High-resolution diffusion tensor imaging and tractography of the human optic chiasm at 9.4 T

The Claustrum and Insula in Microcebus murinus: A High Resolution Diffusion Imaging Study

The claustrum and the insula are closely juxtaposed in the brain of the prosimian primate, the gray mouse lemur (Microcebus murinus). Whether the claustrum has closer affinities with the cortex or the striatum has been debated for many decades. Our observation of histological sections from primate brains and genomic data in the mouse suggest former. Given this, the present study compares the connections of the two structures in Microcebus using high angular resolution diffusion imaging (HARDI, with 72 directions), with a very small voxel size (90 micra), and probabilistic fiber tractography. High angular and spatial resolution diffusion imaging is non-destructive, requires no surgical interventions, and the connection of each and every voxel can be mapped, whereas in conventional tract tracer studies only a few specific injection sites can be assayed. Our data indicate that despite the high genetic and spatial affinities between the two structures, their connectivity patterns are very different. The claustrum connects with many cortical areas and the olfactory bulb; its strongest probabilistic connections are with the entorhinal cortex, suggesting that the claustrum may have a role in spatial memory and navigation. By contrast, the insula connects with many subcortical areas, including the brainstem and thalamic structures involved in taste and visceral feelings. Overall, the connections of the Microcebus claustrum and insula are similar to those of the rodents, cat, macaque, and human, validating our results. The insula in the Microcebus connects with the dorsolateral frontal cortex in contrast to the mouse insula, which has stronger connections with the ventromedial frontal lobe, yet this is consistent with the dorsolateral expansion of the frontal cortex in primates. In addition to revealing the connectivity patterns of the Microcebus brain, our study demonstrates that HARDI, at high resolutions, can be a valuable tool for mapping fiber pathways for multiple sites in fixed brains in rare and difficult-to-obtain species.

Histological validation of DW-MRI tractography in human postmortem tissue

Despite several previous attempts, histological validation of diffusion-weighted magnetic resonance imaging (DW-MRI)-based tractography as true axonal fiber pathways remains difficult. In the present study, we establish a method to compare histological and tractography data precisely enough for statements on the level of single tractography pathways. To this end, we used carbocyanine dyes to trace connections in human postmortem tissue and aligned them to high-resolution DW-MRI of the same tissue processed within the diffusion tensor imaging (DTI) formalism. We provide robust definitions of sensitivity (true positives) and specificity (true negatives) for DTI tractography and characterize tractography paths in terms of receiver operating characteristics. With sensitivity and specificity rates of approximately 80%, we could show a clear correspondence between histological and inferred tracts. Furthermore, we investigated the effect of fractional anisotropy (FA) thresholds for the tractography and identified FA values between 0.02 and 0.08 as optimal in our study. Last, we validated the course of entire tractography curves to move beyond correctness determination based on pairs of single points on a tract. Thus, histological techniques, in conjunction with alignment and processing tools, may serve as an important validation method of DW-MRI on the level of inferred tractography projections between brain areas.

Visuospatial processing in early Alzheimer's disease: a multimodal neuroimaging study

INTRODUCTION

Dorsal pathway dysfunctions are thought to underlie visuospatial processing problems in Alzheimer disease (AD). Prior studies reported compensatory mechanisms in the dorsal or ventral pathway in response to these functional changes. Since functional and structural connectivity are interrelated, these functional changes could be interpreted as a disconnection between both pathways. To better understand functional alterations in the dorsal pathway, we combined functional imaging with diffusion tensor imaging (DTI) in patients with mild cognitive impairment (MCI), a likely prodromal stage of AD.

METHODS

Eighteen older male individuals with amnestic MCI (aMCI) and 18 male cognitively healthy individuals, matched for age (range 59-75 years) and education, performed an object recognition task in the Magnetic Resonance Imaging (MRI) scanner. Neural activation was measured during recognition of non-canonically versus canonically oriented objects. Regions showing activation differences between groups were also investigated by DTI.

RESULTS

Recognition of non-canonical objects elicited increased frontal, temporal and parietal activation. Combining the functional MRI (fMRI) with the DTI results showed less deactivation in areas with decreased diffusion (mediolateral parietal and orbitofrontal) and increased activation in areas with increased diffusion (parietal and temporal) in aMCI patients. Finally, in aMCI patients decreased diffusion was found in the hippocampal cingulum, connecting both pathways.

CONCLUSIONS

Our results showed increased activation in early AD patients in ventral and dorsal pathways. A decrease in deactivation and diffusion suggests functional reorganization, while increased activation and diffusion suggests compensatory processes. This is the first study showing structural evidence for functional reorganization, which may be related to connectivity loss in the cingulum.

A short history of causal modeling of fMRI data

Twenty years ago, the discovery of the blood oxygen level dependent (BOLD) contrast and invention of functional magnetic resonance imaging (MRI) not only allowed for enhanced analyses of regional brain activity, but also laid the foundation for novel approaches to studying effective connectivity, which is essential for mechanistically interpretable accounts of neuronal systems. Dynamic causal modeling (DCM) and Granger causality (G-causality) modeling have since become the most frequently used techniques for inferring effective connectivity from fMRI data. In this paper, we provide a short historical overview of these approaches, describing milestones of their development from our subjective perspectives.

k-space and q-space: combining ultra-high spatial and angular resolution in diffusion imaging using ZOOPPA at 7 T

There is ongoing debate whether using a higher spatial resolution (sampling k-space) or a higher angular resolution (sampling q-space angles) is the better way to improve diffusion MRI (dMRI) based tractography results in living humans. In both cases, the limiting factor is the signal-to-noise ratio (SNR), due to the restricted acquisition time. One possible way to increase the spatial resolution without sacrificing either SNR or angular resolution is to move to a higher magnetic field strength. Nevertheless, dMRI has not been the preferred application for ultra-high field strength (7 T). This is because single-shot echo-planar imaging (EPI) has been the method of choice for human in vivo dMRI. EPI faces several challenges related to the use of a high resolution at high field strength, for example, distortions and image blurring. These problems can easily compromise the expected SNR gain with field strength. In the current study, we introduce an adapted EPI sequence in conjunction with a combination of ZOOmed imaging and Partially Parallel Acquisition (ZOOPPA). We demonstrate that the method can produce high quality diffusion-weighted images with high spatial and angular resolution at 7 T. We provide examples of in vivo human dMRI with isotropic resolutions of 1 mm and 800 μm. These data sets are particularly suitable for resolving complex and subtle fiber architectures, including fiber crossings in the white matter, anisotropy in the cortex and fibers entering the cortex.

Multiscale exploration of mouse brain microstructures using the knife-edge scanning microscope brain atlas

Connectomics is the study of the full connection matrix of the brain. Recent advances in high-throughput, high-resolution 3D microscopy methods have enabled the imaging of whole small animal brains at a sub-micrometer resolution, potentially opening the road to full-blown connectomics research. One of the first such instruments to achieve whole-brain-scale imaging at sub-micrometer resolution is the Knife-Edge Scanning Microscope (KESM). KESM whole-brain data sets now include Golgi (neuronal circuits), Nissl (soma distribution), and India ink (vascular networks). KESM data can contribute greatly to connectomics research, since they fill the gap between lower resolution, large volume imaging methods (such as diffusion MRI) and higher resolution, small volume methods (e.g., serial sectioning electron microscopy). Furthermore, KESM data are by their nature multiscale, ranging from the subcellular to the whole organ scale. Due to this, visualization alone is a huge challenge, before we even start worrying about quantitative connectivity analysis. To solve this issue, we developed a web-based neuroinformatics framework for efficient visualization and analysis of the multiscale KESM data sets. In this paper, we will first provide an overview of KESM, then discuss in detail the KESM data sets and the web-based neuroinformatics framework, which is called the KESM brain atlas (KESMBA). Finally, we will discuss the relevance of the KESMBA to connectomics research, and identify challenges and future directions.

Progressive changes in T₁, T₂ and left-ventricular histo-architecture in the fixed and embedded rat heart

Chemical tissue fixation, followed by embedding in either agarose or Fomblin, is common practice in time-intensive MRI studies of ex vivo biological samples, and is required to prevent tissue autolysis and sample motion. However, the combined effect of fixation and sample embedding may alter tissue structure and MRI properties. We investigated the progressive changes in T(1) and T(2) relaxation times, and the arrangement of locally prevailing cardiomyocyte orientation determined using diffusion tensor imaging, in embedded ex vivo rat hearts fixed using Karnovsky's solution (glutaraldehyde-formaldehyde mix). Three embedding media were investigated: (i) standard agarose (n = 3 hearts); (ii) Fomblin (n = 4 hearts); and (iii) iso-osmotic agarose (n = 3 hearts); in the latter, the osmolarity of the fixative and embedding medium was adjusted to 300 mOsm to match more closely that of native tissue. The T(1) relaxation time in the myocardium showed a pronounced decrease over a 48-h period following embedding in Fomblin (-11.3 ± 6.2%; mean ± standard deviation), but was stable in standard agarose- and iso-osmotic agarose-embedded hearts. The mean myocardial T(2) relaxation time increased in all embedded hearts: by 35.1 ± 14.7% with standard agarose embedding, 13.1 ± 5.6% with Fomblin and 13.3 ± 1.4% with iso-osmotic agarose. Deviation in the orientation of the primary eigenvector of the diffusion tensor occurred in all hearts (mean angular changes of 6.6°, 3.2° and 1.9° per voxel after 48 h in agarose-, Fomblin- and iso-osmotic agarose-embedded hearts, respectively), indicative of progressive structural changes in myocardial histo-architecture, in spite of previous exposure to fast-acting tissue fixation. Our results suggest that progressive structural changes occur in chemically fixed myocardium, and that the extent of these changes is modulated by the embedding medium, and by osmotic gradients between the fixative in the tissue and the surrounding medium.

The prefrontal cortex: comparative architectonic organization in the human and the macaque monkey brains

Detailed cytoarchitectonic studies of the human cerebral cortex appeared during the first quarter of the 20th century. The incorporation of the cytoarchitectonic map by Brodmann (1909) in the Talairach proportional stereotaxic space (Talairach and Tournoux, 1988) has established the Brodmann numerical nomenclature as the basis for describing the cortical location of structural and functional findings obtained with modern neuroimaging. In experimental anatomical and physiological investigations of the macaque monkey performed during the last 50 years, the numerical architectonic nomenclature used to describe findings in the prefrontal cortex has been largely based on the map by Walker (1940). Unfortunately, the map by Walker was not based on a comparative investigation of the cytoarchitecture of the human and macaque monkey prefrontal cortex and, as a result, the nomenclature and the criteria for demarcating areas in the two primate species are not always consistent. These discrepancies are a major obstacle in the ability to compare experimental findings from nonhuman primates with results obtained in functional and structural neuroimaging of the human brain. The present article outlines these discrepancies in the classical maps and describes comparative investigations of the cytoarchitecture of the prefrontal cortex of the macaque monkey and human (Petrides and Pandya, 1994, 1999, 2002a) in order to resolve these discrepancies and enable easy translation of experimental research in the monkey to findings in the human brain obtained with modern neuroimaging.

Ground truth hardware phantoms for validation of diffusion-weighted MRI applications

PURPOSE

To quantitatively validate diffusion-weighted MRI (DW-MRI) applications, a hardware phantom containing crossing fibers at a sub-voxel level is presented. It is suitable for validation of a large spectrum of DW-MRI applications from acquisition to fiber tracking, which is an important recurrent issue in the field.

MATERIALS AND METHODS

Phantom properties were optimized to resemble properties of human white matter in terms of anisotropy, fractional anisotropy, and T(2). Sub-voxel crossings were constructed at angles of 30, 50, and 65 degrees, by wrapping polyester fibers, with a diameter close to axon diameter, into heat shrink tubes. We show our phantoms are suitable for the acquisition of DW-MRI data using a clinical protocol.

RESULTS

The phantoms can be used to successfully estimate both the diffusion tensor and non-Gaussian diffusion models, and perform streamline fiber tracking. DOT (Diffusion Orientation Transform) and q-ball reconstruction of the diffusion profiles acquired at b = 3000 s/mm(2) and 132 diffusion directions reveal multimodal diffusion profiles in voxels containing crossing yarn strands.

CONCLUSION

The highly purpose adaptable phantoms provide a DW-MRI validation platform: applications include optimisation of acquisition schemes, validation of non-Gaussian diffusion models, comparison and validation of fiber tracking algorithms, and quality control in multi-center DWI studies.

A review of diffusion tensor magnetic resonance imaging computational methods and software tools

In this work we provide an up-to-date short review of computational magnetic resonance imaging (MRI) and software tools that are widely used to process and analyze diffusion-weighted MRI data. A review of different methods used to acquire, model and analyze diffusion-weighted imaging data (DWI) is first provided with focus on diffusion tensor imaging (DTI). The major preprocessing, processing and post-processing procedures applied to DTI data are discussed. A list of freely available software packages to analyze diffusion MRI data is also provided.

Cellular-level diffusion tensor microscopy and fiber tracking in mammalian nervous tissue with direct histological correlation

Magnetic resonance imaging techniques have literally revolutionized neuroimaging with an unprecedented ability to explore tissue structure and function. Over the last three decades, the sensitivity and array of imaging techniques available have improved providing ever finer structural information and more sensitive functional techniques. Among these methods, diffusion imaging techniques have facilitated the generation of fiber-tract maps of the brain enabling an examination of issues related to brain structure and neural connectivity. Despite the potential utility of the techniques described, validation has not yet been achieved on biological samples. Recently, using newly developed surface microcoils on small samples at high magnetic fields, we demonstrated the ability of MR microscopy to image individual neurons in mammalian brain tissue. In the present work, we combine MR microscopy with the highest resolution (15microm) fiber tracking yet reported and demonstrate the accuracy of the fiber tract maps with direct histological validation. Thus it becomes possible to delineate fiber structure in tissues at the cellular level. A semi-quantitative approach was used to estimate the cell overlap fraction (cOF) and fiber tract overlap fraction (tOF), with cOFs of 94%, 92% and 100%, and tOFs of 84%, 86% and 100%, in rat cervical, rat lumbar, and pig spinal cord tissue, respectively. These methods provide a way to directly validate fiber tracking techniques with histology so that contemporary tracking techniques may be compared and refined using the microstructural details of a biological template as a ground truth.

Performing real-time interactive fiber tracking

Fiber tracking is a technique that, based on a diffusion tensor magnetic resonance imaging dataset, locates the fiber bundles in the human brain. Because it is a computationally expensive process, the interactivity of current fiber tracking tools is limited. We propose a new approach, which we termed real-time interactive fiber tracking, which aims at providing a rich and intuitive environment for the neuroradiologist. In this approach, fiber tracking is executed automatically every time the user acts upon the application. Particularly, when the volume of interest from which fiber trajectories are calculated is moved on the screen, fiber tracking is executed, even while it is being moved. We present our fiber tracking tool, which implements the real-time fiber tracking concept by using the video card's graphics processing units to execute the fiber tracking algorithm. Results show that real-time interactive fiber tracking is feasible on computers equipped with common, low-cost video cards.

Multiple indicators of age-related differences in cerebral white matter and the modifying effects of hypertension

We investigated differences associated with age and hypertension, a common risk factor for vascular disease, in three aspects of white matter integrity--gross regional volumes of the white matter, volume of the white matter hyperintensities (WMH) and diffusion properties. We acquired MRI scans on 93 adult volunteers (age 50-77 years; 36 with diagnosis of hypertension or elevated blood pressure), and obtained all measures in seven brain regions: frontal, temporal, parietal and occipital white matter, and the genu, body and splenium of the corpus callosum. The results demonstrated robust age-related differences in diffusion-based indices of cerebral white matter integrity and age-related increase in the WMH volume, but no age differences in the gross regional volumes of the white matter. Hypertension was associated with decline in fractional anisotropy, and exacerbated age differences in fractional anisotropy more than those in the volume of WMH. These findings indicate that of all examined measures, diffusion-based indices of white matter integrity may be the most sensitive indicators of global and regional declines and vascular damage in the aging brain.

In vivo diffusion tensor imaging of the human optic chiasm at sub-millimeter resolution

In this work we report findings from an in vivo diffusion tensor imaging (DTI) study of the human optic chiasm at sub-millimeter voxel resolution. Data were collected at 3 T using a diffusion-weighted radial-FSE sequence, which provides images free from typical magnetic susceptibility artifacts. The general DTI features observed in the optic chiasm region were consistent across subjects. They included a central area with high anisotropy and highest diffusivity in a predominately right/left direction corresponding to the decussation of nasal hemiretinae fibers, surrounded by a band of low anisotropy reflecting heterogeneous orientation of fibers within the voxel, and a lateral area with high anisotropy and highest diffusivity in a predominately anterior/posterior direction corresponding to temporal hemiretinae fibers that do not cross. Animal studies indicate that there is a significant dorsal-ventral reorganization of the retinotopic distribution of fibers along the optic pathways. We found that diffusion ellipsoids in the central portion of the optic chiasm show considerable planar anisotropy in the coronal plane indicating fiber crossings in the superior/inferior direction, rather than strictly right/left. This architectural feature of the chiasm suggests that dorso-ventral reorganization of fibers in the optic pathways also occurs in humans. We have shown that by collecting sub-millimeter resolution data, DTI can be used to investigate fine details of small and complex white matter structures, in vivo, with a clinical scanner. High spatial resolution, however, is necessary in the slice direction as well as in-plane to reduce the CSF contribution to the signal and to increase fiber coherence within voxels.

Simple 3D images from fossil and recent micromaterial using light microscopy

Abstract We present a technique for extracting 3D information from small-scale fossil and Recent material and give a summary of other contemporary techniques for 3D methods of investigation. The only hardware needed for the here-presented technique is a microscope that can perform dark field and/or differential interference contrast with a mounted digital camera and a computer. Serial images are taken while the focus is successively shifted from the uppermost end of the specimen to the lowermost end, resulting in about 200 photographs. The data are then processed almost completely automatically by successive use of three freely available programs. Firstly, the stack of images is aligned by the use of CombineZM, which is used to produce a combined image with a high depth of field. Secondly, the aligned images are cropped and sharp edges extracted with the aid of ImageJ. Thirdly, although ImageJ is also capable of producing 3D representations, we preferred to process the image stack further using osirix as it has the facility to export various formats. One of the interesting export formats is a virtual Quicktime movie file (QTVR), which can be used for documentation, and stereo images can also be produced from this Quicktime VR. This method is easy to apply and can be used for documenting specimens in 3D (at least some aspects) without having to prepare them. Therefore, it is particularly useful as a safe method for documenting limited material, before using methods that may destroy the specimen of interest, or to investigate type material that cannot be treated with any preparatory technique. As light microscopes are available in most labs and free computer programs are easily accessible, this method can be readily applied.

High resolution diffusion-weighted imaging in fixed human brain using diffusion-weighted steady state free precession

High resolution diffusion tensor imaging and tractography of ex vivo brain specimens has the potential to reveal detailed fibre architecture not visible on in vivo images. Previous ex vivo diffusion imaging experiments have focused on animal brains or small sections of human tissue since the unfavourable properties of fixed tissue (including short T(2) and low diffusion rates) demand the use of very powerful gradient coils that are too small to accommodate a whole, human brain. This study proposes the use of diffusion-weighted steady-state free precession (DW-SSFP) as a method of extending the benefits of ex vivo DTI and tractography to whole, human, fixed brains on a clinical 3 T scanner. DW-SSFP is a highly efficient pulse sequence; however, its complicated signal dependence precludes the use of standard diffusion tensor analysis and tractography. In this study, a method is presented for modelling anisotropy in the context of DW-SSFP. Markov Chain Monte Carlo sampling is used to estimate the posterior distributions of model parameters and it is shown that it is possible to estimate a tight distribution on the principal axis of diffusion at each voxel using DW-SSFP. Voxel-wise estimates are used to perform tractography in a whole, fixed human brain. A direct comparison between 3D diffusion-weighted spin echo EPI and 3D DW-SSFP-EPI reveals that the orientation of the principal diffusion axis can be inferred on with a higher degree of certainty using a 3D DW-SSFP-EPI even with a 68% shorter acquisition time.

Mapping the human brain white matter tracts relative to cortical and deep gray matter using diffusion tensor imaging at high spatial resolution

The mapping of the human brain white matter fiber networks relative to deep subcortical and cortical gray matter requires high spatial resolution which is challenged by the low signal-to-noise ratio. The purpose of this short report was to introduce a whole brain high spatial resolution diffusion tensor imaging (DTI) protocol that enabled for the first time the mapping of corticopontocerebellar, frontostriatal and thalamofrontal fiber pathways in addition to other limbic, commissural, association and projection white matter pathways relative to the segmented deep gray (e.g., caudate nuclei) and the cortical lobes. Our DTI acquisition protocol and analysis strategy provide important template for brain-behavior research and for teaching brain mapping and are clinically affordable for patient comfort.