cmtk-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-
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.
Opportunity
Personal Opportunity - Free software gives you access to billions of dollars of software at no cost. Use this software for your business, personal use or to develop a profitable skill. Access to source code provides access to a level of capabilities/information that companies protect though copyrights. Open source is a core component of the Internet and it is available to you. Leverage the billions of dollars in resources and capabilities to build a career, establish a business or change the world. The potential is endless for those who understand the opportunity.
Business Opportunity - Goldman Sachs, IBM and countless large corporations are leveraging open source to reduce costs, develop products and increase their bottom lines. Learn what these companies know about open source and how open source can give you the advantage.
Free Software
Free Software provides computer programs and capabilities at no cost but more importantly, it provides the freedom to run, edit, contribute to, and share the software. The importance of free software is a matter of access, not price. Software at no cost is a benefit but ownership rights to the software and source code is far more significant.
Free Office Software - The Libre Office suite provides top desktop productivity tools for free. This includes, a word processor, spreadsheet, presentation engine, drawing and flowcharting, database and math applications. Libre Office is available for Linux or Windows.
Free Books
The Free Books Library is a collection of thousands of the most popular public domain books in an online readable format. The collection includes great classical literature and more recent works where the U.S. copyright has expired. These books are yours to read and use without restrictions.
Source Code - Want to change a program or know how it works? Open Source provides the source code for its programs so that anyone can use, modify or learn how to write those programs themselves. Visit the GNU source code repositories to download the source.
Education
Study at Harvard, Stanford or MIT - Open edX provides free online courses from Harvard, MIT, Columbia, UC Berkeley and other top Universities. Hundreds of courses for almost all major subjects and course levels. Open edx also offers some paid courses and selected certifications.
Linux Manual Pages - A man or manual page is a form of software documentation found on Linux/Unix operating systems. Topics covered include computer programs (including library and system calls), formal standards and conventions, and even abstract concepts.
