327 research outputs found

    Physiological Gaussian Process Priors for the Hemodynamics in fMRI Analysis

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    Background: Inference from fMRI data faces the challenge that the hemodynamic system that relates neural activity to the observed BOLD fMRI signal is unknown. New Method: We propose a new Bayesian model for task fMRI data with the following features: (i) joint estimation of brain activity and the underlying hemodynamics, (ii) the hemodynamics is modeled nonparametrically with a Gaussian process (GP) prior guided by physiological information and (iii) the predicted BOLD is not necessarily generated by a linear time-invariant (LTI) system. We place a GP prior directly on the predicted BOLD response, rather than on the hemodynamic response function as in previous literature. This allows us to incorporate physiological information via the GP prior mean in a flexible way, and simultaneously gives us the nonparametric flexibility of the GP. Results: Results on simulated data show that the proposed model is able to discriminate between active and non-active voxels also when the GP prior deviates from the true hemodynamics. Our model finds time varying dynamics when applied to real fMRI data. Comparison with Existing Method(s): The proposed model is better at detecting activity in simulated data than standard models, without inflating the false positive rate. When applied to real fMRI data, our GP model in several cases finds brain activity where previously proposed LTI models does not. Conclusions: We have proposed a new non-linear model for the hemodynamics in task fMRI, that is able to detect active voxels, and gives the opportunity to ask new kinds of questions related to hemodynamics.Comment: 18 pages, 14 figure

    Fast joint detection-estimation of evoked brain activity in event-related fMRI using a variational approach

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    In standard clinical within-subject analyses of event-related fMRI data, two steps are usually performed separately: detection of brain activity and estimation of the hemodynamic response. Because these two steps are inherently linked, we adopt the so-called region-based Joint Detection-Estimation (JDE) framework that addresses this joint issue using a multivariate inference for detection and estimation. JDE is built by making use of a regional bilinear generative model of the BOLD response and constraining the parameter estimation by physiological priors using temporal and spatial information in a Markovian modeling. In contrast to previous works that use Markov Chain Monte Carlo (MCMC) techniques to approximate the resulting intractable posterior distribution, we recast the JDE into a missing data framework and derive a Variational Expectation-Maximization (VEM) algorithm for its inference. A variational approximation is used to approximate the Markovian model in the unsupervised spatially adaptive JDE inference, which allows fine automatic tuning of spatial regularisation parameters. It follows a new algorithm that exhibits interesting properties compared to the previously used MCMC-based approach. Experiments on artificial and real data show that VEM-JDE is robust to model mis-specification and provides computational gain while maintaining good performance in terms of activation detection and hemodynamic shape recovery

    Spatially Adaptive Mixture Modeling for Analysis of fMRI Time Series.

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    International audienceWithin-subject analysis in fMRI essentially addresses two problems, the detection of brain regions eliciting evoked activity and the estimation of the underlying dynamics. In [1, 2], a detection-estimation framework has been proposed to tackle these problems jointly, since they are connected to one another. In the Bayesian formalism, detection is achieved by modeling activating and non-activating voxels through independent mixture models (IMM) within each region while hemodynamic response estimation is performed at a regional scale in a nonparametric way. Instead of IMMs, in this paper we take advantage of spatial mixture models (SMM) for their non-linear spatial regularizing properties. The proposed method is unsupervised and spatially adaptive in the sense that the amount of spatial correlation is automatically tuned from the data and this setting automatically varies across brain regions. In addition, the level of regularization is specific to each experimental condition since both the signal-to-noise ratio and the activation pattern may vary across stimulus types in a given brain region. These aspects require the precise estimation of multiple partition functions of underlying Ising fields. This is addressed efficiently using first path sampling for a small subset of fields and then using a recently developed fast extrapolation technique for the large remaining set. Simulation results emphasize that detection relying on supervised SMM outperforms its IMM counterpart and that unsupervised spatial mixture models achieve similar results without any hand-tuning of the correlation parameter. On real datasets, the gain is illustrated in a localizer fMRI experiment: brain activations appear more spatially resolved using SMM in comparison with classical General Linear Model (GLM)-based approaches, while estimating a specific parcel-based HRF shape. Our approach therefore validates the treatment of unsmoothed fMRI data without fixed GLM definition at the subject level and makes also the classical strategy of spatial Gaussian filtering deprecated

    Group-level impacts of within- and between-subject hemodynamic variability in fMRI

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    International audienceInter-subject fMRI analyses have specific issues regarding the reliability of the results concerning both the detection of brain activation patterns and the estimation of the underlying dynamics. Among these issues lies the variability of the hemodynamic response function (HRF), that is usually accounted for using functional basis sets in the general linear model context. Here, we use the joint detection-estimation approach (JDE) (Makni et al., 2008; Vincent et al., 2010) which combines regional nonparametric HRF inference with spatially adaptive regularization of activation clusters to avoid global smoothing of fMRI images. We show that the JDE-based inference brings a significant improvement in statistical sensitivity for detecting evoked activity in parietal regions. In contrast, the canonical HRF associated with spatially adaptive regularization is more sensitive in other regions, such as motor cortex. This different regional behavior is shown to reflect a larger discrepancy of HRF with the canonical model. By varying parallel imaging acceleration factor, SNR-specific region-based hemodynamic parameters (activation delay and duration) were extracted from the JDE inference. Complementary analyses highlighted their significant departure from the canonical parameters and the strongest between-subject variability that occurs in the parietal region, irrespective of the SNR value. Finally, statistical evidence that the fluctuation of the HRF shape is responsible for the significant change in activation detection performance is demonstrated using paired t-tests between hemodynamic parameters inferred by GLM and JDE

    Subject-level Joint Parcellation-Detection-Estimation in fMRI

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    Brain parcellation is one of the most important issues in functional MRI (fMRI) data analysis. This parcellation allows establishing homogeneous territories that share the same functional properties. This paper presents a model-based approach to perform a subject-level parcellation into hemodynamic territories with similar hemodynamic features which are known to vary between brain regions. We specifically investigate the use of the Joint Parcellation-Detection-Estimation (JPDE) model initially proposed in [1] to separate brain regions that match different hemodynamic response function (HRF) profiles. A hierarchical Bayesian model is built and a variational expectation maximiza-tion (VEM) algorithm is deployed to perform inference. A more complete version of the JPDE model is detailed. Validation on synthetic data shows the robustness of this model to varying signal-to-noise ratio (SNR) as well as to different initializations. Our results also demonstrate that good parcellation performance is achieved even though the parcels do not involve the same amount of activation. On real fMRI data acquired in children during a language paradigm, we retrieved a parcellation along the superior temporal sulcus of the left hemisphere that matches the gradient of activation dynamics already reported in the literature

    Impact of the joint detection-estimation approach on random effects group studies in fMRI

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    International audienceInter-subject analysis of functional Magnetic Resonance Imaging (fMRI) data relies on single intra-subject studies, which are usually conducted using a massively univariate approach. In this paper, we investigate the impact of an improved intra-subject analysis on group studies. basically the joint detection-estimation (JDE) framework where an explicit characterization of the Hemodynamic Response Function (HRF) is performed at a regional scale and a stimulus-specific adaptive spatial correlation model enables the detection of activation clusters at voxel level. For the group statistics, we conducted several Random effect analyses (RFX) which relied either on the General Linear Model (GLM), or on the JDE analyses, or even on an intermediate approach named Spatially Adaptive GLM (SAGLM). Our comparative study perfomed during a fast-event related paradigm involves 18 subjects and illustrates the regionspecific differences between the GLM, SAGLM and JDE analyses in terms of statistical sensitivity. On different contrasts of interest, spatial regularization is shown to have a beneficial impact on the statistical sensitivity. Also, by studying the spatial variability of the HRF, we demonstrate that the JDE framework provides more robust detection performance in cognitive regions due to the higher hemodynamic variability in these areas

    Hemodynamic-informed parcellation of fMRI data in a Joint Detection Estimation framework

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    International audienceIdentifying brain hemodynamics in event-related functional MRI (fMRI) data is a crucial issue to disentangle the vascular response from the neuronal activity in the BOLD signal. This question is usually addressed by estimating the so-called Hemodynamic Response Function (HRF). Voxelwise or region-/parcelwise inference schemes have been proposed to achieve this goal but so far all known contributions commit to pre-specified spatial supports for the hemodynamic territories by defining these supports either as individual voxels or a priori fixed brain parcels. In this paper, we introduce a Joint Parcellation-Detection-Estimation (JPDE) procedure that incorporates an adaptive parcel identification step based upon local hemodynamic properties. Efficient inference of both evoked activity, HRF shapes and supports is then achieved using variational approximations. Validation on synthetic and real fMRI data demonstrate the JPDE performance over standard detection estimation schemes and suggest it as a new brain exploration tool

    Application and validation of spatial mixture modelling for the joint detection-estimation of brain activity in fMRI.

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    International audienceWithin-subject analysis in event-related functional Magnetic Resonance Imaging (fMRI) first relies on (i) a detection step to localize which parts of the brain are activated by a given stimulus type, and second on (ii) an estimation step to recover the temporal dynamics of the brain response. Recently, a Bayesian detection-estimation approach that jointly addresses (i)-(ii) has been proposed in [1]. This work is based on an independent mixture model (IMM) and provides both a spatial activity map and an estimate of brain dynamics. In [2], we accounted for spatial correlation using a spatial mixture model (SMM) based on a binary Markov random field. Here, we assess the SMM robustness and flexibility on simulations which diverge from the priors and the generative BOLD model and further extend comparison between SMM and IMM on real fMRI data, focusing on a region of interest in the auditory cortex
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