Team, Visitors, External Collaborators
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New Software and Platforms
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Section: New Software and Platforms

BOLD model FIT

Keywords: Functional imaging - FMRI - Health

Scientific Description: Physiological and biophysical models have been proposed to link neuronal activity to the Blood Oxygen Level-Dependent (BOLD) signal in functional MRI (fMRI). Those models rely on a set of parameter values that are commonly estimated using gradient-based local search methods whose initial values are taken from the literature. In some applications, interesting insight into the brain physiology or physiopathology can be gained from an estimation of the model parameters from measured BOLD signals. In this work we focus on the extended Balloon model and propose the estimation of 15 parameters using seven different approaches: three versions of the Expectation Maximization Gauss-Newton (EM/GN) approach (the de facto standard in the neuroscientific community) and four metaheuristics (Particle Swarm Optimization (PSO), Differential Evolution (DE), Real-Coded Genetic Algorithms (GA), and a Memetic Algorithm (MA) combining EM/GN and DE). To combine both the ability to escape local optima and to incorporate prior knowledge, we derive the target function from Bayesian modeling. The general behavior of these algorithms is analyzed and compared, providing very promising results on challenging real and synthetic fMRI data sets involving rats with epileptic activity. These stochastic optimizers provided a better performance than EM/GN in terms of distance to the ground truth in 4 out of 6 synthetic data sets and a better signal fitting in 12 out of 12 real data sets. Non-parametric statistical tests showed the existence of statistically significant differences between the real data results obtained by DE and EM/GN. Finally, the estimates obtained from DE for these parameters seem both more realistic and more stable or at least as stable across sessions as the estimates from EM/GN. This is the largest comparison of optimizers for the estimation of biophysical parameters in BOLD fMRI

Functional Description: This Matlab toolbox performs the automatic estimation of biophysical parameters using the extended Balloon model and BOLD fMRI data. It takes as input a MAT file and provides as output the parameter estimates achieved by using stochastic optimization

News Of The Year: The main differences with our previous work: 1) we also use synthetic data, 2) we use stochastic GN and MCMC+DE, 3) We evaluate results not only in physiological terms but also comparing fitness function values. Also changes were made to allow running on the cluster via MPI