REM control file

A control file is the "top level" that defines the mixed-effects or random-effects  model to be used for analysis.

The first several lines describe options to used in the analysis. After the key-word delimited top section of the file. Subsequently, the keyword “event” denotes that subsequent lines in the file should be interpreted as 1st-level analyses containing maps of signal changes and errors. Generally, one would use square (constant across groups) analysis regressors. However, if a weight is applied to each subject following the file specification, then the 2nd-level regressor will assume the shape specified by the list of weights, which presumably would come from some independently measured variable.

   An example GLM control file follows:

              time-model MEM          # or “REM” , “rem”, “men"

              smoothing 3 6               # [1st level resolution] [smoothing to control sliding scale between fixed and random effects analyses]

              conditions A B A-B        # list of conditions to test

              event A                          # this indicates that following lines will list 1st-level analyses

              ../subject1/S-a-b.nii       # a 1st-level differential test of 2 conditions

              ../subject2/S-a-b.nii       # optionally, a weight could be applied to each subject



              event B                           # “event” or “subjects” or “sessions"

              ../subject21/S-a-b.nii      # a 1st-level differential test of 2 conditions



The following keywords are defined for use in the control file:

    Keyword                     argument        default value           purpose

    time-model                  rem/mem/REM/MEM

    multiple-comparisons  [integer # of resels]                        corrected p-values on output

    conditions                   a list of conditions                          GLM determines these values & errors

    event/subjects/sessions     none                                       separates the file into options (above) and files (below)

    output-format              [type]                   NIFTI                  use “jip” or “nifti” output files

    smooth/smoothing      [resolution] [smoothing factor]       The first number is the effective 1st-level resolution, including smoothing

                                                                                              The 2nd number controls the sliding scale between fixed and random effects

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