from DTI contrasts in the brainstem are segmented and three-dimensionally reconstructed. Further, the ex vivo DTI data are nonlinearly mapped to a widely-used in vivo human brain atlas, to construct a high-resolution atlas of the brainstem in the Montreal Neurological Institute (MNI) stereotaxic coordinate space. The results demonstrate the feasibility of developing a 3D DTI based atlas for detailed characterization of brainstem neuroanatomy with high resolution and contrasts, which will be a useful resource for research and clinical applications.