cmtk-probe(1) [debian man page]
probe(1) The Computational Morphometry Toolkit probe(1) NAME
probe - Probe image data. SYNOPSIS
probe InputImage DESCRIPTION
This tool prints pixel values or symbolic labels at a list of user-provided image coordinates. 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 --coordinates Coordinate specification mode. Supported values: "indexed", "absolute", "relative", "physical", or use one of the following: --indexed Use grid indexes to specify coordinates. For each dimension, the valid value range is [0,Dims-1]. --absolute Use absolute volume coordinates. For each dimension, the valid range is [0,FOV]. --relative Use relative volume coordinates. For each dimension, the valid range is [0,1]. --physical Use physical volume coordinates. Each given location is transformed into image coordinates via the inverse of the images's index- to-physical space matrix. --interpolation Image interpolation method. Supported values: "nn", "linear", "cubic", "pv", "sinc-cosine", "sinc-hamming", where the default is "nn", or use one of the following: --nn Nearest neighbor interpolation [This is the default] --linear Trilinear interpolation --cubic Tricubic interpolation --pv Partial volume interpolation --sinc-cosine Sinc interpolation with cosine window --sinc-hamming Sinc interpolation with Hamming window --sinc-window-radius <integer> Window radius for Sinc interpolation [Default: 3] --no-reorient Disable image reorientation into RAS alignment. 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 probe(1)
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reformatx(1) The Computational Morphometry Toolkit reformatx(1) NAME
reformatx - Volume reformatter SYNOPSIS
reformatx [options] --floating floatingImg target x0 [x1 ...] OR reformatx [options] target [x0 x1 ...] {-j,--jacobian} xx0 [xx1 ...] OR WHERE x0 ... xN and xx0 ... xxN is [{-i,--inverse}] transformation## DESCRIPTION
Extended volume reformatter tool to compute reformatted images and Jacobian maps from arbitrary sequences of concatenated transformations 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). --outputtype Scalar data type for the output image. Supported values: "char", "byte", "short", "ushort", "int", "uint", "float", "double", or use one of the following: --char 8 bits, signed --byte 8 bits, unsigned --short 16 bits, signed --ushort 16 bits, unsigned --int 32 bits signed --uint 32 bits unsigned --float 32 bits floating point --double 64 bits floating point --pad-out <double>, -P <double> Padding value for output image [Default: 0] Options for Plain Reformatting --interpolation Image interpolation method. Supported values: "linear", "nn", "cubic", "pv", "sinc-cosine", "sinc-hamming", where the default is "linear", or use one of the following: --linear Trilinear interpolation [This is the default] --nn Nearest neighbor interpolation --cubic Tricubic interpolation --pv Partial volume interpolation --sinc-cosine Sinc interpolation with cosine window --sinc-hamming Sinc interpolation with Hamming window --sinc-window-radius <integer> Window radius for Sinc interpolation [Default: 3] --preserve-mass Mass-preserving reformatting: multiply every reformatted value with the Jacobian determinant of the applied transformation. Options for Jacobian Map Reformatting --jacobian-correct-global Correct Jacobian maps for global scale. [This is the default] --no-jacobian-correct-global Do not correct Jacobian maps for global scale. Input Options --target-grid <string> Define target grid for reformating as Nx,Ny,Nz:dX,dY,dZ[:Ox,Oy,Oz] (dims:pixel:offset) --mask, -m Use target pixel data as binary mask. --crop <string> Crop target image: x0,y0,z0,x1,y1,z2 --target-offset <string>, -O <string> Override target image offset and set to x,y,z mm --target-offset-pixels <string> Override target image offset and set to dx,dy,dz pixels --floating <string>, -F <string> Format and path of floating image. [Default: NONE] Output Options --outfile <string>, -o <string> Format and path of output image. [Default: reformat.nii ] Image/Transformation Database --db <string> Path to image/transformation database that should be updated with the newly created 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 reformatx(1)