Software

The following programs are provided free of charge, under the terms of the GNU General Public License:

  1. SAfE: Straightforward Analysis of fMRI and EEG-fMRI
  2. ConnExT: Connectivity Explorer Toolbox
  3. MIP-C: Maximum Intensity Projection with colors

SAfE: Straightforward Analysis of fMRI and EEG-fMRI

SAfE is a toolbox for SPM8 written by Guilherme Coco Beltramini. If you use SAfE in a publication, please cite:

  • Beltramini GC, Covolan RJM (2013) Straightforward Analysis of fMRI and EEG-fMRI (SAfE): A toolbox for SPM8. Proceedings of the 19th Annual Meeting of the Organization for Human Brain Mapping, Seattle, WA, USA, June 16-20 2013

SAfE allows one to perform straightforward analyses of almost any fMRI experiment, from the preprocessing until the statistical maps. The user must only complete a spreadsheet with the experimental paradigm and file names. Even a person with little training in fMRI analysis can use this interface very easily.

SAfE is especially suited for situations when the number of conditions and timing of the events vary among subjects. This is one of the reasons why a spreadsheet is used to organize the paradigm. This is particularly the case of one type of EEG-fMRI analysis. When the onset and duration of the events are obtained from the EEG, a VBA macro in Microsoft Excel reads the EEG markers file and creates the spreadsheet that will be used by SAfE.

By requiring little user input, fMRI (or EEG-fMRI) analyses become less prone to human error and can be performed in a fast way. SAfE uses SPM's default options for all the parameters that are not accessible through the GUI or the command line, except when stated otherwise in the manual. The scripts must be manually edited to customize these parameters.

Requirements:

  • SPM8
  • MATLAB (version R2010a or later; no toolbox required)

MS Excel is not required but is recommended, because sometimes the spreadsheets are not fully read by MATLAB.

Downloads

Version 1 (July 2014)

Screenshots

(Click to enlarge)




ConnExT: Connectivity Explorer Toolbox

ConnExT is a toolbox for SPM8 written by Guilherme Coco Beltramini.

ConnExT provides an easy way to visually explore the signal time series and the functional connectivity map of fMRI data. There are various processing options that can be applied to the time series, and the effect is quickly seen. Another very interesting capability is the option to choose the seed region without difficulty for functional connectivity analysis, and the correlation coefficient map is instantaneously displayed. Therefore, ConnExT can be very useful to test different processing alternatives and seed regions. Both GUI and command line are available.

Requirements:

Downloads

Version 1 (July 2014)

Screenshots

(Click to enlarge)




MIP-C: Maximum Intensity Projection with colors

MIP-C is an extension for SPM8 written by Guilherme Coco Beltramini.

MIP-C is a simple program that creates a color image with the maximum intensity projection (MIP) on a glass brain in three orthogonal planes. The documentation is included in the header of the MATLAB files. To execute MIP-C, run the script fmri_mip_color.m.

Requirements:

  • SPM8
  • MATLAB (version R2010a or later; no toolbox required)

Downloads

Version 1 (July 2014)

Screenshots

(Click to enlarge)




Page updated on 2014-07-25 22:37