Provided by: cmtk_3.0.0-1ubuntu1_amd64
jidb - Fix interleaved motion using joint iterative deblurring
jidb [options] inImage outImage
This tool splits an interleaved input image into the pass images, co-registers them, and reconstructs a motion-corrected image
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 following: --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]
Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko
Report bugs at http://nitrc.org/projects/cmtk/
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.