NAME

       glm - General Linear Model

SYNOPSIS

       glm [options] ctlfile imgfile_pattern [ctlfile imgfile_pattern ...]

DESCRIPTION

       Statistical modeling of pixel intensities in multiple images using a General Linear Model.

       The  independent  variables  of  the  model are defined in one of more control files. Each
       control file is a text file with one whitespace-separated column per independent variable.

       The first line of the control file defines the  variable  names,  i.e.,  the  labels  that
       identify each variable. Each following line contains one value per independent variable.

       Example:

         ID  age  sex
         01  20   0
         02  30   1

       Each  control file name is followed by a file name pattern. In that pattern, a single '%s'
       place holder is replaced by the value found in the first column of each control file  row.
       The resulting string is the path of the image read and associated with the model variables
       listed on that particular control file line.

       Using the above control file example, the pattern 'images/subject%s.nii' would  expand  to
       the image file names 'images/subject01.nii' and 'images/subject02.nii'.

       Multiple control files can be used, each with a different image file pattern.

OPTIONS

   Global Toolkit Options (these are shared by all CMTK tools)
       --help
            Write list of basic command line options to standard output.

       --help-all
            Write complete list of basic and advanced command line options to standard output.

       --wiki
            Write list of command line options to standard output in MediaWiki markup.

       --man
            Write man page source in 'nroff' markup to standard output.

       --version
            Write toolkit version to standard output.

       --echo
            Write the current command line to standard output.

       --verbose-level <integer>
            Set verbosity level.

       --verbose, -v
            Increment verbosity level by 1 (deprecated; supported for backward compatibility).

       --threads <integer>
            Set maximum number of parallel threads (for POSIX threads and OpenMP).

   Input Settings
       --crop <string>, -c <string>
            To save space/time, crop images: x0,y0,z0,x1,y1,z2

   Model Settings
       --normalize, -n
            Normalize model parameters w.r.t. data variances.

       --exp, -e
            Use exponential model rather than linear model.

   Selection of Independent Variables
       --exclude-constant, -x
            Exclude automatic constant parameter from model.

       --ignore-parameter <string>, -i <string>
            Ignore parameter with given NUMBER (0..n-1). Can be repeated.

       --select-parameter <string>, -s <string>
            Select parameter with given NAME for model. Can be repeated.

   Output Settings
       --output-pattern <string>, -O <string>
            Filename pattern for output.

              %s is replaced with image type ('fstat', 'tstat', or 'param')
              %d is replaced with independent variable number (0 for entire model)
              %s is replaced with independent variable name ('model' for entire model)

            [Default: model_%s_%02d_%s.nii ]

AUTHORS

       Torsten  Rohlfing,  with  contributions  from  Michael  P. Hasak, Greg Jefferis, Calvin R.
       Maurer, Daniel B. Russakoff, and Yaroslav Halchenko

LICENSE

       http://www.fsf.org/licensing/licenses/gpl.html

BUGS

       Report bugs at http://nitrc.org/projects/cmtk/

ACKNOWLEDGMENTS

       CMTK is developed with support from the NIAAA under Grant AA021697, National Consortium on
       Alcohol  and  Neurodevelopment  in Adolescence (N-CANDA): Data Integration Component. From
       April 2009 through September 2011, CMTK development and maintenance was supported  by  the
       NIBIB under Grant EB008381.