A GLM control file is the "top level" that defines the GLM to be used for analysis.
The first several lines describe options to used in the analysis, such as the number of terms describing baseline signal drift, the conditions to be tested, the hemodynamic impulse response model, as so on. Required options include a list conditions for testing (the whole point of the analysis), and the keyword "runs" or "runs:". Following that line, all subsequent lines are interpreted as containing either 2 or 3 entries. The first 2 entries are required and are the name of the 4-dimensional data file and a file that specifies the stimuli for that run. Optionally, one may also include a table file that has entries for each time point and contains things (eye position, blood pressure, etc) that can only be entered explicitly in this way.
An example GLM control file follows:
baseline-terms 3 # include 3 terms in baseline polynomial
IRF BOLD-rat # use an IRF appropriate for BOLD in rats
convolve-table 3 4 # convolve table events “3” and “4” with the IRF
conditions 1 2 12 1-2 # see conditions page in documentataion
runs: # this indicates that following lines will list runs
../010/data.nii ../010/stim.glm ../010/table.dat
../011/data.nii ../011/stim.glm ../011/table.dat
../012/data.nii ../012/stim.glm ../012/table.dat
The following keywords are defined for use in the GLM control file above the “runs:” line.
Keyword argument default value purpose
baseline-terms [integer] (0-4) 3 baseline polynomial
notify none verbose output
multiple-comparisons [integer # of resels] correct p-values
normalize-BOLD none (default = no normalization)