A GLM control file is the "top level" that defines the GLM to be used for analysis.
The first line defines the type of time model. Following lines describe options to used in the analysis, such as specifying the reference region and the conditions to be tested.
After the key-word delimited top section of the file, use the keyword "runs" or "runs:" to denote that subsequent lines in the file should be interpreted as runs.
Following the "runs:" line, all subsequent lines must contain 3 entries. The first entry is the name of the 4-dimensional data file. The second entry is a file describing the run in terms of SRTM analysis regressors. The third entry is a table file that defines the frame durations in units of seconds, and optionally the table file can contain additional columns that can be used as regressors.
An example GLM control file follows for SRTM:
time-model SRTM # this lets the program know how to interpret subsequent lines
reference-region cerebellum.ovl # reference region for SRTM
target-region putamen.ovl # target region for example analysis
half-life 20.33 # half-life in minutes for the PET tracer (11-C here)
output-format jip # default output-format is NIFTI
conditions A AB 1 # conditions for statistics and parameter evaluation
runs: # this indicates that following lines will list runs (or use “files:”)
../scan1/data.nii pet1.glm ../scan1/pet-timing.table
../scan2/data.nii pet2.glm ../scan2/pet-timing.table
The following keywords are defined for use in the control file above the “runs:” line.
Keyword argument explanation
reference-region overlay file required reference region specified as an image overlay mask
target-region overlay file optional region for example analysis prior to voxel-wise analysis
half-life minutes this defines the noise model used for weighted least squares
conditions list of conditions follows same method as used for fMRI GLM
multiple-comparisons resolution elements follows same method as used for fMRI GLM
output-format jip or nifti specifies the format of output image files
runs/files none separates the file into options (above) and files (below)