After designing an fMRI paradigm and running the experiment and the data
collection, various analysis steps must be applied on resulting data before the
neuroscientists and physicians can achieve answers to the questions about
activities corresponding to the experiment. The goal of computer-based analysis is
to determine automatically, those parts of the brain which respond to stimuli that
presented to the subjects. The fMRI analysis methods are composed of several
basic stages: Pre-processing, signal detection and description and extraction of the
brain connectivity.
The goal of preprocessing is to eliminate different kinds of artifacts such as motion
correction. Pre-processing consist of spatial or temporal filtering of fMRI data and
improving the image resolution.After preprocessing, signal detection is carried out.
The purpose of signal detection is to determine which voxels are activated by the
stimulation and it is commonly achieved by applying a test statistic. The output of
this stage is an activation map which indicates those parts of brain which have been
activated in response to the stimulus. The purpose of signal description is modeling
the BOLD response shape by several parameters and relating these parameters to
the description of the stimulation context. Finally, the connectivity analysis tries to
estimate brain networks. Before statistical analysis and signal detection, it is
necessary to improve the signal quality by preprocessing the raw data obtained
from the MRI scanner, including artifact detection, baseline correction, movement
correction, and image restoration. The pre-processing step applies different image
and signal processing techniques to reduce the noise and the artifacts of the raw
fMRI data. The pre-processing steps are applied individually in particular orders to
the fMRI data.
Nearly all fMRI data are collected using two-dimensional MRI acquisition, in which
the data are acquired one slice at a time, with the timing of the slice acquisition
evenly spread over the repetition time (TR). In some cases, the slices are acquired
in ascending or descending order. In another known method as interleaved
acquisition, every other slice is acquired sequentially. These differences in the
acquisition time of different voxels are problematic for the analysis of fMRI data.
The goal of slice timing correction is to adjust the voxel time series so that common
reference timing exists for all voxels. The time corresponding to the first slice is
often chosen to be the reference.
What does fMRI directly measure? Functional magnetic resonance imaging or
functional MRI (fMRI) measures brain activity by detecting changes associated with
blood flow. This technique relies on the fact that cerebral blood flow and neuronal
activation are coupled. When an area of the brain is in use, blood flow to that region
also increases.