An ex vivo imaging pipeline for producing high-quality and high-resolution diffusion-weighted imaging datasets

Layer-specific intracortical connectivity revealed with diffusion MRI

In this work, we show for the first time that the tangential diffusion component is orientationally coherent at the human cortical surface. Using diffusion magnetic resonance imaging (dMRI), we have succeeded in tracking intracortical fiber pathways running tangentially within the cortex. In contrast with histological methods, which reveal little regarding 3-dimensional organization in the human brain, dMRI delivers additional understanding of the layer dependence of the fiber orientation. A postmortem brain block was measured at very high angular and spatial resolution. The dMRI data had adequate resolution to allow analysis of the fiber orientation within 4 notional cortical laminae. We distinguished a lamina at the cortical surface where diffusion was tangential along the surface, a lamina below the surface where diffusion was mainly radial, an internal lamina covering the Stria of Gennari, where both strong radial and tangential diffusion could be observed, and a deep lamina near the white matter, which also showed mainly radial diffusion with a few tangential compartments. The measurement of the organization of the tangential diffusion component revealed a strong orientational coherence at the cortical surface.

Contrast and stability of the axon diameter index from microstructure imaging with diffusion MRI

The ActiveAx technique fits the minimal model of white matter diffusion to diffusion MRI data acquired using optimized protocols that provide orientationally invariant indices of axon diameter and density. We investigated how limitations of the available maximal gradient strength (G_max) on a scanner influence the sensitivity to a range of axon diameters. Multishell high-angular-diffusion-imaging (HARDI) protocols for G_max of 60, 140, 200, and 300 mT/m were optimized for the pulsed-gradient-spin-echo (PGSE) sequence. Data were acquired on a fixed monkey brain and Monte-Carlo simulations supported the results. Increasing G_max reduces within-voxel variation of the axon diameter index and improves contrast beyond what is achievable with higher signal-to-noise ratio. Simulations reveal an upper bound on the axon diameter (∼10 μm) that pulsed-gradient-spin-echo measurements are sensitive to, due to a trade-off between short T₂ and the long diffusion time needed to probe larger axon diameters. A lower bound (∼2.5 μm) slightly dependent on G_max was evident, below which axon diameters are identifiable as small, but impossible to differentiate. These results emphasize the key-role of G_max for enhancing contrast between axon diameter distributions and are, therefore, relevant in general for microstructure imaging methods and highlight the need for increased G_max on future commercial systems.

A viable isolated tissue system: a tool for detailed MR measurements and controlled perturbation in physiologically stable tissue

In vivo magnetic resonance imaging (MRI) assessment of neuronal tissue is prone to artifacts such as movement, pulsatile flow, and tissue susceptibility. Furthermore, stable in vivo scans of over 3 h are difficult to achieve, experimental design is therefore limited. Using isolated tissue maintained in a viable physiological state can mitigate many of these in vivo issues. This work describes the fabrication and validation of an MRI compatible viable isolated tissue maintenance chamber. Parameters measured from maintained rat optic nerves did not change significantly over 10 h: (i) mean axon radius [electron microscopy--0 h: 0.75±0.46; 5 h: 0.74±0.35; 10 h: 0.76±0.35 μm (P>>0.05, t-test], (ii) action potentials [grease-gap electrophysiology--4.89±0.16 mv, (P>>0.05, Pearson test], and (iii) diffusion tensor imaging parameters [fractional anisotropy: 0.86±0.02 (P>>0.05, Pearson test), mean diffusivity: 1.48E-06±9.74E-08 cm2/s, (P>>0.05, Pearson test)]. In addition, a thorough diffusion-weighted MR protocol demonstrated the comparable stability of viable isolated and chemically fixed rat optic nerve. This MRI compatible viable isolated tissue system allows researchers to probe neuronal physiology in a controlled environment by limiting in vivo artifacts and allowing extended MRI acquisitions.

A DTI tractography analysis of infralimbic and prelimbic connectivity in the mouse using high-throughput MRI

BACKGROUND

High throughput, brain-wide analysis of neural circuit connectivity is needed to understand brain function across species. Combining such tractography techniques with small animal models will allow more rapid integration of systems neuroscience with molecular genetic, behavioral, and cellular approaches.

METHODS

We collected DTI and T2 scans on 3 series of 6 fixed mouse brains ex vivo in a 9.4 Tesla magnet. The DTI analysis of ten mouse brains focused on comparing prelimbic (PL) and Infralimbic (IL) probabilistic tractography. To validate the DTI results a preliminary set of 24 additional mice were injected with BDA into the IL and PL. The DTI results and preliminary BDA results were also compared to previously published rat connectivity.

RESULTS

We focused our analyses on the connectivity of the mouse prelimbic (PL) vs. infralimbic (IL) cortices. We demonstrated that this DTI analysis is consistent across scanned mice, with prior analyses of rat IL/PL connectivity, and with mouse PL and IL projections using the BDA tracer.

CONCLUSIONS

High-throughput ex vivo DTI imaging in the mouse delineated both common and differential connectivity of the IL and PL cortex. The scanning methodology provided a balance of tissue contrast, signal-to-noise ratio, resolution and throughput. Our results are largely consistent with previously published anterograde staining techniques in rats, and the preliminary tracer study of the mouse IL and PL provided here.

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.

Mapping of the mouse olfactory system with manganese-enhanced magnetic resonance imaging and diffusion tensor imaging

As the power of studying mouse genetics and behavior advances, research tools to examine systems level connectivity in the mouse are critically needed. In this study, we compared statistical mapping of the olfactory system in adult mice using manganese-enhanced MRI (MEMRI) and diffusion tensor imaging (DTI) with probabilistic tractography. The primary goal was to determine whether these complementary techniques can determine mouse olfactory bulb (OB) connectivity consistent with known anatomical connections. For MEMRI, 3D T1-weighted images were acquired before and after bilateral nasal administration of MnCl(2) solution. Concomitantly, high-resolution diffusion-tensor images were obtained ex vivo from a second group of mice and processed with a probabilistic tractography algorithm originating in the OB. Incidence maps were created by co-registering and overlaying data from the two scan modalities. The resulting maps clearly show pathways between the OB and amygdala, piriform cortex, caudate putamen, and olfactory cortex in both the DTI and MEMRI techniques that are consistent with the known anatomical connections. These data demonstrate that MEMRI and DTI are complementary, high-resolution neuroimaging tools that can be applied to mouse genetic models of olfactory and limbic system connectivity.

DWI of the brain: postmortal DWI of the brain in comparison with in vivo data

PURPOSE

Changes in water diffusion can be quantified by diffusion-weighted MR imaging. However, there are only few reports about changes in post mortem brain. The aim of this study was to investigate the temporal pattern of the apparent diffusion coefficient (ADC) in the brain after death, to compare the values to in vivo brain and to assess the value of ex vivo DWI as a forensic tool.

MATERIAL AND METHODS

The study was approved by the local Ethics Committee, and informed consent was obtained from all relatives and the control subjects. Twenty-one corpses, died of natural cause, were examined (13 males, 8 females; age: 70.5±8.7 y, weight 74±18 kg). Diffusion-Weighted Imaging (DWI) was performed with b-values of 0 and 1000 s/mm(2) at 1.5 T. Scans were repeated in intervals of 1 h. ADC-maps were calculated in thalamus, cerebrum and cerebellum. The obtained values were statistically compared to healthy volunteers (n=3) and to literature data.

RESULTS

The ADC in the three regions decreased characteristically during the examination time. In the cerebrum there was a significant difference between ex vivo and in vivo ADC (p<0.001) as well as in the other regions (thalamus: p<0.001, cerebellum: p=0.045).

CONCLUSION

DWI of the postmortal brain can be added to the MRI methods for a post mortem imaging.

Diffusion tractography of post-mortem human brains: optimization and comparison of spin echo and steady-state free precession techniques

Diffusion imaging of post-mortem brains could provide valuable data for validation of diffusion tractography of white matter pathways. Long scans (e.g., overnight) may also enable high-resolution diffusion images for visualization of fine structures. However, alterations to post-mortem tissue (T2 and diffusion coefficient) present significant challenges to diffusion imaging with conventional diffusion-weighted spin echo (DW-SE) acquisitions, particularly for imaging human brains on clinical scanners. Diffusion-weighted steady-state free precession (DW-SSFP) has been proposed as an alternative acquisition technique to ameliorate this tradeoff in large-bore clinical scanners. In this study, both DWSE and DW-SSFP are optimized for use in fixed white matter on a clinical 3-Tesla scanner. Signal calculations predict superior performance from DW-SSFP across a broad range of protocols and conditions. DW-SE and DW-SSFP data in a whole, post-mortem human brain are compared for 6- and 12-hour scan durations. Tractography is performed in major projection, commissural and association tracts (corticospinal tract, corpus callosum, superior longitudinal fasciculus and cingulum bundle). The results demonstrate superior tract-tracing from DW-SSFP data, with 6-hour DW-SSFP data performing as well as or better than 12-hour DW-SE scans. These results suggest that DW-SSFP may be a preferred method for diffusion imaging of post-mortem human brains. The ability to estimate multiple fibers in imaging voxels is also demonstrated, again with greater success in DW-SSFP data.

Diffusion-weighted MRI and quantitative biophysical modeling of hippocampal neurite loss in chronic stress

Chronic stress has detrimental effects on physiology, learning and memory and is involved in the development of anxiety and depressive disorders. Besides changes in synaptic formation and neurogenesis, chronic stress also induces dendritic remodeling in the hippocampus, amygdala and the prefrontal cortex. Investigations of dendritic remodeling during development and treatment of stress are currently limited by the invasive nature of histological and stereological methods. Here we show that high field diffusion-weighted MRI combined with quantitative biophysical modeling of the hippocampal dendritic loss in 21 day restraint stressed rats highly correlates with former histological findings. Our study strongly indicates that diffusion-weighted MRI is sensitive to regional dendritic loss and thus a promising candidate for non-invasive studies of dendritic plasticity in chronic stress and stress-related disorders.

Diffusion imaging of whole, post-mortem human brains on a clinical MRI scanner

Diffusion imaging of post mortem brains has great potential both as a reference for brain specimens that undergo sectioning, and as a link between in vivo diffusion studies and "gold standard" histology/dissection. While there is a relatively mature literature on post mortem diffusion imaging of animals, human brains have proven more challenging due to their incompatibility with high-performance scanners. This study presents a method for post mortem diffusion imaging of whole, human brains using a clinical 3-Tesla scanner with a 3D segmented EPI spin-echo sequence. Results in eleven brains at 0.94 × 0.94 × 0.94 mm resolution are presented, and in a single brain at 0.73 × 0.73 × 0.73 mm resolution. Region-of-interest analysis of diffusion tensor parameters indicate that these properties are altered compared to in vivo (reduced diffusivity and anisotropy), with significant dependence on post mortem interval (time from death to fixation). Despite these alterations, diffusion tractography of several major tracts is successfully demonstrated at both resolutions. We also report novel findings of cortical anisotropy and partial volume effects.

Distribution of collateral fibers in the monkey cervical spinal cord detected with diffusion-weighted magnetic resonance imaging

Diffusion anisotropy monitored with diffusion-weighted magnetic resonance imaging (DWMRI) is a sensitive marker to monitor developmental or pathological microstructural changes in spinal cord. The white matter is often treated as a unidirectional axonal bundle but collateral fibers branching off the main spinal pathways contradicts this assumption and affects the diffusion anisotropy. It is the aim of this study to investigate to what extent collateral fibers are apparent in diffusion tensor data and if collaterals can be detected as individual fiber directions using crossing fiber detection techniques. We calculate the diffusion tensor and the persistent angular structure (PAS), a multi-fiber reconstruction technique, from high quality post mortem data of a perfusion-fixed vervet monkey cervical spinal cord sample and simulated crossing fiber data. Our results show that (i) cylindrical geometry in the white matter of the spinal cord is an invalid assumption due to collateral fibers. We also demonstrate that (ii) collateral fibers can be resolved as distinct peaks in the water diffusion propagator in white matter using multi-fiber models. Finally, we show that (iii) crossing fibers are mainly located laterally and increase towards the cervical enlargement.

Axon diameter mapping in crossing fibers with diffusion MRI

This paper proposes a technique for a previously unaddressed problem, namely, mapping axon diameter in crossing fiber regions, using diffusion MRI. Direct measurement of tissue microstructure of this kind using diffusion MRI offers a new class of biomarkers that give more specific information about tissue than measures derived from diffusion tensor imaging. Most existing techniques for axon diameter mapping assume a single axon orientation in the tissue model, which limits their application to only the most coherently oriented brain white matter, such as the corpus callosum, where the single orientation assumption is a reasonable one. However, fiber crossings and other complex configurations are widespread in the brain. In such areas, the existing techniques will fail to provide useful axon diameter indices for any of the individual fiber populations. We propose a novel crossing fiber tissue model to enable axon diameter mapping in voxels with crossing fibers. We show in simulation that the technique can provide robust axon diameter estimates in a two-fiber crossing with the crossing angle as small as 45 degrees. Using ex vivo imaging data, we further demonstrate the feasibility of the technique by establishing reasonable axon diameter indices in the crossing region at the interface of the cingulum and the corpus callosum.

Symmetric positive-definite Cartesian tensor orientation distribution functions (CT-ODF)

A novel method for estimating a field of orientation distribution functions (ODF) from a given set of DW-MR images is presented. We model the ODF by Cartesian tensor basis using a parametrization that explicitly enforces the positive definite property to the computed ODF. The computed Cartesian tensors, dubbed Cartesian Tensor-ODF (CT-ODF), are symmetric positive definite tensors whose coefficients can be efficiently estimated by solving a linear system with non-negative constraints. Furthermore, we show how to use our method for converting higher-order diffusion tensors to CT-ODFs, which is an essential task since the maxima of higher-order tensors do not correspond to the underlying fiber orientations. We quantitatively evaluate our method using simulated DW-MR images as well as a real brain dataset from a post-mortem porcine brain. The results conclusively demonstrate the superiority of the proposed technique over several existing multi-fiber reconstruction methods.