BACKGROUND: Dynamic causal modeling (DCM) for fMRI is an established method for Bayesian system identification and inference on effective brain connectivity. DCM relies on a biophysical model that links hidden neuronal activity to measurable BOLD signals. Currently, biophysical simulations from DCM constitute a serious computational hindrance. Here, we present Massively Parallel Dynamic Causal Modeling (mpdcm), a toolbox designed to address this bottleneck.
NEW METHOD: mpdcm delegates the generation of simulations from DCM's biophysical model to graphical processing units (GPUs). Simulations are generated in parallel by implementing a low storage explicit Runge-Kutta's scheme on a GPU architecture. mpdcm is publicly available under the GPLv3 license.
RESULTS: We found that mpdcm efficiently generates large number of simulations without compromising their accuracy. As applications of mpdcm, we suggest two computationally expensive sampling algorithms: thermodynamic integration and parallel tempering.
COMPARISON WITH EXISTING METHOD(S): mpdcm is up to two orders of magnitude more efficient than the standard implementation in the software package SPM. Parallel tempering increases the mixing properties of the traditional Metropolis-Hastings algorithm at low computational cost given efficient, parallel simulations of a model.
CONCLUSIONS: Future applications of DCM will likely require increasingly large computational resources, for example, when the likelihood landscape of a model is multimodal, or when implementing sampling methods for multi-subject analysis. Due to the wide availability of GPUs, algorithmic advances can be readily available in the absence of access to large computer grids, or when there is a lack of expertise to implement algorithms in such grids.
- Access to Information
- Bayes Theorem
- Brain Mapping
- Cerebrovascular Circulation
- Computer Graphics
- Computer Simulation
- Magnetic Resonance Imaging
- Neurological Models
- Statistical Models
- Computer-Assisted Signal Processing
- Comparative Study
- School of Psychology - Professor in Psychology
- Centre for Behavioural and Experimental Social Science
Person: Research Group Member, Academic, Teaching & Research