Functional Magnetic Resonance Imaging

Functional Magnetic Resonance Imaging (fMRI) maps brain activity by detecting changes in image intensity related to neural activity by the blood oxygenation level–dependent (BOLD) contrast. Functional MRI data essentially consist of time series of 3D images associated with a description of the experimental conditions. The chapter outlines an analysis pipeline for functional Magnetic Resonance Imaging (fMRI) experiments completely based on R packages. Thereby, we focus on a single-subject analysis with the full pipeline of data pre-processing, the General Linear Model, and inference with correction for the multiplicity of the statistical tests. Part of the chapter elaborates on the use of structural adaptive smoothing procedure in fMRI, which we specifically developed. We also include alternative fMRI analysis methods, i.e., other than the mass-univariate approach. The chapter concludes with a section on functional connectivity.