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Sensing activity-induced cell swellings and ensuing neurotransmitter releases for in-vivo functional imaging sans hemodynamics

Total Cost €


EC-Contrib. €






 DIRECT-fMRI project word cloud

Explore the words cloud of the DIRECT-fMRI project. It provides you a very rough idea of what is the project "DIRECT-fMRI" about.

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Project "DIRECT-fMRI" data sheet

The following table provides information about the project.


Organization address
city: LISBOA
postcode: 1400-038

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country Portugal [PT]
 Project website
 Total cost 1˙787˙500 €
 EC max contribution 1˙787˙500 € (100%)
 Programme 1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC))
 Code Call ERC-2015-STG
 Funding Scheme ERC-STG
 Starting year 2016
 Duration (year-month-day) from 2016-03-01   to  2021-02-28


Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 


 Project objective

Functional-Magnetic Resonance Imaging (fMRI) has transformed our understanding of brain function due to its ability to noninvasively tag ‘active’ brain regions. Nevertheless, fMRI only detects neural activity indirectly, by relying on slow hemodynamic couplings whose relationships with underlying neural activity are not fully known. We have recently pioneered two unique MR approaches: Non-Uniform Oscillating-Gradient Spin-Echo (NOGSE) MRI and Relaxation Enhanced MR Spectroscopy (RE MRS). NOGSE-MRI is an exquisite microstructural probe, sensing cell sizes (l) with an unprecedented l^6 sensitivity (compared to l^2 in conventional approaches); RE MRS is a new spectral technique capable of recording metabolic signals with extraordinary fidelity at ultrahigh fields. This proposal aims to harness these novel concepts for mapping neural activity directly, without relying on hemodynamics. The specific objectives of this proposal are: (1) Mapping neural activity via sensing cell swellings upon activity (μfMRI): we hypothesize that NOGSE can robustly sense subtle changes in cellular microstructure upon neural firings and hence convey neural activity directly. (2) Probing the nature of elicited activity via detection of neurotransmitter release: we posit that RE MRS is sufficiently sensitive to robustly detect changes in Glutamate and GABA signals upon activation. (3) Network mapping in optogenetically-stimulated, behaving mice: we propose to couple our novel approaches with optogenetics to resolve neural correlates of behavior in awake, behaving mice. Simulations for μfMRI predict >4% signal changes upon subtle cell swellings; further, our in vivo RE MRS experiments have detected metabolites with SNR>50 in only 6 seconds. Hence, these two complementary –and importantly, hemodynamics-independent– approaches will represent a true paradigm shift: from indirect detection of neurovasculature couplings towards direct and noninvasive mapping of neural activity in vivo.


year authors and title journal last update
List of publications.
2017 Daniel Nunes, Tomás L. Cruz, Sune N. Jespersen, Noam Shemesh
Mapping axonal density and average diameter using non-monotonic time-dependent gradient-echo MRI
published pages: 117-130, ISSN: 1090-7807, DOI: 10.1016/j.jmr.2017.02.017
Journal of Magnetic Resonance 277 2020-01-29
2017 Guilherme Blazquez Freches, Cristina Chavarrias, Noam Shemesh
BOLD-fMRI in the mouse auditory pathway
published pages: , ISSN: 1053-8119, DOI: 10.1016/j.neuroimage.2017.10.027
NeuroImage 2020-01-29
2017 Andrada IanuÅŸ, Noam Shemesh
Incomplete initial nutation diffusion imaging: An ultrafast, single-scan approach for diffusion mapping
published pages: , ISSN: 0740-3194, DOI: 10.1002/mrm.26894
Magnetic Resonance in Medicine 2020-01-29
2019 Rafael Neto Henriques, Sune N. Jespersen, Noam Shemesh
Microscopic anisotropy misestimation in spherical-mean single diffusion encoding MRI
published pages: 3245-3261, ISSN: 0740-3194, DOI: 10.1002/mrm.27606
Magnetic Resonance in Medicine 81/5 2020-01-29
2019 Daniel Nunes, Andrada Ianus, Noam Shemesh
Layer-specific connectivity revealed by diffusion-weighted functional MRI in the rat thalamocortical pathway
published pages: 646-657, ISSN: 1053-8119, DOI: 10.1016/j.neuroimage.2018.09.050
NeuroImage 184 2020-01-29
2019 Mark D. Does, Jonas Lynge Olesen, Kevin D. Harkins, Teresa Serradas‐Duarte, Daniel F. Gochberg, Sune N. Jespersen, Noam Shemesh
Evaluation of principal component analysis image denoising on multi‐exponential MRI relaxometry
published pages: , ISSN: 0740-3194, DOI: 10.1002/mrm.27658
Magnetic Resonance in Medicine 2020-01-29
2018 Teresa Serradas Duarte, Noam Shemesh
Two-dimensional magnetization-transfer – CPMG MRI reveals tract-specific signatures in fixed rat spinal cord
published pages: 124-137, ISSN: 1090-7807, DOI: 10.1016/j.jmr.2018.10.014
Journal of Magnetic Resonance 297 2020-01-29
2019 Sune Nørhøj Jespersen, Jonas Lynge Olesen, Andrada Ianuş, Noam Shemesh
Effects of nongaussian diffusion on “isotropic diffusion” measurements: An ex-vivo microimaging and simulation study
published pages: 84-94, ISSN: 1090-7807, DOI: 10.1016/j.jmr.2019.01.007
Journal of Magnetic Resonance 300 2020-01-29
2018 Andrada IanuÅŸ, Sune N. Jespersen, Teresa Serradas Duarte, Daniel C. Alexander, Ivana Drobnjak, Noam Shemesh
Accurate estimation of microscopic diffusion anisotropy and its time dependence in the mouse brain
published pages: 934-949, ISSN: 1053-8119, DOI: 10.1016/j.neuroimage.2018.08.034
NeuroImage 183 2020-01-29
2018 Noam Shemesh
Axon Diameters and Myelin Content Modulate Microscopic Fractional Anisotropy at Short Diffusion Times in Fixed Rat Spinal Cord
published pages: , ISSN: 2296-424X, DOI: 10.3389/fphy.2018.00049
Frontiers in Physics 6 2020-01-29
2018 Marco Palombo, Noam Shemesh, Itamar Ronen, Julien Valette
Insights into brain microstructure from in vivo DW-MRS
published pages: 97-116, ISSN: 1053-8119, DOI: 10.1016/j.neuroimage.2017.11.028
NeuroImage 182 2020-01-29

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