Installation instructions

Download the zip package containing the current version, unzip it to the directory of your choice, and run setISCToolboxPath.m (this should be done on every time a new Matlab session is started unless you save the path). The package contains NiFTI tools by Jimmy Shen for convenience. The visualization tool require Harvard Oxford atlases as well as the MNI152 standard brains (2mm versions), which are available as a part of the FSL software package. These are NOT provided with the toolbox since they are distributed under a different license, so you should copy these files into templates sub-directory. See the readme.txt in the zip-package for details.

User Guide

User Guide : New Updated Userguide (pre v.3.0)

References

The main references explaining the analyses are:

J.-P. Kauppi, J. Pajula J and J. Tohka (2014). A Versatile Software Package for Inter-subject Correlation Based Analyses of fMRI. Frontiers in Neuroinformatics, 8:2. Available here.

J.-P. Kauppi, I.P. Jääskeläinen, M. Sams and J. Tohka (2010). Inter-subject correlation of brain hemodynamic responses during watching a movie: localization in space and frequency, Frontiers in Neuroinformatics, 4:5. Available here.

Please cite these papers if you use the toolbox in your research.

A validation of the analysis methods in this toolbox against a stimulus model (GLM) based approach with simple block design stimuli is presented in

J. Pajula, J.-P. Kauppi, and J. Tohka (2012). Inter-Subject Correlation in fMRI: Method Validation against Stimulus-model Based Analysis, PLoS ONE, 8(8):e41196. Available here.

Effects of Gaussian smoothing on inter-subject correlation analysis are studied in:

J. Pajula and J. Tohka (2014). Effects of spatial smoothing on inter-subject correlation based analysis of FMRI, Magnetic Resonance Imaging, Volume 32, Issue 9, Pages 1114-1124, Available: here and preprint here.

Other wiki-pages

User's guide is available here

Known matlab errors : explains the known Matlab errors related to the ISC toolbox

Memory mapping error and fix