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cmtk-split(1) [debian man page]

split(1)					       The Computational Morphometry Toolkit						  split(1)

NAME
split - Split images SYNOPSIS
split InputImage OutputImagePattern DESCRIPTION
Split volume image into sub-images, i.e., to separate interleaved images into passes 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 --axial, -a Interleaved axial images [This is the default] --sagittal, -s Interleaved sagittal images --coronal, -c Interleaved coronal images --interleave-x, -x Interleaved along x axis --interleave-y, -y Interleaved along y axis --interleave-z, -z Interleaved along z axis [This is the default] --factor <integer>, -f <integer> Interleave factor. This is the number of subimages generated. [Default: 2] --padded, -p Padded output, i.e., fill in removed slices --output-xform-path <string> Optional path template (fprintf-style) for output affine transformation that maps input image coordinates to each output image. [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 split(1)

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jidb(1) 					       The Computational Morphometry Toolkit						   jidb(1)

NAME
jidb - Fix interleaved motion using joint iterative deblurring SYNOPSIS
jidb [options] inImage outImage DESCRIPTION
This tool splits an interleaved input image into the pass images, co-registers them, and reconstructs a motion-corrected image 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). Interleaving Options --interleave-axis Define interleave axis: this is the through-slice direction of the acquisition. Supported values: "guess-from-input", "axial", "sagittal", "coronal", "interleave-x", "interleave-y", "interleave-z", where the default is "guess-from-input", or use one of the fol- lowing: --guess-from-input Guess from input image [This is the default] --axial, -a Interleaved axial images --sagittal, -s Interleaved sagittal images --coronal, -c Interleaved coronal images --interleave-x, -x Interleaved along x axis --interleave-y, -y Interleaved along y axis --interleave-z, -z Interleaved along z axis --passes <integer>, -p <integer> Number of interleaved passes [Default: 2] --pass-weight <string>, -W <string> Set contribution weight for a pass in the form 'pass:weight' Motion Correction / Registration Options --reference-image <image-path>, -R <image-path> Use a separate high-resolution reference image for registration [Default: NONE] --registration-metric Registration metric for motion estimation by image-to-image registration. Supported values: "nmi", "mi", "cr", "msd", "cc", where the default is "msd", or use one of the following: --nmi Use Normalized Mutual Information for pass-to-refereence registration --mi Use standard Mutual Information for pass-to-refereence registration --cr Use Correlation Ratio for pass-to-refereence registration --msd Use Mean Squared Differences for pass-to-refereence registration [This is the default] --cc Use Cross-Correlation for pass-to-refereence registration --import-xforms-path <path> Path of file from which to import transformations between passes. [Default: NONE] --export-xforms-path <path> Path of file to which to export transformations between passes. [Default: NONE] Volume Injection Options --injection-kernel-sigma <double>, -S <double> Standard deviation of Gaussian kernel for volume injection [Default: 1] --injection-kernel-radius <integer>, -r <integer> Truncation radius of injection kernel [Default: 4] Deblurring Options --psf Kernel for the inverse interpolation reconstruction Supported values: "box", "gaussian", or use one of the following: --box Box-shaped PSF --gaussian Gaussian-shaped PSF --psf-scale <double> Set global scale factor for point spread function size, which itself is derived from the input image. [Default: 1] Optimization Options --fourth-order-error, -f Use fourth-order (rather than second-order) error for optimization. --num-iterations <integer>, -n <integer> Maximum number of inverse interpolation iterations [Default: 20] --no-truncation, -T Turn off regional intensity truncatrion --l-norm-weight <double> Set constraint weight for Tikhonov-type L-Norm regularization (0 disables constraint) [Default: 0] Output Options --write-injected-image <image-path> Write initial volume injection image to path [Default: NONE] --write-images-as-float, -F Write output images as floating point [default: same as input] 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 jidb(1)
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