xenial (1) cmtk-glm.1.gz

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.