cmtk-destripe(1) [debian man page]

destripe(1)					       The Computational Morphometry Toolkit					       destripe(1)

NAME

       destripe - Destripe volume image data.

SYNOPSIS

       destripe InputImage OutputImage

DESCRIPTION

       This program corrects stripe artifacts in acquired image stacks which can result from between-slice intensity scale differences.

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).

   Slice Orientation
       --slice-axis
	    Define  slice  direction axis: this is the through-slice direction of the acquisition.  Supported values: "guess-from-input", "axial",
	    "sagittal", "coronal", "slice-x", "slice-y", "slice-z", where the default is "guess-from-input", or use one of the following:

	    --guess-from-input
		 Guess from input image [This is the default]

	    --axial, -a
		 Sliced axial images

	    --sagittal, -s
		 Sliced sagittal images

	    --coronal, -c
		 Sliced coronal images

	    --slice-x, -x
		 Sliced along x axis

	    --slice-y, -y
		 Sliced along y axis

	    --slice-z, -z
		 Sliced along z axis

       --kernel-fwhm <double>
	    Gaussian kernel full width at half maximum (FWHM) in units of slice indexes.  [Default: 1]

       --kernel-radius <integer>
	    Truncate kernel radius to this many samples. By default, kernel width is determined to limit approximation error.  [Default: 0]

       --write-float
	    Write output image in floating point representation. By default, write using input image pixel data type.

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 						       destripe(1)

mk_analyze_hdr(1)				       The Computational Morphometry Toolkit					 mk_analyze_hdr(1)

NAME

       mk_analyze_hdr - Make Analyze header file

SYNOPSIS

       mk_analyze_hdr [options] [output.nii]

DESCRIPTION

       Make header file according Analzye 7.5 format based on user-supplied parameters for geometry, data type, orientation, etc.

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).

   Main Options
       --dims <string>, -D <string>
	    Set dimensions in voxels

       --voxel <string>, -V <string>
	    Set voxel size in [mm]

       --offset <float>, -O <float>
	    Binary data file offset [Default: disabled]

       --char, -c
	    8 bits, signed

       --byte, -b
	    8 bits, unsigned

       --short, -s
	    16 bits, signed

       --ushort, -u
	    16 bits, unsigned

       --int, -i
	    32 bits signed

       --float, -f
	    32 bits floating point

       --double, -d
	    64 bits floating point

       --big-endian, -B
	    Big endian data [This is the default]

       --little-endian, -L
	    Little endian data

       --axial
	    Set slice orientation to axial

       --axial-flip
	    Set slice orientation to reverse axial

       --sagittal
	    Set slice orientation to sagittal

       --sagittal-flip
	    Set slice orientation to reverse sagittal

       --coronal
	    Set slice orientation to corona;

       --coronal-flip
	    Set slice orientation to reverse coronal

       --legacy
	    Legacy mode; do not write 'SRI1' tag into header

       --SRI1
	    Force 'SRI1' tag even if not present in imported header

       --import <string>, -I <string>
	    Import data from given header file.  [Default: NONE]

       --description <string>
	    Set description string [max. 80 characters] [Default: NONE]

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 						 mk_analyze_hdr(1)