Neuroscience and Quantitative Neuroimaging

Abstract: The project Neuroscience and Quantitative Neuroimaging (NQN) studies the dynamics of brain networks using quantitative experimental approaches based on nuclear magnetic resonance imaging (MRI), combined with biophysical models. The experimental activity is focused on the study of coherent spontaneous fluctuations in cerebral blood oxygenation – which indirectly reflect the network properties of brain function – in particular in presence of functional dynamics elicited by sensory (vision) or cognitive (memory, perception) stimulations. To this end, NQN promotes innovation in the field of MRI technologies, such as the optimization of acquisition processes, and the development of new multimodal analysis methods.

The project has a strong interdisciplinary connotation, and aims at contributing to the development of advanced and optimized diagnostic tools tailored to individual patients’ specificities, for the characterization, diagnosis and treatment of neurological and psychiatric pathologies.

The Neuroscience and Quantitative Neuroimaging (NQN) project is aimed at the study of brain function and some neurological and psychiatric pathologies. The project associates technological development and applications for the characterization of brain networks and metabolic dynamics at functional, structural and molecular level. General aims of the project include the determination of the relationships between brain function and its physiological and biochemical substrates, or more generally between function and structure. The dominant view is that the structure conditions, but does not uniquely determine the function. Regardless of the controversial philosophical and evolutionary aspects, our approach is eminently multimodal and interdisciplinary. It deals with Magnetic Resonance Imaging (MRI), image processing and computational modeling techniques, and fully exploits the intrinsic multi-parametric properties of (MRI).

Pubmed hits (June 2020) for the key “functional Magnetic Resonance Imaging” OR fMRI. The vertical line identifies the invention of modern functional imaging, based on BOLD (Blood Oxygenation Level Dependent) contrast, and therefore ideally marks the transition between the search for a valid method and its development in terms of technology and applications.

It is difficult to overestimate the importance of MR-based neuroimaging for the advancement of neuroscience, and more generally for the understanding of the human brain and how it is capable of generating behavior. In this interdisciplinary and frontier field, no other technology has had a greater impact in quantitative and also qualitative terms. From a quantitative point of view, the exponential growt of the number of scientific publications associated with functional imaging is eloquent enough (see side figure). The qualitative importance derives instead from the unique properties of MRI. On the one hand MRI is completely non-invasive, and can therefore be extensively applied to humans, even for repeated and longitudinal studies. On the other hand it is characterized by being an intrinsically multiparametric technique. Through appropriate manipulation of nuclear spins, MR imaging can in fact be sensitized to multiple phenomena of interest for neuroscience. Thanks to these properties, MRI has totally revolutionized medical diagnostics and offered an important set of quantitative and non-invasive investigation methods, which give information that are both functional (blood flow, oxygen consumption, temperature, pH, metabolic dynamics), structural (images weighted in parameters related to rapid molecular dynamics, called T1 e T2) and microstructural (water diffusion, slow molecular dynamics).

The functional neuroimaging methods, in particular thanks to the BOLD (Blood Oxigenation Level-Dependent) contrast, initially made feasible to identify the areas “activated” during the performance of motor, sensory or cognitive functions. The BOLD effect allows to indirectly study the brain function through its hemodynamic and metabolic correlates. Electrophysiological activity is indeed associated with a localized increase in blood flow and volume, and with an increase in oxygen consumption. The hemodynamic modulations are in fact overcompensatory compared to the increase of aerobic metabolism, which causes a focal increase in blood oxygenation, which in turn can be revealed by rapid fMRI (functional MRI) techniques. Since 1995 it has been realized that the areas that are presumed to cooperate during function, responding to it with a measurable increase in activity, show slow oscillations of the BOLD signal even in the absence of stimulation. In other words, the cortex constantly maintains a low level of activity, with apparently random but spatially coherent temporal characteristics.

Connettomics and brain networks

The first sector that we intend to develop in the three-year period is the study of the properties of brain networks using fMRI and associated techniques.

The study of brain connectivity is continuously expanding its scope and scale, on the one hand towards the investigation of connectivity at the cortical layer level, on the other hand with the use of connectomics on a global level, for example for early fingerprinting of neurological diseases or psychiatric. In any case, the connectomic analysis is based on the characterization of differences with respect to a reference. These changes can be induced by a pathology, or simply a statistical comparison with a blank. This is a complex procedure and prone to false positives. In fact, it should be remembered that the connectomic analysis techniques, being based on the appreciation of the covariance structure of the data, are sensitive to coherent spurious signals, including the so-called “physiological noise” (ie the variations induced by physiological rhythms such as breathing , movement or heartbeat).

Dynamics of brain networks

A first line of activity, which we intend to complete within a year, is the development of methods for the mitigation of physiological noise. At the same time we will deepen the dynamic characterization of the signal. The relationship between plastic modulation of networks and behavior is a question of utmost importance in terms of basic knowledge of brain function and its implications for the understanding of major neurological and psychiatric pathologies. Our group is among the first to have studied the issue of the dynamic modulation of brain networks induced by brain function, in multiple experimental models, as shown in figure.

Left: brain networks during spontaneous pupillary diameter modulation associated with a visual attention task. Right: Granger causality analysis between the rate of variation of the pupillary diameter dP/dT and the brain networks. Although Locus Coeruleus is physiologically associated with pupil diameter, Granger Causality indicates the presence of a complex pattern of interdependence between networks, with LC and pupil diameter separated by numerous stages of cortical processing (From DiNuzzo et al 2019).

In particular, we confirmed that the topology of the resting brain networks is globally conserved during the execution of a continuous cognitive task. However, we have highlighted two phenomena that deserve further study. The first is that a small number of brain network nodes actually change their topological relationships during activity, suggesting that the networks are globally stable, but undergo short-term plastic remodeling phenomena. We plan to investigate this modulation, both in terms of the modalities with which it occurs, and in terms of functional significance.

Correlation matrix at rest (top left) and during a cognitive task (bottom), and t-test (unthresholded) on the difference between the two (top right, from Tommasin et al. 2018).

The second point that we will study is the significance of the amplitude of the modulation of functional connectivity in MRI (fcMRI). As well seen in figure (on the side), intra-network connectivity, which is normally higher than connectivity between networks, tends to decrease during tasks, while the opposite occurs for connectivity between networks. With our work we have shown that the functional connectivity variation ΔFC as a function of resting connectivity FCR is well described by a simple linear model, ∆FC=βFCR0. Interestingly the amplitude of this modulation is irrelevant from a behavioral point of view (percentage of exact responses during the cognitive task), while the slope β shows a significant inverse correlation with cognitive performance in some areas involved in the execution of the task. These results indicate that, without proper normalization, the amplitude of connectivity changes could be an irrelevant parameter from the physiological point of view. This result would have a significant impact, considering the increasing use of this parameter to study neurodegeneration. We will then investigate the physiological origins of stimulation-induced modulation of fcMRI, to identify the determinant of the behaviorally irrelevant component. It is important to note that vascular reactivity is a potent modulator of fMRI response and vascular reactivity has been reported to spatially modulate functional connectivity at rest and the amplitude of BOLD fluctuations. We believe we can hypothesize a role of vascular reactivity and/or the autonomic system in determining the connectivity changes associated with activity. If this hypothesis, subjected to experimental verification, proves to be correct, we will develop methods of renormalization of the signal aimed at excluding the vascular component from the analysis.


The second line is partially linked to the first, and in particular aims to investigate the mechanisms of plasticity induced by electrical stimulation. This is a study in collaboration with the Santa Lucia Foundation (Prof. Marangolo), aimed in particular at studying the effects of transpinal electrical stimulation in patients suffering from Alzheimer’s dementia (AD). Transpinal direct current stimulation is a non-invasive stimulation tool that involves the application of a weak electric current (1-2 mA) using electrodes applied to the back. The current modulates neuronal excitability, with protracted effects similar to the mechanisms of long-term enhancement and depression. While there is some fMRI evidence of the plastic effect in the case of cortical stimulation, the effects of transpinal stimulation on brain networks are still unknown. In this series of experiments we intend first of all to study the focal effect of tsDCS as such, by means of task-based studies, and secondly to determine its plastic-type effects and the relative temporal duration (a relevant characteristic for therapeutic applications). To this end, we will develop a technique capable of taking into account the spatial scale of the modulations. In fcMRI studies, the nodes of the network are identified a priori and the evolution of the branches is studied, often assuming the spatial stationarity of the network. However, plastic phenomena occur at multiple scales, starting from the minimum functional unit (canonical microcircuit), and can modulate by definition the physiological substrate of the network. We will therefore develop two optimized approaches to characterize plasticity by fcMRI: 1) a method based on the extraction of exemplary dynamic components by constrained Independent Vector Analysis (SED-cIVA), adapted to the very high temporal resolution data that we will acquire through multiband approaches (0.8 s against the ordinary 2-3s). SED-cIVA is an iterative approach, which in a first phase extracts models with independent component analysis approaches (ICA), and in a second time determines the spatiotemporal dynamics by means of fit on a sliding window. 2) We will then develop a univariate approach based on the connectivity radius. The techniques to identify fMRI networks are usually of multivariate nature. In this way it is inherently difficult to define the location and directionality of the modulations. Preliminary tests conducted over the past year suggest that a metric based on the average of the Fisher transformation of the correlation coefficients of a voxel with the voxels included in spherical shells of increasing radius has the potential to capture local modulations of connectivity. We therefore propose to develop this metric and show its adequacy to describe phenomena of neuronal plasticity.

Metabolism of brain function

Brain activity is mainly based on oxidative metabolism. For this reason, the measurement of the metabolic oxygen consumption rate (CMRO2) is an excellent biomarker for the quantification of brain activity and the physiological state of tissues, with potential applications in the early diagnosis of carcinomas, strokes, neurological and neurodegenerative diseases. Currently, positron emission tomography techniques based on oxygen isotopes are the gold standard for obtaining CMRO2 maps of the whole brain. However, the technical complexity of the tests and the level of invasiveness of the same constitute a huge limit to their use.

There are several MRI methods for measuring CMRO2, based on different technological approaches and physiological characteristics. We cite for example the exploitation of the magnetic field differences associated to tissue differences between the superior sagittal sinus or main veins and the surrounding parenchyma, the T2 oxygenation calibration curves with speed selective techniques, or the quantification approaches of venous oxygen saturation through the T2 of venous blood.

Davis and Hoge introduced in the late 1990s another group of techniques, based on BOLD calibration methods, which aim to estimate CMRO2 from BOLD and ASL (Arterial Spin Labeling) signals, exploiting respiratory tasks (hypercapnia and hyperoxia) and mathematical models that describe the complex relationship between oxygen metabolism, BOLD signal and cerebral blood flow (CBF). CBF is a direct biomarker for cerebrovascular function and neurovascular health, and the correlation between CBF, local neuronal activity and metabolism, known as neurovascular coupling, is a surrogate marker for brain function. Detecting CBF at rest without carrying out complex cognitive tasks is a fairly easy operation to conduct in clinical practice. For example, CBF can be measured with ASL, perfusion, or phase contrast MRI techniques. Recently, an extension of these techniques has made it possible to record in the same experiment the changes in CBF, induced by hypercapnia, and in BOLD induced by hyperoxia (increased concentration of oxygen in the blood), and to exploit them to characterize the cerebral metabolic state through the estimation of various parameters, including the concentration of deoxyhemoglobin in venous blood, the fraction of oxygen extracted (OEF), the absolute CMRO2, the CBF and the vascular reactivity (CVR). This innovative approach is called quantitative oxygen imaging or dual calibrated fMRI (dcfMRI), and overcomes one of the basic problems of the method initially proposed by Davis and Hoge, namely the dependence on an unknown parameter, the signal baseline, M. The dcfMRI techniques have technological requirements that can be matched with those of vascular reactivity techniques (described in the Dynamics of brain networks paragraph), therefore the development of both techniques has clear synergistic aspects. In this part, the tissue segmentation work based on AI methods developed in collaboration with the University of Kuopio will also be exploited, in order to obtain structurally homogeneous areas on which to average the signals.

The quantification of CMRO2 will allow us to continue the study of the metabolic dynamics that has characterized the activity of our group from the beginning. Many of the problems we have successfully studied actually concern the functional characterization of the cells of the nervous system (neurons and glial cells) in biophysical and biochemical terms. Neurons are the components of neural circuits, whose task is to process specific types of information, whose integration represents the substrate of brain function. Glial cells, which are in a 10: 1 ratio with neurons, have functions that are not yet completely clear, but which certainly include the modulation of nutrient transport, ionic homeostasis and the modulation of cellular excitability.

From the experimental point of view we have in the past focused attention on lactate. The importance that lactate plays in the functional metabolism of the brain derives from the paradigm shift that has invested this scientific field after the introduction of the hypothesis of the lactate shuttle, Astrocyte – Neuron Lactate Shuttle (ANLSH), proposed by Pellerin and Magistretti in 1994. This hypothesis has revolutionized the concept that neurons use exclusively glucose, while providing a nutritional role for astrocytes (a type of glial cell). According to ANLSH, astrocytes would couple the increase in electrical activity of neurons to the absorption of glucose from the blood for production of energy. In other words, ANLSH affirms that the primary energy substrate of neurons would not be glucose, but the lactate produced by astrocytes at activity-dependent rate.

We have repeatedly challenged the ANSL hypothesis on experimental and modeling grounds, associating the increase in lactate that is observed during stimulation with a generalized increase in metabolic intermediates during the rapid increase in aerobic metabolism. However, there is no direct experimental demonstration that the change in lactate in vivo is associated with oxygen consumption. We therefore intend to carry out a combined spectroscopy and CMRO2 experiment aimed at functionally characterizing the link between CMRO2 and lactate.

Left: brain metabolic network, including astrocytic and neuronal subcellular compartments and extracellular compartments (extracellular matrix, vessels). The part subject to the latest steady-state modeling studies (DiNuzzo et al. 2017) is highlighted in gray and amplified on the right.

From the modeling point of view, the basic idea is to continue past efforts by capitalizing on the research of the last ten years in the field of kinetic and stoichiometric models, research that has received strong interest in the scientific community and has recently led to the important strategic collaboration. with Yale School of Medicine.

In particular, the aim is to formalize compartmentalized models (neuron, astrocyte, extracellular space, perivascular space, vessels) in which the cellular components are described by detailed metabolic networks at the genomic level in order to implement simulations of cerebral metabolism (with significant impact also on the interpretation of MRS and fMRI signals) with a level of detail never achieved before (side figure). This effort is aimed among other things at clarifying the role of astrocytic glycogen, for which our group first hypothesized and modeled a modulatory role. This research activity would also allow to acquire general skills in the study of metabolic networks from a more purely bioinformatic point of view (in particular, systems biology). In turn, this would favor the birth of new international collaborations and the expansion of the research line towards biotechnology.

The model development will initially focus on the determination of metabolic fluxes at steady state (Flux Balance Analysis). Our methodology proved to be qualitatively superior to the standard algorithms used to estimate the distributions of metabolic flows. On the other hand, the computational efficiency of our method is lower and the first step will be aimed at optimizing and implementing strategies, many of which are already known, to reduce the computational load of our method.

Main publications

On brain networks

  • DiNuzzo et al. 2019. Brain Networks Underlying Eye’s Pupil Dynamics. Front Neurosci. doi: 10.3389/fnins.2019.00965
  • Tommasin et al. 2018. Scale-invariant Rearrangement of Resting State Networks in the Human Brain under Sustained Stimulation. Neuroimage. doi: 10.1016/j.neuroimage.2018.06.006
  • Mascali et al. 2018. Disruption of Semantic Network in Mild Alzheimer’s Disease Revealed by Resting-State fMRI. Neuroscience. doi: 10.1016/j.neuroscience.2017.11.030
  • Mascali et al. 2015. Intrinsic Patterns of Coupling Between Correlation and Amplitude of Low-Frequency fMRI Fluctuations Are Disrupted in Degenerative Dementia Mainly Due to Functional Disconnection. PLoS One. doi: 10.1371/journal.pone.0120988

On brain metabolic dynamic, modeling

  • DiNuzzo et al. 2017. Computational Flux Balance Analysis Predicts that Stimulation of Energy Metabolism in Astrocytes and their Metabolic Interactions with Neurons Depend on Uptake of K+ Rather than Glutamate. Neurochemical Research. doi: 10.1007/s11064-016-2048-0
  • Massucci et al. 2013. Energy metabolism and glutamate-glutamine cycle in the brain: a stoichiometric modeling perspective. BMC Systems Biology. doi: 10.1186/1752-0509-7-103.
  • Mangia et al. 2011. Response to ‘comment on recent modeling studies of astrocyte-neuron metabolic interactions’: much ado about nothing. J Cereb Blood Flow Metab. doi: 10.1038/jcbfm.2011.29
  • DiNuzzo et al. 2010b. Glycogenolysis in astrocytes supports blood-borne glucose channeling not glycogen-derived lactate shuttling to neurons: evidence from mathematical modelling. J Cereb Blood Flow Metab. doi: 10.1038/jcbfm.2010.151
  • DiNuzzo et al. 2010a. Changes in glucose uptake rather than lactate shuttle take center stage in subserving neuroenergetics: evidence from mathematical modeling. J Cereb Blood Flow Metab. doi: 10.1038/jcbfm.2009.232

On brain metabolic dynamic, experimental

  • Bednarik et al. 2018. Neurochemical Responses to Chromatic and Achromatic Stimuli in the Human Visual Cortex. J Cereb Blood Flow Metab. doi: 10.1177/0271678X17695291
  • Bednarik et al. 2015. Neurochemical and BOLD Responses During Neuronal Activation Measured in the Human Visual Cortex at 7 Tesla. J Cereb Blood Flow Metab. doi: 10.1038/jcbfm.2014.233.

Main collaborations

  • University of Minnesota, Center for Magnetic Resonance Research (CMRR), Minneapolis. (Prof. S. Mangia)
  • Yale University, Magnetic Resonance Research Center, New Haven. (Prof. D. Rothman)
  • University of Eastern Finland, A.I. Virtanen Institute for Molecular Sciences, Kuopio. (Prof. O. Gröhn, Prof. J. Tohka)
  • Fondazione Santa Lucia, Roma (Prof. M Bozzali, Prof. P Marangolo)
  • Università di Chieti-Pescara, Dipartimento di Neuroscienze, Chieti (Prof. R. G. Wise)
  • Sapienza Università di Roma, Dipartimenti di Ingegneria dell’Informazione Elettronica e Telecomunicazioni (Prof. F. Frezza) e di Fisica (Prof. S. Giagu)
  • IMT Lucca (Dr. T. Gili)
  • CNR, Istituto dei sistemi complessi, (Dr. S. Capuani) e Istituto di Nanotecnologia (Dr. M. Fratini)

Grants, last 5 years

  • 2015–2019 H2020 MSCA-RISE 691110 “MICROBRADAM: Advanced MR methods for characterization of microstructural brain damage”.
  • 2015–2018 Regione Lazio POR-FESR 2014-2020 RU-2014-1092, “PAMINA: Piattaforma per l’Analisi Multimodale Integrata in Neuroscienze Applicate”.