• FsFastParadigmFile

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).

• The first column is the onset time (in seconds) of the stimulus relative to the acquisition of the first STORED image in the series (i.e., not including discarded acquisitions or dummy scans).
• The second column is a numeric ID that codes the condition/event type that was presented at that time.
• The third column is the stimulus duration.

• The fourth column is a weight used for parametric modulation analysis (see FsFastParametricModulation)

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

• There are 5 event types, 4 task-related and 1 fixation (NULL).
• The NULL/Fixation condition is ALWAYS 0.
• The rest of the conditions must be numbered sequentially starting at 1.
• The NULL condition does not have to be explicitly represented.
• These condition codes will be used later in FSFAST when constructing contrasts.
• The onset time does not need to be a multiple of the TR or linked in any way (e.g., the onset time could be something like 11.340).

• The weight is always 1.0. See FsFastParametricModulation for cases where you would set the weight.

• The 5th column is ignored.
• Any lines that begin with a hash character (#) are ignored (ie, treated as a comment)

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.