Data Analysis Lab

Data Analysis

Available Software


AFNI is a collection of command-line programs for processing and analyzing functional MRI data. Primarily designed for command-line use, it has a simple GUI viewer for visualizing activation maps and time series and runs best in Linux.


Developed at the University of Minnesota, eConnectome (Electrophysiological Connectome) is a MATLAB toolbox for imaging brain functional connectivity from electrophysiological signal. It provides interactive graphical interfaces for EEG/ECoG/MEG preprocessing, source estimation, connectivity analysis and visualization.

Egg LabEEGLab

A full-featured MATLAB toolbox for processing and analyzing EEG and MEG data. It includes a user-friendly GUI and a variety of visualization tools, and lends itself to complex scripting. In addition to typical averaging approaches, EEGLAB also includes functions for ICA and time/frequency analysis.

Field TripFieldtrip

A MATLAB toolbox for analysis of EEG, MEG, and other electrophysiological data. It has capabilities for time-frequency analysis, source reconstruction using dipoles, distributed sources and beamformers, and non-parametric statistical testing, in addition to a variety of signal processing tools.


A set of automated tools for reconstruction of the brain’s cortical surface from structural MRI data, and overlay of functional MRI data onto the reconstructed surface. It has functions for skull stripping, nonlinear registration, surface region labeling, labeling of subcortical structures, statistical analysis of group morphometry differences, and more. It is primarily a command-line tool and runs on Linux and Mac.


One of the most popular software suites for the analysis of MR data (including structural MRI, fMRI, and DTI). Developed at Oxford, it has a robust point-and-click GUI as well as command-line scripting capabilities. FSL runs on Linux, Mac, and Windows.


MATLAB is a computing environment for numerical analysis and engineering. It includes a simple language for scripting tasks and extending the set of available functions. MATLAB's rich functionality can be further extended with a wide array of commercial and open-sources toolboxes, such as those for signal processing, wavelet analysis, and the analysis of neuroimaging data.


MRIcron is a free visualization tool for MRI data. It has an intuitive GUI and is capable of layered, overlay, multislice, and 3D render views. MRIcron runs on Linux, Mac, and Windows.


Developed at University College, London, SPM is a full-featured MATLAB package of brain data analysis tools, including fMRI, PET, EEG, and MEG. SPM uses the NIfTI file format and has a comprehensive GUI.

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