Note: this applies to FreeSurfer version 4.5

The paradigm file is a simple text file that describes which stimulus was present when. You will need a separate paradigm file for each run/series in the visit. It contains at least 2 columns and may contain as many as 4. The first column is the onset time 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 (optional) third column is the stimulus duration (redundant with column 1). The (optional) fourth column is a name of the condition/event type (redundant with column 2). An example of a paradigm file is given below:
<<BR>>
  0.0000    2    3.000    Neutral-Long  <<BR>>   
  3.0000    3    3.000    Fearful-Short    <<BR>>  
  6.0000    0    1.000          NULL      <<BR>> 
  7.0000    4    3.000    Fearful-Long    <<BR>>  
 10.0000    0    2.000          NULL      <<BR>> 
 12.0000    1    3.000    Neutral-Short    <<BR>>   
 15.0000    0    3.000          NULL      <<BR>> 
 18.0000    2    3.000    Neutral-Long      <<BR>> 
<<BR>>
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. These condition codes will be used later in fsfast when constructing contrasts. FSFAST only pays attention to the first 2 columns; the rest are for making them easier to read. 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). There are a few cases where you might need to re-code the paradigm file to indicate how long the stimulus lasts, but these are rare.

Create a file for each functional run/series and copy each one into the same directory as your functional data. E.g., if you have four functional runs, then you would create four paradigm files (note that they can all have the same content). When you copy the paradigm files to the functional data, you must give it the same name in each directory. E.g., if the functional data is stored in targetdir/bold/002, 003, 004, 005 and you have four paradigm files emotion1.par, emotion2.par, emotion3.par, emotion4.par, then:
<<BR>>
cp emotion1.par argetdir/bold/002/emotion.par <<BR>>
cp emotion2.par argetdir/bold/003/emotion.par <<BR>>
cp emotion3.par argetdir/bold/004/emotion.par <<BR>>
cp emotion4.par argetdir/bold/005/emotion.par <<BR>>
<<BR>>
Note that the paradigm file is always called "emotion.par" regardless of the run. There is no conflict because they are in different directories.