A simulation toolbox for fMRI data: SimTB

Update: both papers have been published, simulation toolbox and inter-subject variability.

Elena Allen and I recently submitted two papers that detail a simulation toolbox for fMRI data (SimTB) and capturing inter-subject variability with group independent component analysis (ICA) using simulations. It’s been an exciting and interesting project because we can at last generate interesting and complex datasets to use as a “ground truth” to compare estimation and processing techniques.  We’ve learned a lot about the limits of some methods, as well as their robustness.  The papers will be submitted next week.  For those with MATLAB, it’s available at http://mialab.mrn.org/software.

SimTB, a simulation toolbox for fMRI data under a model of spatiotemporal separability
EB Erhardt, EA Allen, Y Wei, T Eichele, VD Calhoun. (2011)

We introduce SimTB, a MATLAB toolbox designed to simulate functional magnetic resonance imaging (fMRI) datasets under a model of spatiotemporal separability. The toolbox meets the increasing need of the fMRI community to more comprehensively understand the effects of complex processing strategies by providing a ground truth that estimation methods may be compared against. SimTB captures the fundamental structure of real data, but data generation is fully parameterized and fully controlled by the user, allowing for accurate and precise comparisons. The toolbox offers a wealth of options regarding the number and configuration of spatial sources, implementation of experimental paradigms, inclusion of tissue-specific properties, addition of noise and head movement, and much more. A straightforward data generation method and short computation time (3-10 seconds for each dataset) allow a practitioner to simulate and analyze many datasets to potentially understand a problem from many angles. Beginning MATLAB users can use the SimTB graphical user interface (GUI) to design and execute simulations while experienced users can write batch scripts to automate and customize this process. The toolbox is freely available at http://mialab.mrn.org/software together with sample scripts and tutorials.

Capturing inter-subject variability with group independent component analysis of fMRI data: a simulation study
EA Allen, EB Erhardt, Y Wei, T Eichele, VD Calhoun. (2011)

A key challenge in functional neuroimaging is the meaningful combination of results across subjects. Even in a sample of healthy participants, brain morphology and functional organization exhibit considerable variability, such that no two individuals have the same neural activation at the same location in response to the same stimulus. This inter-subject variability limits inferences at the group-level as average activation patterns may fail to represent the patterns seen in individuals. A promising approach to multi-subject analysis is group independent components analysis (GICA), which identities group components and reconstructs activations at the individual level. GICA has gained considerable popularity, particularly in studies where temporal response models cannot be speci ed. However, a comprehensive understanding of the performance of GICA under realistic conditions of inter-subject variability is lacking. In this study we use simulated functional magnetic resonance imaging (fMRI) data to determine the capabilities and limitations of GICA under conditions of spatial, temporal, and amplitude variability. Simulations, generated with the SimTB toolbox, address questions that commonly arise in GICA studies, such as: (1) How well can individual subject activations be estimated and when will spatial variability preclude estimation? (2) Why does component splitting occur and how is it a ected by model order? (3) How should we analyze component features to maximize sensitivity to intersubject differences? Overall, our results indicate an excellent capability of GICA to capture between-subject differences and we make a number of recommendations regarding analytic choices for application to functional imaging data.

SimTB flowchart for simulation of fMRI data

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