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 of "conditions", which specify statistical tests and also parameter estimation for output.
After the key-word delimited top section of the file, use the keyword "runs” (or “files”, with or without “:”) to denote that subsequent lines in the file should be interpreted as runs.
Following the "runs:" 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:
time-model GLM # define the format of the file to follow
baseline-terms 3 # include 3 terms in baseline polynomial
IRF IRON-rat # use an IRF appropriate for IRON fMRI 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 documentation
runs: # this indicates that following lines will list runs
../010/data.nii ../010/stim.glm ../010/table.dat # data file and GLM description are mandatory, table is optional
../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] corrected p-values on output
normalize-BOLD none (default = no normalization) equalize average signal values across runs
IRF built-in IRF or file name describe the hemodynamic IRF
conditions a list of conditions GLM determines these values & errors
convolve-table [list of events] convolve table events with IRF
drift-correct [order] [list of events] default drift correction is baseline-terms; overwrite this way for specified events
output-format [type] NIFTI use “jip” or “nifti” output files
frequency-filter [low] [high] pre-GLM frequency band for filtering data
residue-filter [low] [high] post-GLM frequency band for filtering data; used with “-r” option
AR [auto-regression order] 0 this feature currently is broken: don’t use it without verifying a fix!
runs/files none separates the file into options (above) and files (below)