Conditional granger causality analysis of fMRI data shows a direct connection from LGN to hMT+ bypassing V1

The human middle temporal complex (hMT+) is devoted to motion perception. To determine whether motion-related neural information may reach hMT+ directly from the thalamus, by-passing the primary visual cortex (V1), we measured effective connectivity in an optic flow fMRI experiment in humans. Conditional Granger Causality analysis was employed to measure direct influences between the lateral geniculate nucleus (LGN) and hMT+, discarding indirect effects mediated by V1. Results indicated the existence of a bilateral alternative pathway for visual motion processing that allows for a direct flow of information from LGN to hMT+. This direct link may play a role in blindsight

Diagnostic accuracy of quantitative susceptibility mapping in multiple system atrophy: The impact of echo time and the potential of histogram analysis

The non-invasive quantification of iron stores via Quantitative Susceptibility Mapping (QSM) could play an important role in the diagnosis and the differential diagnosis of atypical Parkinsonisms. However, the susceptibility (χ) values measured via QSM depend on echo time (TE). This effect relates to the microstructural organization within the voxel, whose composition can be altered by the disease. Moreover, pathological iron deposition in a brain area may not be spatially uniform, and conventional Region of Interest (ROI)-based analysis may fail in detecting alterations. Therefore, in this work we evaluated the impact of echo time on the diagnostic accuracy of QSM on a population of patients with Multiple System Atrophy (MSA) of either Parkinsonian (MSAp) or cerebellar (MSAc) phenotypes. In addition, we tested the potential of histogram analysis to improve QSM classification accuracy. We enrolled 32 patients (19 MSAp and 13 MSAc) and 16 healthy controls, who underwent a 7T MRI session including a gradient-recalled multi-echo sequence for χ mapping. Nine histogram features were extracted from the χ maps computed for each TE in atlas-based ROIs covering deep brain nuclei, and compared among groups. Alterations of susceptibility distribution were found in the Putamen, Substantia Nigra, Globus Pallidus and Caudate Nucleus for MSAp and in the Substantia Nigra and Dentate Nucleus for MSAc. Increased iron deposition was observed in a larger number of ROIs for the two shortest TEs and the standard deviation, the 75th and the 90th percentile were the most informative features yielding excellent diagnostic accuracy with area under the ROC curve > 0.9. In conclusion, short TEs may enhance QSM diagnostic performances, as they can capture variations in rapidly-decaying contributions of high χ sources. The analysis of histogram features allowed to reveal fine heterogeneities in the spatial distribution of susceptibility alteration, otherwise undetected by a simple evaluation of ROI χ mean values

Mapping tissue microstructure across the human brain on a clinical scanner with soma and neurite density image metrics

Soma and neurite density image (SANDI) is an advanced diffusion magnetic resonance imaging biophysical signal model devised to probe in vivo microstructural information in the gray matter (GM). This model requires acquisitions that include b values that are at least six times higher than those used in clinical practice. Such high b values are required to disentangle the signal contribution of water diffusing in soma from that diffusing in neurites and extracellular space, while keeping the diffusion time as short as possible to minimize potential bias due to water exchange. These requirements have limited the use of SANDI only to preclinical or cutting‐edge human scanners. Here, we investigate the potential impact of neglecting water exchange in the SANDI model and present a 10‐min acquisition protocol that enables to characterize both GM and white matter (WM) on 3 T scanners. We implemented analytical simulations to (i) evaluate the stability of the fitting of SANDI parameters when diminishing the number of shells; (ii) estimate the bias due to potential exchange between neurites and extracellular space in such reduced acquisition scheme, comparing it with the bias due to experimental noise. Then, we demonstrated the feasibility and assessed the repeatability and reproducibility of our approach by computing microstructural metrics of SANDI with AMICO toolbox and other state‐of‐the‐art models on five healthy subjects. Finally, we applied our protocol to five multiple sclerosis patients. Results suggest that SANDI is a practical method to characterize WM and GM tissues in vivo on performant clinical scanners

Multi-centre and multi-vendor reproducibility of a standardized protocol for quantitative susceptibility Mapping of the human brain at 3T

: Quantitative Susceptibility Mapping (QSM) is an MRI-based technique allowing the non-invasive quantification of iron content and myelination in the brain. The RIN - Neuroimaging Network established an optimized and harmonized protocol for QSM across ten sites with 3T MRI systems from three different vendors to enable multicentric studies. The assessment of the reproducibility of this protocol is crucial to establish susceptibility as a quantitative biomarker. In this work, we evaluated cross-vendor reproducibility in a group of six traveling brains. Then, we recruited fifty-one volunteers and measured the variability of QSM values in a cohort of healthy subjects scanned at different sites, simulating a multicentric study. Both voxelwise and Region of Interest (ROI)-based analysis on cortical and subcortical gray matter were performed. The traveling brain study yielded high structural similarity (∼0.8) and excellent reproducibility comparing maps acquired on scanners from two different vendors. Depending on the ROI, we reported a quantification error ranging from 0.001 to 0.017 ppm for the traveling brains. In the cohort of fifty-one healthy subjects scanned at nine different sites, the ROI-dependent variability of susceptibility values, of the order of 0.005-0.025 ppm, was comparable to the result of the traveling brain experiment. The harmonized QSM protocol of the RIN - Neuroimaging Network provides a reliable quantification of susceptibility in both cortical and subcortical gray matter regions and it is ready for multicentric and longitudinal clinical studies in neurological and pychiatric diseases

Recommended Implementation of Quantitative Susceptibility Mapping for Clinical Research in The Brain: A Consensus of the ISMRM Electro-Magnetic Tissue Properties Study Group

This article provides recommendations for implementing quantitative susceptibility mapping (QSM) for clinical brain research. It is a consensus of the ISMRM Electro-Magnetic Tissue Properties Study Group. While QSM technical development continues to advance rapidly, the current QSM methods have been demonstrated to be repeatable and reproducible for generating quantitative tissue magnetic susceptibility maps in the brain. However, the many QSM approaches available give rise to the need in the neuroimaging community for guidelines on implementation. This article describes relevant considerations and provides specific implementation recommendations for all steps in QSM data acquisition, processing, analysis, and presentation in scientific publications. We recommend that data be acquired using a monopolar 3D multi-echo GRE sequence, that phase images be saved and exported in DICOM format and unwrapped using an exact unwrapping approach. Multi-echo images should be combined before background removal, and a brain mask created using a brain extraction tool with the incorporation of phase-quality-based masking. Background fields should be removed within the brain mask using a technique based on SHARP or PDF, and the optimization approach to dipole inversion should be employed with a sparsity-based regularization. Susceptibility values should be measured relative to a specified reference, including the common reference region of whole brain as a region of interest in the analysis, and QSM results should be reported with - as a minimum - the acquisition and processing specifications listed in the last section of the article. These recommendations should facilitate clinical QSM research and lead to increased harmonization in data acquisition, analysis, and reporting

European Ultrahigh-Field Imaging Network for Neurodegenerative Diseases (EUFIND).

INTRODUCTION: The goal of European Ultrahigh-Field Imaging Network in Neurodegenerative Diseases (EUFIND) is to identify opportunities and challenges of 7 Tesla (7T) MRI for clinical and research applications in neurodegeneration. EUFIND comprises 22 European and one US site, including over 50 MRI and dementia experts as well as neuroscientists. METHODS: EUFIND combined consensus workshops and data sharing for multisite analysis, focusing on 7 core topics: clinical applications/clinical research, highest resolution anatomy, functional imaging, vascular systems/vascular pathology, iron mapping and neuropathology detection, spectroscopy, and quality assurance. Across these topics, EUFIND considered standard operating procedures, safety, and multivendor harmonization. RESULTS: The clinical and research opportunities and challenges of 7T MRI in each subtopic are set out as a roadmap. Specific MRI sequences for each subtopic were implemented in a pilot study presented in this report. Results show that a large multisite 7T imaging network with highly advanced and harmonized imaging sequences is feasible and may enable future multicentre ultrahigh-field MRI studies and clinical trials. DISCUSSION: The EUFIND network can be a major driver for advancing clinical neuroimaging research using 7T and for identifying use-cases for clinical applications in neurodegeneration

Bayesian Source Separation of Astrophysical Images Using Particle Filters (Separazione Bayesiana di Sorgenti in Immagini Astrofisiche Utilizzando "Particle Filters")

The problem of separating a superposition of different, simultaneous signals from their mixture appears very frequently in various fields of engineering, such as speech processing, telecommunications, biomedical imaging and financial data analysis. In this thesis, we will confront the problem of source separation in the field of astrophysics, where the contributions of various Galactic and extra-Galactic components need to be separated from a set of observed noisy mixtures. Most of the previous work on the problem perform a blind separation, assume noiseless models, and in the few cases when noise is taken into account it is generally assumed to be Gaussian and space-invariant. Our objective is to study a novel technique named particle filtering, and implement it for the non-blind solution of the source separation problem. Particle filtering is an advanced Bayesian estimation method which can deal with non-Gaussian and nonlinear models, and additive space-varying noise, in the sense that it is a generalization of the Kalman Filter. In this work, particle filters are utilized with objectives of both noise filtering and separation of signals: this approach is extremely flexible, as it is possible to exploit the available a-priori information about the statistical properties of the sources through the Bayesian theory. Especially in case of low SNR, our simulations show that the output quality of the separated signals is better than that of ICA, which is one of the most widespread methods for source separation. On the other hand, since a wide set of parameters, which can take from a large range of values, has to be initialized, the use of this approach needs extensive experimentation and testing

High-field functional magnetic resonance imaging reveals different patterns of responses elicited by transient changes in visual motion coherency

Previous work on human visual cortex demonstrated that when contrast is transiently increased or decreased from an intermediate, baseline level, neuronal activity in areas V1 through V3 follows the sign and the magnitude of the change. However, human area V4 (hV4) was reported to behave in a fundamentally different way, by responding always positively to both increments and decrements in contrast. This interesting behavior has been suggested to be part of the mechanisms responsible for signaling less salient changes in the visual stimulus – a function that cannot otherwise be performed by earlier areas, whose response to lesser stimuli is weak. However, despite the interestingness of this property of hV4 and its importance to advance knowledge about important aspects of early visual processing, this behavior has not been thoroughly investigated further and is not well documented in the literature. In particular, two main questions are of special interest: does hV4 respond positively to lesser stimuli in the presence of decrements of other stimulus attributes, besides image contrast? And do other cortical areas in the visual cortex behave in a similar way? To answer to these questions, we investigated the behavior of the visual cortex in response to transient increments and decrements in visual motion coherency. Two main response patterns were observed in the extrastriate visual cortex. In particular, the human MT complex, the parieto-occipital area V6, and V3A share the same kind of response pattern, in the sense that they are characterized by hemodynamic responses whose sign follows that of the change in motion coherency. On the other hand, areas in ventral occipital areas, including hV4, and in the vicinity of the intra-parietal sulcus exhibit a different kind of response, since they respond always positively to both increments and decrements in the level of motion coherency. Thus, we are able to provide evidence that hV4 signals transient decrements with positive responses, not only in the case of contrast, but also in the case of motion coherency – and, importantly, such a property is not restricted to hV4, but it is observed elsewhere as well, in other visual areas that are hierarchically located beyond V3. This previously unknown diversity in response patterns constitutes a new important finding for further understanding the mechanisms involved in visual processing in the human brain

The impact of white matter fiber orientation in single-acquisition quantitative susceptibility mapping

The aim of this work was to assess the impact of tissue structural orientation on quantitative susceptibility mapping (QSM) reliability, and to provide a criterion to identify voxels in which measures of magnetic susceptibility (Ï\u87) are most affected by spatial orientation effects. Four healthy volunteers underwent 7-T magnetic resonance imaging (MRI). Multi-echo, gradient-echo sequences were used to obtain quantitative maps of frequency shift (FS) and Ï\u87. Information from diffusion tensor imaging (DTI) was used to investigate the relationship between tissue orientation and FS measures and QSM. After sorting voxels on the basis of their fractional anisotropy (FA), the variations in FS and Ï\u87 values over tissue orientation were measured. Using a K-means clustering algorithm, voxels were separated into two groups depending on the variability of measures within each FA interval. The consistency of FS and QSM values, observed at low FA, was disrupted for FA > 0.6. The standard deviation of Ï\u87 measured at high FA (0.0103 ppm) was nearly five times that at low FA (0.0022 ppm). This result was consistent through data across different head positions and for different brain regions considered separately, which confirmed that such behavior does not depend on structures with different bulk susceptibility oriented along particular angles. The reliability of single-orientation QSM anticorrelates with local FA. QSM provides replicable values with little variability in brain regions with FA < 0.6, but QSM should be interpreted cautiously in major and coherent fiber bundles, which are strongly affected by structural anisotropy and magnetic susceptibility anisotropy