Functional magnetic resonance imaging (fMRI) simulator

Arslankoz, Kamil
Functional magnetic resonance imaging (fMRI) utilizes the change in the oxygenation of blood to predict active areas in the brain. fMRI consists of multiple low resolution whole brain images, for which, the contrast difference in corresponding voxels among all images are studied. In this study, an fMRI simulator has been developed which generates customized 4D fMRI data that can be used as a ground truth for comparing/benchmarking different fMRI analysis methods. This simulator can be also used for educational purposes for hands-on study of several aspects of the fMRI time series. Some of the strengths of this simulator with respect to other simulators are as follows. The simulator is programmed in MATLAB and it contains a GUI which facilitates its use. It allows an atlas (ICBM) to generate multiple brain activations within pre-defined anatomical structures. It utilizes T2 MRI images to construct task related (event/block/mixed paradigms) or DMN (Default Mode Network) 4D fMRI data. It is capable of simulating the effects of head movement, habituation, scanner drift and Gaussian noise. The simulator completes realistic fMRI data generation on the order of minutes. The results produced by the simulator are analyzed by popular fMRI analysis tools, FSL and AFNI. The estimation of brain activations and the prediction of the embodied artifacts by FSL and AFNI matched the simulation parameters with great certainty, verifying the quality of the simulations.


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Citation Formats
K. Arslankoz, “Functional magnetic resonance imaging (fMRI) simulator,” M.S. - Master of Science, Middle East Technical University, 2015.