scholarly journals Correcting for Superficial Bias in 7T Gradient Echo fMRI

2021 ◽  
Vol 15 ◽  
Author(s):  
Pei Huang ◽  
Marta M. Correia ◽  
Catarina Rua ◽  
Christopher T. Rodgers ◽  
Richard N. Henson ◽  
...  
Keyword(s):  
Blood Oxygenation ◽  
Fmri Data ◽  
Bold Signal ◽  
Gradient Echo ◽  
Cortical Layers ◽  
Ultra High Field ◽  
Additional Advantage ◽  
Deming Regression ◽  
Oxygenation Level ◽  
7T Fmri

The arrival of submillimeter ultra high-field fMRI makes it possible to compare activation profiles across cortical layers. However, the blood oxygenation level dependent (BOLD) signal measured by gradient echo (GE) fMRI is biased toward superficial layers of the cortex, which is a serious confound for laminar analysis. Several univariate and multivariate analysis methods have been proposed to correct this bias. We compare these methods using computational simulations of 7T fMRI data from regions of interest (ROI) during a visual attention paradigm. We also tested the methods on a pilot dataset of human 7T fMRI data. The simulations show that two methods–the ratio of ROI means across conditions and a novel application of Deming regression–offer the most robust correction for superficial bias. Deming regression has the additional advantage that it does not require that the conditions differ in their mean activation over voxels within an ROI. When applied to the pilot dataset, we observed strikingly different layer profiles when different attention metrics were used, but were unable to discern any differences in laminar attention across layers when Deming regression or ROI ratio was applied. Our simulations demonstrates that accurate correction of superficial bias is crucial to avoid drawing erroneous conclusions from laminar analyses of GE fMRI data, and this is affirmed by the results from our pilot 7T fMRI data.

scholarly journals Correcting for Superficial Bias in 7T Gradient Echo fMRI

2020 ◽  
Author(s):  
Pei Huang ◽  
Marta M. Correia ◽  
Catarina Rua ◽  
Christopher T. Rodgers ◽  
Richard N. Henson ◽  
...  
Keyword(s):  
Blood Oxygenation ◽  
Fmri Data ◽  
Gradient Echo ◽  
Cortical Layers ◽  
Visual Stream ◽  
Additional Advantage ◽  
Deming Regression ◽  
Oxygenation Level ◽  
Ventral Visual Stream ◽  
7T Fmri

1AbstractThe arrival of submillimetre ultra high-field fMRI makes it possible to compare activation profiles across cortical layers. However, the Blood Oxygenation Level Dependent (BOLD) signal measured by Gradient-Echo fMRI is biased towards superficial layers of the cortex, which is a serious confound for laminar analysis. Several univariate and multivariate analysis methods have been proposed to correct this bias. We compare these methods using computational simulations and example human 7T fMRI data from Regions-of-Interest (ROIs) during a visual attention paradigm. The simulations show that two methods - the ratio of ROI means across conditions and a novel application of Deming regression - offer the most robust correction for superficial bias. Deming regression has the additional advantage that it does not require that the conditions differ in their mean activation over voxels within an ROI. When applied to the example dataset, these methods suggest that attentional modulation of activation is similar across cortical layers within the ventral visual stream, despite a naïve activation-based analysis producing stronger modulation in superficial layers. Our study demonstrates that accurate correction of superficial bias is crucial to avoid drawing erroneous conclusions from laminar analyses of Gradient-Echo fMRI data.

scholarly journals Validating Linear Systems Analysis for Laminar fMRI: Temporal Additivity for Stimulus Duration Manipulations

2020 ◽  
Author(s):  
Jelle A. van Dijk ◽  
Alessio Fracasso ◽  
Natalia Petridou ◽  
Serge O. Dumoulin
Keyword(s):  
Systems Theory ◽  
Linear Systems ◽  
Blood Oxygenation ◽  
Ultra High Field ◽  
Feedback Information ◽  
Oxygenation Level ◽  
Early Visual Cortex ◽  
Magnetic Resonance Imaging Mri ◽  
And Function ◽  
The Relationship

AbstractAdvancements in ultra-high field (7 T and higher) magnetic resonance imaging (MRI) scanners have made it possible to investigate both the structure and function of the human brain at a sub-millimeter scale. As neuronal feedforward and feedback information arrives in different layers, sub-millimeter functional MRI has the potential to uncover information processing between cortical micro-circuits across cortical depth, i.e. laminar fMRI. For nearly all conventional fMRI analyses, the main assumption is that the relationship between local neuronal activity and the blood oxygenation level dependent (BOLD) signal adheres to the principles of linear systems theory. For laminar fMRI, however, directional blood pooling across cortical depth stemming from the anatomy of the cortical vasculature, potentially violates these linear system assumptions, thereby complicating analysis and interpretation. Here we assess whether the temporal additivity requirement of linear systems theory holds for laminar fMRI. We measured responses elicited by viewing stimuli presented for different durations and evaluated how well the responses to shorter durations predicted those elicited by longer durations. We find that BOLD response predictions are consistently good predictors for observed responses, across all cortical depths, and in all measured visual field maps (V1, V2, and V3). Our results suggest that the temporal additivity assumption for linear systems theory holds for laminar fMRI. We thus show that the temporal additivity assumption holds across cortical depth for sub-millimeter gradient-echo BOLD fMRI in early visual cortex.

Coherent Spontaneous Activity Identifies a Hippocampal-Parietal Memory Network

2006 ◽  
Vol 96 (6) ◽  
pp. 3517-3531 ◽  
Author(s):  
Justin L. Vincent ◽  
Abraham Z. Snyder ◽  
Michael D. Fox ◽  
Benjamin J. Shannon ◽  
Jessica R. Andrews ◽  
...  
Keyword(s):  
Parietal Cortex ◽  
Hippocampal Formation ◽  
Normal Subjects ◽  
Blood Oxygenation Level Dependent ◽  
Retrosplenial Cortex ◽  
Blood Oxygenation ◽  
Bold Signal ◽  
Inferior Parietal Lobule ◽  
Oxygenation Level ◽  
Memory Network

Despite traditional theories emphasizing parietal contributions to spatial attention and sensory-motor integration, functional MRI (fMRI) experiments in normal subjects suggest that specific regions within parietal cortex may also participate in episodic memory. Here we examined correlations in spontaneous blood-oxygenation-level-dependent (BOLD) signal fluctuations in a resting state to identify the network associated with the hippocampal formation (HF) and determine whether parietal regions were elements of that network. In the absence of task, stimuli, or explicit mnemonic demands, robust correlations were observed between activity in the HF and several parietal regions (including precuneus, posterior cingulate, retrosplenial cortex, and bilateral inferior parietal lobule). These HF-correlated regions in parietal cortex were spatially distinct from those correlated with the motion-sensitive MT+ complex. Reanalysis of event-related fMRI studies of recognition memory showed that the regions spontaneously correlated with the HF (but not MT+) were also modulated during directed recollection. These regions showed greater activity to successfully recollected items as compared with other trial types. Together, these results associate specific regions of parietal cortex that are sensitive to successful recollection with the HF.

scholarly journals Dynamic Forcing of End-Tidal Carbon Dioxide and Oxygen Applied to Functional Magnetic Resonance Imaging

2007 ◽  
Vol 27 (8) ◽  
pp. 1521-1532 ◽  
Author(s):  
Richard G Wise ◽  
Kyle TS Pattinson ◽  
Daniel P Bulte ◽  
Peter A Chiarelli ◽  
Stephen D Mayhew ◽  
...  
Keyword(s):  
Carbon Dioxide ◽  
Blood Oxygenation ◽  
Dynamic Responses ◽  
Bold Signal ◽  
Tidal Forcing ◽  
Partial Pressures ◽  
Oxygenation Level ◽  
Mri Environment ◽  
Dynamic Forcing ◽  
End Tidal

Investigations into the blood oxygenation level-dependent (BOLD) functional MRI signal have used respiratory challenges with the aim of probing cerebrovascular physiology. Such challenges have altered the inspired partial pressures of either carbon dioxide or oxygen, typically to a fixed and constant level (fixed inspired challenge (FIC)). The resulting end-tidal gas partial pressures then depend on the subject's metabolism and ventilatory responses. In contrast, dynamic end-tidal forcing (DEF) rapidly and independently sets end-tidal oxygen and carbon dioxide to desired levels by altering the inspired gas partial pressures on a breath-by-breath basis using computer-controlled feedback. This study implements DEF in the MRI environment to map BOLD signal reactivity to CO2. We performed BOLD (T2*) contrast FMRI in four healthy male volunteers, while using DEF to provide a cyclic normocapnichypercapnic challenge, with each cycle lasting 4 mins (PetCO2 mean±s.d., from 40.9 ± 1.8 to 46.4 ± 1.6 mm Hg). This was compared with a traditional fixed-inspired (FiCO2 = 5%) hypercapnic challenge (PetCO2 mean±s.d., from 38.2 ± 2.1 to 45.6 ± 1.4 mm Hg). Dynamic end-tidal forcing achieved the desired target PetCO2 for each subject while maintaining PetCO2 constant. As a result of CO2-induced increases in ventilation, the FIC showed a greater cyclic fluctuation in PetCO2. These were associated with spatially widespread fluctuations in BOLD signal that were eliminated largely by the control of PetCO2 during DEF. The DEF system can provide flexible, convenient, and physiologically well-controlled respiratory challenges in the MRI environment for mapping dynamic responses of the cerebrovasculature.

A NEW MATHEMATICAL APPROACH FOR DETECTION OF ACTIVE AREA IN HUMAN BRAIN fMRI USING NONLINEAR MODEL

2010 ◽  
Vol 22 (05) ◽  
pp. 409-418 ◽  
Author(s):  
Ali Taalimi ◽  
Emad Fatemizadeh
Keyword(s):  
Moving Average ◽  
Simulated Data ◽  
Nonlinear Behavior ◽  
Blood Oxygenation ◽  
Superior Performance ◽  
Model Parameters ◽  
Bold Signal ◽  
Mathematical Approach ◽  
Region Detection ◽  
Oxygenation Level

Functional magnetic resonance imaging (fMRI) is widely-used for detection of the brain's neural activity. The signals and images acquired through this imaging technique demonstrate the human brain's response to pre-scheduled tasks. Several studies on blood oxygenation level-dependent (BOLD) signal responses demonstrate nonlinear behavior in response to a stimulus. In this paper we propose a new mathematical approach for modeling BOLD signal activity, which is able to model nonlinear and time variant behaviors of this physiological system. We employ the Nonlinear Auto Regressive Moving Average (NARMA) model to describe the mathematical relationship between output signals and predesigned tasks. The model parameters can be used to distinguish between rest and active states of a brain region. We applied our proposed method for active region detection on real as well as simulated data sets. The results show superior performance in comparison with existing methods.

Widespread and intense BOLD changes during brief focal electrographic seizures

Neurology ◽  
2006 ◽  
Vol 66 (7) ◽  
pp. 1049-1055 ◽  
Author(s):  
E. Kobayashi ◽  
C. S. Hawco ◽  
C. Grova ◽  
F. Dubeau ◽  
J. Gotman
Keyword(s):  
Blood Oxygenation Level Dependent ◽  
Blood Oxygenation ◽  
Angular Gyrus ◽  
Temporal Region ◽  
Bold Signal ◽  
Hemodynamic Response Function ◽  
Focal Seizures ◽  
Blood Oxygenation Level ◽  
Oxygenation Level ◽  
Electrographic Seizures

Background: Combined recording of EEG and fMRI has shown changes in blood oxygenation level dependent (BOLD) signal during focal interictal epileptic spikes. Due to difficult assessment of seizures inside the scanner little is known about BOLD changes during seizures.Objectives: To describe BOLD changes related to brief focal electrographic seizures in a patient with right temporo-parietal gray matter nodular heterotopia.Methods: The patient underwent two EEG-fMRI sessions during which several focal seizures were recorded. EEG was acquired continuously during scanning and seizure timing was used for statistical analysis. Functional maps were thresholded to disclose positive (activation) and negative (deactivation) BOLD changes.Results: Twenty-five focal electrographic seizures were analyzed, consisting of runs of polyspikes lasting 2 to 6 s in the right temporal region. Activation included a large volume, involving the heterotopia and the abnormal temporo-parietal cortex overlying the nodule, with a clear maximum over the angular gyrus. Deactivation was bilateral and maximum in the occipital regions. The hemodynamic response function showed a return to baseline of the BOLD signal 30 s after seizure end.Conclusions: The brief focal seizures resulted in high amplitude and widespread blood oxygenation level dependent (BOLD) responses taking 30 s to return to baseline. This suggests that such brief events could have important behavioral consequences despite absent overt manifestations. A clear focal BOLD peak was found at some distance from the main EEG discharge, raising the possibility that the seizure could have started in a region that did not generate a visible EEG change despite its superficial location.

scholarly journals Diffusion-Informed Spatial Smoothing of fMRI Data in White Matter Using Spectral Graph Filters

2020 ◽  
Author(s):  
David Abramian ◽  
Martin Larsson ◽  
Anders Eklund ◽  
Iman Aganj ◽  
Carl-Fredrik Westin ◽  
...  
Keyword(s):  
White Matter ◽  
Blood Oxygenation ◽  
Fmri Data ◽  
Bold Signal ◽  
Spatial Filters ◽  
Gaussian Filters ◽  
Temporal Correlations ◽  
Spatial Correlation Structure ◽  
Spatio Temporal ◽  
Activation Mapping

AbstractBrain activation mapping using functional magnetic resonance imaging (fMRI) has been extensively studied in brain gray matter (GM), whereas in large disregarded for probing white matter (WM). This unbalanced treatment has been in part due to controversies in relation to the nature of the blood oxygenation level-dependent (BOLD) contrast in WM and its detachability. However, an accumulating body of studies has provided solid evidence of the functional significance of the BOLD signal in WM and has revealed that it exhibits anisotropic spatio-temporal correlations and structure-specific fluctuations concomitant with those of the cortical BOLD signal. In this work, we present an anisotropic spatial filtering scheme for smoothing fMRI data in WM that accounts for known spatial constraints on the BOLD signal in WM. In particular, the spatial correlation structure of the BOLD signal in WM is highly anisotropic and closely linked to local axonal structure in terms of shape and orientation, suggesting that isotropic Gaussian filters conventionally used for smoothing fMRI data are inadequate for denoising the BOLD signal in WM. The fundamental element in the proposed method is a graph-based description of WM that encodes the underlying anisotropy observed across WM, derived from diffusion-weighted MRI data. Based on this representation, and leveraging graph signal processing principles, we design subject-specific spatial filters that adapt to a subject’s unique WM structure at each position in the WM that they are applied at. We use the proposed filters to spatially smooth fMRI data in WM, as an alternative to the conventional practice of using isotropic Gaussian filters. We test the proposed filtering approach on two sets of phantoms, showcasing its greater sensitivity and specificity for the detection of slender anisotropic activations, compared to that achieved with isotropic Gaussian filters. We also present WM activation mapping results on the Human Connectome Project’s 100-unrelated subject dataset, across seven functional tasks, showing the capacity of the proposed method for detecting streamline-like activations within axonal bundles.

Optogenetic fMRI Sheds Light on the Neural Basis of the BOLD Signal

2010 ◽  
Vol 104 (4) ◽  
pp. 1838-1840 ◽  
Author(s):  
Helen. S. Palmer
Keyword(s):  
Magnetic Resonance Imaging ◽  
Blood Oxygenation Level Dependent ◽  
Blood Oxygenation ◽  
Bold Signal ◽  
Functional Magnetic Resonance ◽  
Resonance Imaging ◽  
Neural Basis ◽  
Bold Responses ◽  
Blood Oxygenation Level ◽  
Oxygenation Level

Blood oxygenation level dependent (BOLD) functional magnetic resonance imaging (fMRI) is widely used as a measure of neuronal activity, despite an incomplete understanding of the hemodynamic and neural bases for BOLD signals. Recent work by Lee and colleagues investigated whether activating genetically specified neurons elicits BOLD responses. Integrating optogenetic control of specific cells and fMRI showed that stimulating excitatory neurons triggers a positive BOLD signal with conventional kinetics locally and delayed weaker BOLD signals distally.

Representation of Umami Taste in the Human Brain

2003 ◽  
Vol 90 (1) ◽  
pp. 313-319 ◽  
Author(s):  
I.E.T. de Araujo ◽  
M. L. Kringelbach ◽  
E. T. Rolls ◽  
P. Hobden
Keyword(s):  
Orbitofrontal Cortex ◽  
Anterior Part ◽  
Monosodium Glutamate ◽  
Blood Oxygenation ◽  
Anterior Cingulate ◽  
Bold Signal ◽  
Taste System ◽  
Umami Taste ◽  
Oxygenation Level ◽  
Cortical Regions

Umami taste stimuli, of which an exemplar is monosodium glutamate (MSG) and which capture what is described as the taste of protein, were shown using functional MRI (fMRI) to activate similar cortical regions of the human taste system to those activated by a prototypical taste stimulus, glucose. These taste regions included the insular/opercular cortex and the caudolateral orbitofrontal cortex. A part of the rostral anterior cingulate cortex (ACC) was also activated. When the nucleotide 0.005 M inosine 5′-monophosphate (IMP) was added to MSG (0.05 M), the blood oxygenation-level dependent (BOLD) signal in an anterior part of the orbitofrontal cortex showed supralinear additivity; this may reflect the subjective enhancement of umami taste that has been described when IMP is added to MSG. These results extend to humans previous studies in macaques showing that single neurons in these taste cortical areas can be tuned to umami stimuli.

scholarly journals Simultaneous Blood Oxygenation Level-Dependent and Cerebral Blood Flow Functional Magnetic Resonance Imaging during Forepaw Stimulation in the Rat

1999 ◽  
Vol 19 (8) ◽  
pp. 871-879 ◽  
Author(s):  
Afonso C. Silva ◽  
Sang-Pil Lee ◽  
Guang Yang ◽  
Costantino Iadecola ◽  
Seong-Gi Kim
Keyword(s):  
Correlation Coefficient ◽  
Cerebral Blood Volume ◽  
Blood Oxygenation Level Dependent ◽  
Blood Oxygenation ◽  
Single Shot ◽  
Bold Signal ◽  
Doppler Flowmetry ◽  
Blood Oxygenation Level ◽  
Oxygenation Level ◽  
Signal Changes

The blood oxygenation level-dependent (BOLD) contrast mechanism can be modeled as a complex interplay between CBF, cerebral blood volume (CBV), and CMRO2. Positive BOLD signal changes are presumably caused by CBF changes in excess of increases in CMRO2. Because this uncoupling between CBF and CMRO2 may not always be present, the magnitude of BOLD changes may not be a good index of CBF changes. In this study, the relation between BOLD and CBF was investigated further. Continuous arterial spin labeling was combined with a single-shot, multislice echo-planar imaging to enable simultaneous measurements of BOLD and CBF changes in a well-established model of functional brain activation, the electrical forepaw stimulation of a-chloralose-anesthetized rats. The paradigm consisted of two 18- to 30-second stimulation periods separated by a 1-minute resting interval. Stimulation parameters were optimized by laser Doppler flowmetry. For the same cross-correlation threshold, the BOLD and CBF active maps were centered within the size of one pixel (470 µm). However, the BOLD map was significantly larger than the CBF map. Measurements taken from 15 rats at 9.4 T using a 10-millisecond echo-time showed 3.7 ± 1.7% BOLD and 125.67 ± 81.7% CBF increases in the contralateral somatosensory cortex during the first stimulation, and 2.6 ± 1.2% BOLD and 79.3 ± 43.6% CBF increases during the second stimulation. The correlation coefficient between BOLD and CBF changes was 0.89. The overall temporal correlation coefficient between BOLD and CBF time-courses was 0.97. These results show that under the experimental conditions of the current study, the BOLD signal changes follow the changes in CBF.

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