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.
Statistical Analysis Methods
At the pre-processing stages, the quality of the fMR images is improved. After that,
statistical analysis is attempted to determine which voxels are activated by the
stimulation. Most fMRI studies are established upon the correlation of
hemodynamic response function with stimulation. Activation defines the local
intensity changes in the images. These methods can be grouped into two broad
categories: the univariate methods (hypothesis testing methods), and the
multivariate methods (exploratory methods).
The univariate methods attempt to define which voxels can be characterized as
activated given one signal model. This allows the parameterization of the response
and then the estimation of the model parameters. The univariate methods are
widely used to analyze brain images obtained from fMR imaging. In these methods,
signal estimation and the presence or the absence of activation are defined by the
statistical test. One of the typical methods is Statistic Parametric Mapping (SPM),
which is based upon the hypothesis of linear correlation between neuro-activities
and the tasks.
Multivariate methods are also applied to fMRI data analysis, which extract
information from dataset, often with any prior knowledge of the experimental
conditions. They use some structural properties, such as decorrelation,
independence, similarity measures, that can discriminate between features of
interest present in the data. Unlike the univariate methods which carry out voxelwise statistical analysis, multivariate methods provide statistical inference about
the whole brain so as to describe brain responses in terms of spatial patterns. A
wide range of multivariate statistical methods is being increasingly employed to
analyze the fMRI time series. fMRI data are essentially multi-variate in nature, since
information about thousands of measured locations (voxels) are being impacted in
each scan. The univariate or voxel based analysis approaches have been
traditionally used to analyze neuroimaging data.
The vast majority of fMRI data analysis techniques employed by neuroscientists use
a GLM. The GLM is one of the most common approaches in fMRI statistical analysis
which is the construction of a model that describes the way in which the BOLD
response depends on the stimulus. In general linear modeling first a model must
be set up and then this model has to be fit to the data.
How is fMRI data processed? Preprocessing of raw fMRI data involves recognition
of outlier data followed by multiple steps to correct for noise, motion, signal drifts,
slice timing discrepancies, and spatial distortions.
Does fMRI measure blood flow? Functional magnetic resonance imaging (fMRI)
uses MR imaging to measure the tiny changes in blood flow that take place in an
active part of the brain.
