Modelling the depth-dependent VASO and BOLD responses in human primary visual cortex

Akbari, Atena; Bollmann, Saskia; Ts, Ali; Barth, Markus

doi:10.1101/2021.05.07.443052

Cited by 7 publications

(6 citation statements)

References 120 publications

(284 reference statements)

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“…As expected, we find that the VASO contrast is largely insensitive to unwanted contributions from large draining veins at the cortical surface. This is in line with previous layer-fMRI VASO experiments at 7T (Akbari et al 2021;Beckett et al 2020;Persichetti et al 2020).…”

Section: Discussionsupporting

confidence: 93%

Evaluating the capabilities and challenges of layer-fMRI VASO at 3T

Huber

Kronbichler

Stirnberg

et al. 2022

Preprint

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Sub-millimeter functional imaging has the potential to capture cortical layer-specific functional information flow within and across brain systems. Recent sequence advancements of fMRI signal readout and contrast generations resulted in wide adaptation of layer-fMRI protocols across the global ultra high-field (UHF) neuroimaging community. However, most layer-fMRI applications are confined to one of ≈100 privileged UHF imaging centers, and sequence contrasts with unwanted sensitivity to large draining veins. In this work, we propose the application of vein-signal free vascular space occupancy (VASO) sequences at widely accessible 3T scanners. Specifically, we implement, characterize, and apply a cerebral blood volume (CBV)-sensitive VASO fMRI at a 3T scanner setup, as it is typically used in the majority of cognitive neuroscience and clinical neuroscience fMRI studies. We find that the longer T2*, and stronger relative T1 contrast at 3T can account for some of the lower z-magnetization in the inversion-recovery VASO sequence compared to 7T and 9.4T. In the main series of experiments (N=16), we test the utility of this setup for motor tasks and find that -while being limited by thermal noise- 3T layer-fMRI VASO is feasible within conventional scan durations. In a series of auxiliary studies, we furthermore explore the generalizability of the developed protocols for a larger range of study designs including: visual stimulation, whole brain movie watching paradigms, and cognitive tasks with weaker effect sizes. We hope that the developed imaging protocols will help to increase accessibility of vein-free layer-fMRI imaging tools to a wider community of neuroimaging centers.

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Section: Discussionsupporting

confidence: 93%

Evaluating the capabilities and challenges of layer-fMRI VASO at 3T

Huber

Kronbichler

Stirnberg

et al. 2022

Preprint

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“…The cortical vascular model was implemented in MATLAB (2018b, The MathWorks, Inc.). The code is available on gitlab (https://gitlab.com/AtenaAkbari/cortical-vascular-model) including the original version used in Markuerkiaga et al (2016) (branch: originalCode), the implementation used for an earlier version of this work presented at the ISMRM 2020 in which intracortical arteries were not yet added (Akbari et al, 2020) (branch: vasoSignal), and the implementation used in this manuscript (branch: master).…”

Section: Experimental Methodsmentioning

confidence: 99%

Modelling the depth‐dependent VASO and BOLD responses in human primary visual cortex

Akbari

Bollmann

Ali

et al. 2022

Human Brain Mapping

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Functional magnetic resonance imaging (fMRI) using a blood‐oxygenation‐level‐dependent (BOLD) contrast is a common method for studying human brain function noninvasively. Gradient‐echo (GRE) BOLD is highly sensitive to the blood oxygenation change in blood vessels; however, the spatial signal specificity can be degraded due to signal leakage from activated lower layers to superficial layers in depth‐dependent (also called laminar or layer‐specific) fMRI. Alternatively, physiological variables such as cerebral blood volume using the VAscular‐Space‐Occupancy (VASO) contrast have shown higher spatial specificity compared to BOLD. To better understand the physiological mechanisms such as blood volume and oxygenation changes and to interpret the measured depth‐dependent responses, models are needed which reflect vascular properties at this scale. For this purpose, we extended and modified the “cortical vascular model” previously developed to predict layer‐specific BOLD signal changes in human primary visual cortex to also predict a layer‐specific VASO response. To evaluate the model, we compared the predictions with experimental results of simultaneous VASO and BOLD measurements in a group of healthy participants. Fitting the model to our experimental data provided an estimate of CBV change in different vascular compartments upon neural activity. We found that stimulus‐evoked CBV change mainly occurs in small arterioles, capillaries, and intracortical arteries and that the contribution from venules and ICVs is smaller. Our results confirm that VASO is less susceptible to large vessel effects compared to BOLD, as blood volume changes in intracortical arteries did not substantially affect the resulting depth‐dependent VASO profiles, whereas depth‐dependent BOLD profiles showed a bias towards signal contributions from intracortical veins.

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“…In recent years, the research field of layer-fMRI methods development has invested some efforts into laminar vascular deconvolution models (Markuerkiaga, Barth, and Norris 2016; Akbari et al 2021; Havlicek et al 2015; Heinzle et al 2016; Huber et al 2021). The purpose of these models is to account for unwanted venous biases of layer-fMRI signals in conventional gradient echo BOLD.…”

Section: Resultsmentioning

confidence: 99%

Acquisition and processing methods of whole-brain layer-fMRI VASO and BOLD: The Kenshu dataset

Koiso

Mueller

Akamatsu

et al. 2022

Preprint

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Cortical depth-dependent functional magnetic resonance image (fMRI), also known as layer-fMRI, has the potential to capture directional neural information flow of brain computations within and across large-scale cortical brain networks. E.g., layer-fMRI can differentiate feedforward and feedback cortical input in hierarchically organized brain networks. Recent advancements in 3D-EPI sampling approaches and MR contrast generation strategies have allowed proof-of-principle studies showing that layer-fMRI can provide sufficient data quality for capturing laminar changes in functional connectivity. These studies have however not shown how reliable the signal is and how repeatable the respective results are. It is especially unclear whether whole-brain layer-fMRI functional connectivity protocols are widely applicable across common neuroscience-driven analysis approaches. Moreover, there are no established preprocessing fMRI methods that are optimized to work for whole-brain layer-fMRI datasets. In this work, we aimed to serve the field of layer-fMRI and build tools for future routine whole-brain layer-fMRI in application-based neuroscience research. We have developed publicly available sequences, acquisition protocols, and processing pipelines for whole-brain layer-fMRI. These protocols are validated across 60 hours of scanning in nine participants. Specifically, we identified and exploited methodological advancements for maximizing tSNR efficiency and test-retest reliability. We are sharing an extensive multi-modal whole-brain layer-fMRI dataset (20 scan hours of movie-watching in a single participant) for the purpose of benchmarking future method developments: The Kenshu dataset. With this dataset, we are also exemplifying the usefulness of whole brain layer-fMRI for commonly applied analysis approaches in modern cognitive neuroscience fMRI studies. This includes connectivity analyses, representational similarity matrix estimations, general linear model analyses, principal component analysis clustering, etc. We believe that this work paves the road for future routine measurements of directional functional connectivity across the entire brain.

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Modelling the depth-dependent VASO and BOLD responses in human primary visual cortex

Cited by 7 publications

References 120 publications

Evaluating the capabilities and challenges of layer-fMRI VASO at 3T

Evaluating the capabilities and challenges of layer-fMRI VASO at 3T

Modelling the depth‐dependent VASO and BOLD responses in human primary visual cortex

Acquisition and processing methods of whole-brain layer-fMRI VASO and BOLD: The Kenshu dataset

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