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1.  The effects of brain tissue decomposition on diffusion tensor imaging and tractography 
NeuroImage  2007;36(1):64-68.
There have been numerous high resolution diffusion tensor imaging studies in fixed animal brains, but relatively few studies in human brains. While animal tissues are generally fixed pre-mortem or directly postmortem, this is not possible for human tissue, therefore there is always some delay between death and tissue fixation. The elapsed time between death and tissue fixation, the postmortem interval (PMI), will most likely adversely affect the tissue's diffusion properties. We studied the effects of PMI on the diffusion properties of rodent brain. Eight mice were euthanized and the brains (kept in the skull) were placed in formalin at PMIs of 0, 1, 4 and 14 days. Post fixation they were placed in a solution of GdDTPA and phosphate buffered saline. Brains were scanned with a 3D EPI DTI sequence at 4.7T. DTI data were processed to generate apparent diffusion coefficient (ADC) and fractional anisotropy (FA) maps. DTI tractography was also performed. The temporal changes in regional ADC and FA values were analyzed statistically using a one-way ANOVA, followed by individual Student's T-tests. Regional FA and ADC of gray and white matter decreased significantly with time (p<0.05). DTI tractography showed a decrease in the number and coherence of reconstructed fiber pathways between PMIs 0 and 14. Elapsed time between death and tissue fixation has a major effect upon the brain's diffusion properties and should be born in mind when interpreting fixed brain DTI.
doi:10.1016/j.neuroimage.2007.02.039
PMCID: PMC4039353  PMID: 17433879
2.  Probing Tissue Microstructure with Restriction Spectrum Imaging: Histological and Theoretical Validation 
Human brain mapping  2012;34(2):327-346.
Diffusion magnetic resonance imaging (dMRI) is a powerful tool for studying biological tissue microarchitectures in vivo. Recently, there has been increased effort to develop quantitative dMRI methods to probe both length scale and orientation information in diffusion media. Diffusion spectrum imaging (DSI) is one such approach that aims to resolve such information on the basis of the three-dimensional diffusion propagator at each voxel. However, in practice only the orientation component of the propagator function is preserved when deriving the orientation distribution function. Here, we demonstrate how a straightforward extension of the linear spherical deconvolution (SD) model can be used to probe tissue orientation structures over a range (or “spectrum”) of length scales with minimal assumptions on the underlying microarchitecture. Using high b-value Cartesian q-space data on a fixed rat brain sample, we demonstrate how this “restriction spectrum imaging” (RSI) model allows for separating the volume fraction and orientation distribution of hindered and restricted diffusion, which we argue stems primarily from diffusion in the extra- and intra-neurite water compartment, respectively. Moreover, we demonstrate how empirical RSI estimates of the neurite orientation distribution and volume fraction capture important additional structure not afforded by traditional DSI or fixed-scale SD-like reconstructions, particularly in grey matter. We conclude that incorporating length scale information in geometric models of diffusion offers promise for advancing state-of-the-art dMRI methods beyond white matter into grey matter structures while allowing more detailed quantitative characterization of water compartmentalization and histoarchitecture of healthy and diseased tissue.
doi:10.1002/hbm.21454
PMCID: PMC3538903  PMID: 23169482
Diffusion MRI; DTI; HARDI; DSI; FOD; Fiber Orientation; Tractography; Histology; Cerebellum; Cerebral Cortex; Striatum; Basal Ganglia; Rat
3.  Dynamic Diffusion Magnetic Resonance Imaging of Infarct Formation and Peri-infarct Spreading Depression after Middle Cerebral Artery Occlusion (MCAO) in macacca fasicularis 
Dynamic diffusion MRI was used to visualize hyperacute stroke formation in the brain of a cynomolgus macaque. Under fluoroscopic guidance, a microcatheter was placed into the middle cerebral artery (MCA). The animal was immediately transferred to a 1.5T clinical scanner. Dynamic T2-weighted imaging during bolus injection of Oxygen-17 enriched water through the microcatheter mapped out the territory perfused by the MCA segment. Serial diffusion measurements were made using diffusion-weighted echo-planar imaging, with a temporal resolution of 15 seconds, during injection of a glue embolus into the microcatheter. The apparent diffusion coefficient declined within the lesion core. A wave of transient diffusion decline spread through peripheral uninvolved brain immediately following stroke induction. The propagation speed and pattern is consistent with spreading peri-infarct depolarizations (PID). The detection of PIDs following embolic stroke in a higher nonhuman primate brain supports the hypothesis that spreading depressions may occur following occlusive stroke in humans.
doi:10.2174/1874440001105010153
PMCID: PMC3257554  PMID: 22253657
Non-human primates; MCAo; Stroke; Oxygen-17; Cortical spreading depression (CSD); Diffusion MRI.
4.  Topography of connections between human prefrontal cortex and mediodorsal thalamus studied with diffusion tractography 
Neuroimage  2010;51(2):555-564.
Studies in monkeys show clear anatomical and functional distinctions among networks connecting with subregions within the prefrontal cortex. Three such networks are centered on lateral orbitofrontal cortex, medial frontal and cingulate cortex, and lateral prefrontal cortex and all have been identified with distinct cognitive roles. Although these areas differ in a number of their cortical connections, some of the first anatomical evidence for these networks came from tracer studies demonstrating their distinct patterns of connectivity with the mediodorsal (MD) nucleus of the thalamus. Here, we present evidence for a similar topography of MD thalamus prefrontal connections, using non-invasive imaging and diffusion tractography (DWI–DT) in human and macaque. DWI–DT suggested that there was a high probability of interconnection between medial MD and lateral orbitofrontal cortex, between caudodorsal MD and medial frontal/cingulate cortex, and between lateral MD and lateral prefrontal cortex, in both species. Within the lateral prefrontal cortex a dorsolateral region (the principal sulcus in the macaque and middle frontal gyrus in the human) was found to have a high probability of interconnection with the MD region between the regions with a high probability of interconnection with other parts of the lateral prefrontal cortex and with the lateral orbitofrontal cortex. In addition to suggesting that the thalamic connectivity in the macaque is a good guide to human prefrontal cortex, and therefore that there are likely to be similarities in the cognitive roles played by the prefrontal areas in both species, the present results are also the first to provide insight into the topography of projections of an individual thalamic nucleus in the human brain.
doi:10.1016/j.neuroimage.2010.02.062
PMCID: PMC2877805  PMID: 20206702
Anatomy; DTI; Human; Macaque; Thalamus
5.  Quantitative Histological Validation of Diffusion MRI Fiber Orientation Distributions in the Rat Brain 
PLoS ONE  2010;5(1):e8595.
Diffusion MRI (dMRI) is widely used to measure microstructural features of brain white matter, but commonly used dMRI measures have limited capacity to resolve the orientation structure of complex fiber architectures. While several promising new approaches have been proposed, direct quantitative validation of these methods against relevant histological architectures remains missing. In this study, we quantitatively compare neuronal fiber orientation distributions (FODs) derived from ex vivo dMRI data against histological measurements of rat brain myeloarchitecture using manual recordings of individual myelin stained fiber orientations. We show that accurate FOD estimates can be obtained from dMRI data, even in regions with complex architectures of crossing fibers with an intrinsic orientation error of approximately 5–6 degrees in these regions. The reported findings have implications for both clinical and research studies based on dMRI FOD measures, and provide an important biological benchmark for improved FOD reconstruction and fiber tracking methods.
doi:10.1371/journal.pone.0008595
PMCID: PMC2802592  PMID: 20062822
6.  3D micro-CT imaging of the Postmortem Brain 
Journal of neuroscience methods  2008;171(2):207-213.
Magnetic resonance microscopy (μMRI) is becoming an important tool for non-destructive analysis of fixed brain tissue. However, unlike MRI, X-ray computed tomography (CT) scans show little native soft tissue contrast. In this paper, we explored the use of contrast enhanced (brains immersion staining in iodinated CT contrast media) micro-CT (μCT) for high resolution 3D imaging of fixed normal and pathological brains, compared to μMRI and standard histopathology. An optimum iodine concentration of 0.27M resulted in excellent contrast between gray and white matter in normal brain and a wide range of anatomical structures were identified. In glioma bearing mouse brains, there was clear deliniation of tumor margin which closely matched that seen on histopathology sections. μCT tumor volume was strongly correlated with histopathology volume. Our data suggests that μCT image contrast in the immersion-stained brains is related to axonal density and myelin content. Compared to traditional histopathology, our μCT approach is relatively rapid and less labor intensive. In addition, compared to μMRI, μCT is robust and requires much lower equipment and maintenance costs. For simple measurements, such as tumor volume and non-destructive post-mortem brain screening, μCT may prove to be a valuable alternative to standard histopathology or μMRI.
doi:10.1016/j.jneumeth.2008.03.006
PMCID: PMC2693019  PMID: 18462802
brain; micro-CT; magnetic resonance microscopy; post mortem; pathology; tumor
7.  Near-infrared spectroscopy measurement of the pulsatile component of cerebral blood flow and volume from arterial oscillations 
Journal of biomedical optics  2007;12(1):014033.
We describe a near-infrared spectroscopy (NIRS) method to noninvasively measure relative changes in the pulsate components of cerebral blood flow (pCBF) and volume (pCBV) from the shape of heartbeat oscillations. We present a model that is used and data to show the feasibility of the method. We use a continuous-wave NIRS system to measure the arterial oscillations originating in the brains of piglets. Changes in the animals' CBF are induced by adding CO2 to the breathing gas. To study the influence of scalp on our measurements, comparative, invasive measurements are performed on one side of the head simultaneously with noninvasive measurements on the other side. We also did comparative measurements of CBF using a laser Doppler system to validate the results of our method. The results indicate that for sufficient source-detector separation, the signal contribution of the scalp is minimal and the measurements are representative of the cerebral hemodynamics. Moreover, good correlation between the results of the laser Doppler system and the NIRS system indicate that the presented method is capable of measuring relative changes in CBF. Preliminary results show the potential of this NIRS method to measure pCBF and pCBV relative changes in neonatal pigs.
doi:10.1117/1.2710250
PMCID: PMC2637815  PMID: 17343508
cerebral blood flow; cerebral blood volume; near-infrared spectroscopy; arterial oscillations
8.  Probabilistic Tractography Recovers a Rostrocaudal Trajectory of Connectivity Variability in the Human Insular Cortex 
Human Brain Mapping  2011;33(9):2005-2034.
The insular cortex of macaques has a wide spectrum of anatomical connections whose distribution is related to its heterogeneous cytoarchitecture. Although there is evidence of a similar cytoarchitectural arrangement in humans, the anatomical connectivity of the insula in the human brain has not yet been investigated in vivo. In the present work, we used in vivo probabilistic white-matter tractography and Laplacian eigenmaps (LE) to study the variation of connectivity patterns across insular territories in humans. In each subject and hemisphere, we recovered a rostrocaudal trajectory of connectivity variation ranging from the anterior dorsal and ventral insula to the dorsal caudal part of the long insular gyri. LE suggested that regional transitions among tractography patterns in the insula occur more gradually than in other brain regions. In particular, the change in tractography patterns was more gradual in the insula than in the medial premotor region, where a sharp transition between different tractography patterns was found. The recovered trajectory of connectivity variation in the insula suggests a relation between connectivity and cytoarchitecture in humans resembling that previously found in macaques: tractography seeds from the anterior insula were mainly found in limbic and paralimbic regions and in anterior parts of the inferior frontal gyrus, while seeds from caudal insular territories mostly reached parietal and posterior temporal cortices. Regions in the putative dysgranular insula displayed more heterogeneous connectivity patterns, with regional differences related to the proximity with either putative granular or agranular regions. Hum Brain Mapp 33:2005–2034, 2012. © 2011 Wiley Periodicals, Inc.
doi:10.1002/hbm.21338
PMCID: PMC3443376  PMID: 21761507
DTI; insula; laplacian eigenmaps; diffusion-weighted imaging; connectivity-based parcellation

Results 1-8 (8)