All SAM analyses are directed by a named parameter file. The format of this file is plain text and can be created using any convenient text editor (i.e., vi, gedit, emacs, etc.). The parameter file is normally specified with -m.
Parameters may be abbreviated, and except where noted may also be specified on the command line prefixed with two dashes, e.g., --DataSet. Some also have single dash option flags (-h), and some (e.g., ds) may be specified as exported environment variables.
Parameters specified on the command line or environment override those specified in a parameter file. If command line options are used, the actual parameters that the analysis was run with will be reconstituted as a .param file in the SAM director of the MEG dataset.
Finally, you may also define an optional parameter file called .samrc in the directory from which the program is run, which may contain parameters common to a set of analyses.
All parameters appear below. User defined input is given in all capital letters.
Specifies the MEG dataset to be analyzed.
Parameter File: DataSet DNAME Command Line: -r DNAME
Only used for 4D/BTi datasets, this specifies the additional PDF file.
Parameter File: PDFName PDFNAME Command Line: -d PDFNAME
N specifies the number of unique event marker names found in the dataset that are to be used in the analysis. Up to six markers are currently permitted. If no named markers are present, the user must specify zero markers for analyses that are not state dependent. The sam_cov and sam_wts programs, together, read this parameter and parse the dataset for the named markers, generating up to six named SAM beamformer coefficient files plus Global and Sum coefficients.
Parameter File: NumMarkers N