This page describes the paradigm file format for FreeSurfer version 5.0 and higher

The paradigm file is a simple ASCII text file that describes which stimulus was present when. You will need a separate paradigm file for each fMRI run/series. It contains at least 4 columns (any extra columns are ignored).

An example of a paradigm file is given below:

  0.0000    2    3.000   1.0 Neutral-Long
  3.0000    3    3.000   1.0 Fearful-Short
  6.0000    0    1.000   1.0 NULL
  7.0000    4    3.000   1.0 Fearful-Long
 10.0000    0    2.000   1.0 NULL
 12.0000    1    3.000   1.0 Neutral-Short
 15.0000    0    3.000   1.0 NULL
 18.0000    2    3.000   1.0 Neutral-Long

This file would go into the run directory (ie, in the same folder as the raw fMRI data). When making an analysis with mkanalysis-sess, specify this file with "-paradigm paradigmfile", where "paradigmfile" is the name of the file. It must be named the same name for all runs (though the content can change).

When making a contrast, refer to the condition IDs in the 2nd column. Eg, Neutral-Long vs Fearful-Short would be

mkcontrast-sess -a 2 -c 3 ...

The software that reads in the paradigm file is $FREESURFER_HOME/fsfast/toolbox/fast_ldpar4.m. This file effectively defines the format.

FsFastParadigmFile (last edited 2017-02-22 18:19:27 by AllisonMoreau)