glm(1)						       The Computational Morphometry Toolkit						    glm(1)

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-sepa-
       rated 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, and Daniel B. Russakoff

LICENSE

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

BUGS

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

ACKNOWLEDGMENTS

       From April 2009 through September 2011, CMTK Development and Maintenance was supported by the National Institute of Biomedical Imaging  and
       Bioengineering under Grant No.R01 EB008381 (PI: Torsten Rohlfing).

CMTK 2.2.2							    Jul 20 2012 							    glm(1)