A software for fMRI experiments using naturalistic stimuli

The mt_tools code is a collection of Matlab functions to support the analysis of experiments involving complex and dynamic naturalistic stimuli. The software comprises three main parts:

A) Computation of saliency and feature-specific maps, for visual and auditory stimuli

This part of the software computes saliency maps based on feature discontinuities at different scales, which are then combined into a single saliency map (Itti and Koch 2001, in Nat Rev Neurosci). For vision, the software can utilise Intensity, Orientation, Colour, Motion, Flicker and binocular Disparity contrasts. For audition, the saliency maps consider discontinuities in Intensity, Frequency, Time and Orientation (Kalinli and Narayanan 2009, in IEEE Trans Audio Speech Lang Process). This part of the code includes functions from the SaliencyToolbox and the SIFTflow.

B) Processing of eye-movement data

This set of functions process eye-movement data that we typically acquire while subjects view complex naturalistic stimuli. Following some initial processing (e.g. conversion to visual degrees, exclusion of blinks and artefacts), the eye-tracking data are combined with information about “what stimulus was presented when” and fixations/saccades are identified.

C) Data-driven analyses of fMRI time series (brain Modes)

This part of the software combines inter-subjects synchronization analyses (Hasson et al., 2004, in Science) and cluster analyses to isolate functionally-relevant brain networks during viewing of complex and dynamic stimuli (bModes). The procedure is fully data-driven and can identify transient coupling between brain areas, irrespective of the signal shape within each area. This new approach is particularly suited to investigate multi-components control processes using naturalistic stimuli during fMRI.

The software is developed with funding from the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) / ERC grant agreement n.242809 (MindTravel).

The current version of mt_tools runs only in Linux and requires several Matlab toolboxes (see User Guide for details).

Please email Emiliano Macaluso (emiliano.macaluso [at] to obtain the MT_TOOLS code.

NO WARRANTY: mt_tools is for research purposes only and is provided as-it-is without warranty of any kind.