SRTM control file (PET)

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

    time-model                  srtm/SRTM/MRTM/LSRRM

    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)

Joseph B. Mandeville, Athinoula A. Martinos Center for Biomedical Imaging at MGH/MIT/Harvard