Anat-SFSeg: Anatomically-guided superficial fiber segmentation with point-cloud deep learning.

Diffusion magnetic resonance imaging (dMRI) tractography is a critical technique to map the brain's structural connectivity. Accurate segmentation of white matter, particularly the superficial white matter (SWM), is essential for neuroscience and clinical research. However, it is challenging to segment SWM due to the short adjacent gyri connection in a U-shaped pattern. In this work, we propose an Anatomically-guided Superficial Fiber Segmentation (Anat-SFSeg) framework to improve the performance on SWM segmentation. The framework consists of a unique fiber anatomical descriptor (named FiberAnatMap) and a deep learning network based on point-cloud data. The spatial coordinates of fibers represented as point clouds, as well as the anatomical features at both the individual and group levels, are fed into a neural network. The network is trained on Human Connectome Project (HCP) datasets and tested on the subjects with a range of cognitive impairment levels. One new metric named fiber anatomical region proportion (FARP), quantifies the ratio of fibers in the defined brain regions and enables the comparison with other methods. Another metric named anatomical region fiber count (ARFC), represents the average fiber number in each cluster for the assessment of inter-subject differences. The experimental results demonstrate that Anat-SFSeg achieves the highest accuracy on HCP datasets and exhibits great generalization on clinical datasets. Diffusion tensor metrics and ARFC show disorder severity associated alterations in patients with Alzheimer's disease (AD) and mild cognitive impairments (MCI). Correlations with cognitive grades show that these metrics are potential neuroimaging biomarkers for AD. Furthermore, Anat-SFSeg could be utilized to explore other neurodegenerative, neurodevelopmental or psychiatric disorders.

Language function of the superior longitudinal fasciculus in patients with arteriovenous malformation as evidenced by automatic fiber quantification.

The superior longitudinal fasciculus (SLF) is a major fiber tract involved in language processing and has been used to investigate language impairments and plasticity in many neurological diseases. The SLF is divided into four main branches that connect with different cortex regions, with two branches (SLF II, SLF III) being directly related to language. However, most white matter analyses consider the SLF as a single bundle, which may underestimate the relationship between these fiber bundles and language function. In this study, we investigated the differences between branches of the SLF in patients with arteriovenous malformation (AVM), which is a unique model to investigate language reorganization. We analyzed diffusion tensor imaging data of AVM patients and healthy controls to generate whole-brain fiber tractography, and then segmented the SLF into SLF II and III based on their distinctive waypoint regions. The SLF, SLF II, and III were further quantified, and four diffusion parameters of three branches were compared between the AVMs and controls. No significant diffusivity differences of the whole SLF were observed between two groups, however, the right SLF II and III in AVMs showed significant reorganization or impairment patterns as compared to the controls. Results demonstrating the need to subtracting SLF branches when studying structure-function relationship in neurological diseases that have SLF damage.

The language-related cerebro-cerebellar pathway in humans: a diffusion imaging-based tractographic study.

Background: The cerebellum and cerebral cortex form the most important cortico-cerebellar system in the brain. However, diffusion magnetic resonance imaging (MRI)-based tractography of the connecting white matter between the cerebellum and cerebral cortex, which support language function, has not been extensively reported on. This work aims to serve as a guideline for facilitating the analysis of white matter tracts along the language-related cerebro-cerebellar pathway (LRCCP), which includes the corticopontine, pontocerebellar, corticorubral, rubroolivary, olivocerebellar, and dentatorubrothalamic tracts. Methods: The LRCCP templates were developed via processing the high-resolution, population-averaged atlas available in the Human Connectome Project (HCP)-1065 dataset (2017 Q4, 1,200-subject release) in DSI Studio. The deterministic tracking was performed with the manually selected regions of interest (ROIs) on this atlas according to prior anatomic knowledge. Templates were then applied to the MRI datasets of 30 health participants acquired from a single hospital to verify the practicability of the tracking. The diffusion tensor and shape analysis metrics were calculated for all LRCCP tracts. Differences in the tracking metrics between the left and right hemispheres were compared, and the related white matter asymmetry was discussed. Results: The LRCCP templates were successfully created and applied to healthy participants for quantitative analysis. Significantly higher mean fractional anisotropy (FA) values were discovered on the left (L) corticorubral tract [L, 0.43±0.02 vs. right (R), 0.41±0.02; P<0.01] and left dentatorubrothalamic tract (L, 0.47±0.02 vs. R, 0.46±0.02; P<0.01). Significant differences in tract volume and streamline number were observed between the corticopontine, corticorubral, and dentatorubrothalamic tracts. The size of the right corticopontine and corticorubral tracts were smaller, and both had smaller streamline numbers and innervation areas when compared with the contralateral sides. The R dentatorubrothalamic tract showed a larger volume (R, 23,582.47±4,160.71 mm3 vs. L, 19,821.27±2,983.91 mm3; P<0.01) and innervation area (R, 2,117.37±433.98 mm2 vs. L, 1,610.00±356.19 mm2; P<0.01) than did the L side. No significant differences were observed in the rubroolivary tracts. Conclusions: This work suggests the feasibility of applying tractography templates of the LRCCP to quantitatively evaluate white matter properties associated with language function. Lateralized diffusion metrics were observed in preliminary experiments. LRCCP tractography-based research may provide a potential quantitative method to better understanding neuroplasticity.

Resting-state functional alterations in patients with brain arteriovenous malformations involving language areas.

Brain arteriovenous malformations (AVMs) may involve language areas but usually do not lead to aphasia. This study evaluated resting-state functional alterations and investigated the language reorganization mechanism in AVM patients. Thirty-nine patients with AVMs involving language areas and 32 age- and sex-matched healthy controls were prospectively enrolled. The AVM patients were categorized into three subgroups according to lesion location: the frontal (15 patients), temporal (14 patients), and parietal subgroups (10 patients). All subjects underwent resting-state functional magnetic resonance imaging (rs-fMRI), and the amplitude of low-frequency fluctuation (ALFF) approach was applied to analyze rs-fMRI data. Language abilities were normal in all participants based on the Western Aphasia Battery. Compared with those of healthy subjects, ALFF values significantly increased (FDR corrected p < .01) in the anterior part of the right putamen in the frontal AVM subgroup, in the posterior part of the right inferior and middle temporal gyrus in the temporal AVM subgroup, and in the inferior lateral part of the left cerebellar hemisphere (lobule VIII) and the right inferior parietal lobule in the parietal AVM subgroup. Functional annotation using Neurosynth indicated that the ALFF t-map was only significantly positively associated with the language-related domain (FDR corrected p < .01). In patients with AVMs involving the language cortex, language network reorganization occurs to maintain normal language abilities. The brain areas recruited into the reorganized language network were located in the right cerebral and left cerebellar hemispheres, both of which are nondominant hemispheres. Differences in lesion location led to distinct reorganization patterns.

Human ESC-derived immunity- and matrix- regulatory cells ameliorated white matter damage and vascular cognitive impairment in rats subjected to chronic cerebral hypoperfusion.

OBJECTIVES: This study investigated the ability of immunity- and matrix- regulatory cells (IMRCs) to improve cognitive function in a rat model of vascular cognitive impairment. MATERIALS AND METHODS: A chronic cerebral hypoperfusion (CCH) model was established in rats via permanent bilateral occlusion of the common carotid arteries (two-vessel occlusion, 2VO). The rats then received intravenous injections of IMRCs or saline. A single injection of different doses of IMRCs (1 × 106 cells/rat, 2 × 106 cells/rat, or 4 × 106 cells/rat) was administered via tail vein 72 h after establishment of the model. To evaluate functional recovery, the rats were subjected to behavioural tests after 30 days of CCH. Imaging, western blotting, immunofluorescence staining, and quantitative real-time PCR were used to analyse neuroinflammation and white matter injury after 14 and 40 days of CCH. RNA sequencing (RNA-seq) was used to profile gene expression changes in copine 1 (CPNE1) in response to IMRCs treatment. RESULTS: Intravenous injection of 4 × 106 IMRCs alleviated white matter damage and ameliorated cognitive deficits in rats subjected to CCH. Immunofluorescence staining suggested that activation of microglia and astrocytes was reduced, and RNA sequencing showed that CPNE1 expression was significantly elevated following treatment with IMRCs. CONCLUSIONS: Intravenous injection of IMRCs protected against CCH-induced white matter injury and cognitive impairment inhibition of microglial activation and regulation of microglia polarization.

Impairment and Plasticity of Language-Related White Matter in Patients With Brain Arteriovenous Malformations.

BACKGROUND: Language dysfunction is rarely seen in patients with unruptured brain arteriovenous malformation (AVM) albeit the AVM nidus involving language areas, which provides a unique disease model to study language reorganization. The objective of this study was to investigate the impairment and reorganization patterns and characteristics of language-related white matter in AVMs located at different brain areas. METHODS: Thirty-three patients with AVMs involving language areas were prospectively enrolled. Patients were categorized into 3 groups according to the lesion locations: the frontal (14 patients), temporal (15 patients), and parietal groups (4 patients). Thirty age- and sex-matched healthy controls were enrolled as comparison. All participants underwent diffusion tensor imaging scans, and automated fiber quantification method was applied to quantitatively study the difference of segmented language-related white matter connectivity between 3 AVM groups and control group. RESULTS: Language functions were normal in all subjects according to Western Aphasia Battery test. In the frontal group, fractional anisotropy (FA) value decreased in the left arcuate fascicle and increased in left superior longitudinal fasciculus and uncinate fascicle; in the temporal group, FA values decreased in left inferior fronto-occipital fascicle and inferior longitudinal fascicle and increased in right anterior thalamic radiation and uncinate fascicle; in the parietal group, FA values decreased in left arcuate fascicle and inferior longitudinal fascicle and increased in bilateral anterior thalamic radiations and uncinate fascicles and right inferior fronto-occipital fascicle. In fascicles with decreased FA values, the increase of radial diffusivity was common, and fascicles with increased FA values usually presented along with increased axial diffusivity values. CONCLUSIONS: Remodeling of language-related white matter occurs when traditional language areas are involved by AVM nidus, and its reorganization patterns vary with locations of AVM nidus. Fascicle impairment is mainly caused by the myelin deficits, and its plasticity may be dominated by the axon remodeling procedure.

Right-hemispheric language reorganization in patients with brain arteriovenous malformations: A functional magnetic resonance imaging study.

Brain arteriovenous malformation (AVM), a presumed congenital lesion, may involve traditional language areas but usually does not lead to language dysfunction unless it ruptures. The objective of this research was to study right-hemispheric language reorganization patterns in patients with brain AVMs using functional magnetic resonance imaging (fMRI). We prospectively enrolled 30 AVM patients with lesions involving language areas and 32 age- and sex-matched healthy controls. Each subject underwent fMRI during three language tasks: visual synonym judgment, oral word reading, and auditory sentence comprehension. The activation differences between the AVM and control groups were investigated by voxelwise analysis. Lateralization indices (LIs) for the frontal lobe, temporal lobe, and cerebellum were compared between the two groups, respectively. Results suggested that the language functions of AVM patients and controls were all normal. Voxelwise analysis showed no significantly different activations between the two groups in visual synonym judgment and oral word reading tasks. In auditory sentence comprehension task, AVM patients had significantly more activations in the right precentral gyrus (BA 6) and right cerebellar lobule VI (AAL 9042). According to the LI results, the frontal lobe in oral word reading task and the temporal lobe in auditory sentence comprehension task were significantly more right-lateralized in the AVM group. These findings suggest that for patients with AVMs involving language cortex, different language reorganization patterns may develop for different language functions. The recruitment of brain areas in the right cerebral and cerebellar hemispheres may play a compensatory role in the reorganized language network of AVM patients.

Inside-out azimuthally selective NMR tool using array coil and capacitive decoupling.

Inside-out nuclear magnetic resonance (NMR) is a unique technique for investigating large in-situ objects outside of tools, to provide pore structure and pore-bearing fluids properties. However, in borehole, objects towards azimuthal orientations pose different properties, referred to as azimuthal spatial heterogeneity. This may lead to ambiguous evaluations by utilizing present inside-out NMR measurement, which hardly resolves azimuthal information and loses the location information of oil/gas. In this paper, we for the first time design and construct an innovative tool to investigate the heterogeneity of large in-situ samples. The most key component, array coil, which performs with azimuthal selection, measurement consistency and interactive isolation, configured in this novel tool to capture heterogeneity information. Whereas, strong coupling between neighboring coil elements largely decrease the coil sensitivity. Capacitive decoupling network is bridged into adjacent ports without segmenting coils to be decoupled and could be easily adjusted by electrical relays. The coil model and numerical simulation are firstly given to demonstrate the array coil configuration, B1 field map and mutual coupling effects on coil sensitivity. Capacitive network is then introduced to be theoretically and practically analyzed to minimize coupling effects. Simulation and experimental results demonstrate that these coil elements have excellent consistency and independence to feasibly acquire the azimuthal NMR data.

Altered Motor and Motor Perceptual Cognitive Imagery Task-Related Activation in Diabetic Peripheral Neuropathy: Insights From Functional MRI.

OBJECTIVE: To compare central nervous system (CNS) activation in patients with and without diabetic peripheral neuropathy (DPN) during motor and motor imagery tasks and to correlate activation with functional performance. RESEARCH DESIGN AND METHODS: Twenty-six participants (13 with DPN, 13 without DPN) underwent functional MRI during three tasks: ankle dorsi plantar flexion (motor task [MT]) and motor imagery tasks of walking on a smooth surface (SMIT) and rough surface (RMIT). Functional assessment included gait analysis, ankle muscle strength, and ankle range of motion. RESULTS: The tasks activated the sensorimotor, motor preparation, visual processing, and decision-making regions. Activation was significantly lower in patients with DPN than in those without DPN during MT and SMIT but not RMIT. Poor functional performance in patients with DPN was associated with greater activation in motor preparation regions. CONCLUSIONS: In patients with DPN, CNS responses appear muted compared with patients without DPN, but they remain capable of enhancing CNS activation when tasks are more challenging or when functional deficits are substantial.

Threshold Isocontouring on High b-Value Diffusion-Weighted Images in Magnetic Resonance Mammography.

OBJECTIVES: Motivated by the similar appearance of malignant breast lesions in high b-value diffusion-weighted imaging (DWI) and positron emission tomography, the purpose of this work was to evaluate the applicability of a threshold isocontouring approach commonly used in positron emission tomography to analyze DWI data acquired from female human breasts with minimal interobserver variability. METHODS: Twenty-three female participants (59.4 ± 10.0 years) with 23 lesions initially classified as suggestive of cancers in x-ray mammography screening were subsequently imaged on a 1.5-T magnetic resonance imaging scanner. Diffusion-weighted imaging was performed prior to biopsy with b values of 0, 100, 750, and 1500 s/mm. Isocontouring with different threshold levels was performed on the highest b-value image to determine the voxels used for subsequent evaluation of diffusion metrics. The coefficient of variation was computed by specifying 4 different regions of interest drawn around the lesion. Additionally, a receiver operating statistical analysis was performed. RESULTS: Using a relative threshold level greater than or equal to 0.85 almost completely suppresses the intra-individual and inter-individual variability. Among 4 studied diffusion metrics, the diffusion coefficients from the intravoxel incoherent motion model returned the highest area under curve value of 0.9. The optimal cut-off diffusivity was found to be 0.85 µm/ms with a sensitivity of 87.5% and specificity of 90.9%. CONCLUSION: Threshold isocontouring on high b-value maps is a viable approach to reliably evaluate DWI data of suspicious focal lesions in magnetic resonance mammography.

Quantifying NMR relaxation correlation and exchange in articular cartilage with time domain analysis.

Measured nuclear magnetic resonance (NMR) transverse relaxation data in articular cartilage has been shown to be multi-exponential and correlated to the health of the tissue. The observed relaxation rates are dependent on experimental parameters such as solvent, data acquisition methods, data analysis methods, and alignment to the magnetic field. In this study, we show that diffusive exchange occurs in porcine articular cartilage and impacts the observed relaxation rates in T1-T2 correlation experiments. By using time domain analysis of T2-T2 exchange spectroscopy, the diffusive exchange time can be quantified by measurements that use a single mixing time. Measured characteristic times for exchange are commensurate with T1 in this material and so impacts the observed T1 behavior. The approach used here allows for reliable quantification of NMR relaxation behavior in cartilage in the presence of diffusive fluid exchange between two environments.

Bone volume-to-total volume ratio measured in trabecular bone by single-sided NMR devices.

PURPOSE: Reduced bone strength is associated with a loss of bone mass, usually evaluated by dual-energy X-ray absorptiometry, although it is known that the bone microstructure also affects the bone strength. Here, a method is proposed to measure (in laboratory) the bone volume-to-total volume ratio by single-sided NMR scanners, which is related to the microstructure of the trabecular bone. METHODS: Three single-sided scanners were used on animal bone samples. These low-field, mobile, low-cost devices are able to detect the NMR signal, regardless of the sample sizes, without the use of ionizing radiations, with the further advantage of signal localization offered by their intrinsic magnetic field gradients. RESULTS: The performance of the different single-sided scanners have been discussed. The results have been compared with bone volume-to-total volume ratio by micro CT and MRI, obtaining consistent values. CONCLUSIONS: Our results demonstrate the feasibility of the method for laboratory analyses, which are useful for measurements like porosity on bone specimens. This can be considered as the first step to develop an NMR method based on the use of a mobile single-sided device, for the diagnosis of osteoporosis, through the acquisition of the signal from the appendicular skeleton, allowing for low-cost, wide screening campaigns. Magn Reson Med 79:501-510, 2018. © 2017 International Society for Magnetic Resonance in Medicine.

Multimodal analysis of aged wild-type mice exposed to repeated scanning ultrasound treatments demonstrates long-term safety.

The blood-brain barrier presents a major challenge for the delivery of therapeutic agents to the brain; however, it can be transiently opened by combining low intensity ultrasound with microbubble infusion. Studies evaluating this technology have largely been performed in rodents, including models of neurological conditions. However, despite promising outcomes in terms of drug delivery and the amelioration of neurological impairments, the potential for long-term adverse effects presents a major concern in the context of clinical applications. Methods: To fill this gap, we repeatedly treated 12-month-old wild-type mice with ultrasound, followed by a multimodal analysis for up to 18 months of age. Results: We found that spatial memory in these aged mice was not adversely affected as assessed in the active place avoidance test. Sholl analysis of Golgi impregnations in the dentate gyrus of the hippocampus did not reveal any changes to the neuronal cytoarchitecture. Long-term potentiation, a cellular correlate of memory, was still achievable, magnetic resonance spectroscopy revealed no major changes in metabolites, and diffusion tensor imaging revealed normal microstructure and tissue integrity in the hippocampus. More specifically, all measures of diffusion appeared to support a neuroprotective effect of ultrasound treatment on the brain. Conclusion: This multimodal analysis indicates that therapeutic ultrasound for blood-brain barrier opening is safe and potentially protective in the long-term, underscoring its validity as a potential treatment modality for diseases of the brain.

Determining mean fractional anisotropy using DDCOSY: preliminary results in biological tissues.

Complex materials are ubiquitous in science, engineering and nature. One important parameter for characterising their morphology is the degree of anisotropy. Magnetic resonance imaging offers non-invasive methods for quantitative measurements of the materials anisotropy, most commonly via diffusion tensor imaging and the subsequent extraction of the spatially resolved fractional anisotropy (FA) value. Here, we propose an alternative way of determining the FA as a sample average for cases where spatially resolved methods are not needed or not applicable. It is based on a particular diffusion-diffusion correlation spectroscopy protocol, allowing for the extraction of the mean (i.e. sample averaged) FA value. We demonstrate that mean FA values obtained from three anisotropic biological tissues are consistent with those extracted using diffusion tensor imaging. Moreover, we show that differences of mean FA values in healthy and tumour-bearing mouse brains allow to distinguish these tissue types. We anticipate that the proposed method will be beneficial in the wider context of medical and material science. Copyright © 2016 John Wiley & Sons, Ltd.

Fast reconstruction of highly undersampled MR images using one and two dimensional principal component analysis.

Recent compressed sensing techniques allow signal acquisition with less sampling than required by the Nyquist-Shannon theorem which reduces the data acquisition time in magnetic resonance imaging (MRI). However, prior knowledge becomes essential to reconstruct detailed features when the sampling rate is exceedingly low. In this work, one compressed sensing scheme developed in wireless sensing networks was adapted for the purpose of reconstructing magnetic resonance images by using one-dimensional principal component analysis (1D-PCA). Moreover, another related reconstruction method was proposed based on two-dimensional principal component analysis (2D-PCA). When comparing with one wavelet compressed sensing method, we demonstrate that these techniques are feasible and efficient at high undersampling rates.

Symmetry of the gradient profile as second experimental dimension in the short-time expansion of the apparent diffusion coefficient as measured with NMR diffusometry.

The time-dependent apparent diffusion coefficient as measured by pulsed gradient NMR can be used to estimate parameters of porous structures including the surface-to-volume ratio and the mean curvature of pores. In this work, the short-time diffusion limit and in particular the influence of the temporal profile of diffusion gradients on the expansion as proposed by Mitra et al. (1993) is investigated. It is shown that flow-compensated waveforms, i.e. those whose first moment is zero, are blind to the term linear in observation time, which is the term that is proportional to mean curvature and surface permeability. A gradient waveform that smoothly interpolates between flow-compensated and bipolar waveform is proposed and the degree of flow-compensation is used as a second experimental dimension. This two-dimensional ansatz is shown to yield an improved precision when characterizing the confining domain. This technique is demonstrated with simulations and in experiments performed with cylindrical capillaries of 100 µm radius.