vbim(1) [debian man page]

vbim(1) 							 The VoxBo Manual							   vbim(1)

NAME

       vbim - manipulate 3D and 4D volumes

SYNOPSIS

       vbim <flag> ...

DESCRIPTION

       vbim is part of the VoxBo suite of tools for brain image analysis.

       vbim is a multi-purpose program that applies various simple manipulations to 3D and 4D images.

OPTIONS

       vbim performs a set of operations, specified by option flags, in sequence.  To get a complete list of available flags, run the program with
       no arguments.

EXAMPLES

       To get very basic info about a file:

	      vbim foo.nii -info

       To get more detailed information about the data within a mask:

	      vbim foo.nii -regioninfo mask.nii

       To apply a mask to a 3D image and write out the result:

	      vbim image.nii -mask mask.nii -write maskedimage.nii

       To mask a 4D image:

	      vbim image.nii -mask mask.nii -write4D maskedimage.nii

       To average a bunch of 3D volumes:

	      vbim *.nii.gz -average -write mean.nii.gz

       To create a lesion count map from a set of lesion masks:

	      vbim *.nii -count -write count.nii.gz

       To create a 4D volume (20x20x20 voxels, 32-bit int, 10 time points) of random data with a mean of 100 and sd of 10:

	      vbim -newvol 20 20 20 10 int32 -addnoise 100 10 -write3d myvol.nii

NOTES

AVAILABILITY

       Pre-built VoxBo binaries are available for Linux, OSX, and Cygwin, and via the NeuroDebian project (neuro.debian.net)  for  Debian  deriva-
       tives.

CAVEATS

       VoxBo is provided with no warranty whatsoever.

AUTHOR

       For an historical roster of the VoxBo development team, visit www.voxbo.org.

SEE ALSO

       For  detailed  help  on	any VoxBo command-line program, run it with no arguments.  For graphical programs, use the -h flag.  For more help
       with VoxBo, for information about the mailing list, or to report bugs, visit the web site at www.voxbo.org.

       For information about file format support in VoxBo, see voxbo-fileformats(7).  For general information about VoxBo, see voxbo(7).

VoxBo							      January, 2011 (v1.8.5)							   vbim(1)

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)