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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volume_reconstruction(1) The Computational Morphometry Toolkit volume_reconstruction(1) NAME
volume_reconstruction - Volume reconstruction SYNOPSIS
volume_reconstruction [options] refImage xform0 inImage0 [xform1 inImage1 ...] DESCRIPTION
Iterative volume reconstruction from co-registered images using inverse interpolation or joint deblurring 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 Options --exclude-first-image, -x Exclude first image from reconstruction as a separate registration target image) --crop <string> Crop reference to pixel region x0,y0,z1:x1,y1,z1 --pass-weight <string>, -W <string> Set contribution weight for a pass in the form 'pass:weight' Reconstruction Grid --recon-grid <string> Define reconstruction grid as Nx,Ny,Nz:dX,dY,dZ[:Ox,Oy,Oz] (dims:pixel:offset) --recon-grid-path <string>, -R <string> Give path to grid that defines reconstructed image grid [including offset] [Default: NONE] Initial Volume Injection Parameters --isotropic-injection Use isotropic volume injection [otherwise: scaled with pass image pixel size per dimension] --injection-kernel-sigma <double>, -S <double> Standard deviation of Gaussian kernel for volume injection in multiples of pixel size in each direction. [Default: 1] --injection-kernel-radius <double>, -r <double> Truncation radius factor of injection kernel. The kernel is truncated at sigma*radius, where sigma is the kernel standard deviation. [Default: 2] Volume Reconstruction Options --inverse-interpolation-kernel Kernel for the inverse interpolation reconstruction Supported values: "cubic", "linear", "hamming-sinc", "cosine-sinc", where the default is "cubic", or use one of the following: --cubic, -C Tricubic interpolation [This is the default] --linear, -L Trilinear interpolation (faster but less accurate) --hamming-sinc, -H Hamming-windowed sinc interpolation --cosine-sinc, -O Cosine-windowed sinc interpolation (most accurate but slowest) --deblurring Kernel shape to approximate the point spread function for joint deblurring reconstruction (selecting one of these disables inverse interpolation reconstruction) Supported values: "box", "gaussian", or use one of the following: --box Box-shaped kernel --gaussian Gaussian kernel --psf <string> Explicitly set point spread function size as x,y,z. Use with 'deblurring' kernel reconstrunction. --psf-scale <double> Scale point spread function size by this value. Use with 'deblurring' kernel reconstrunction. [Default: 1] Optimization Parameters --num-iterations <integer>, -n <integer> Maximum number of inverse interpolation iterations [Default: 20] --fourth-order-error, -f Use fourth-order (rather than second-order) error for optimization. Regularization Parameters --l-norm-weight <double> Set constraint weight for Tikhonov-type L-Norm regularization (0 disables constraint) [Default: 0] --no-truncation, -T Turn off non-linear regional intensity truncation Output Options --output <string>, -o <string> Output path for final reconstructed image [Default: reconstructed.nii ] --write-injected-image <string> Write initial volume-injected image to this path [Default: NONE] --write-lowest-max-error-image <string> Optional path to write reconstructed image with lowest MAXIMUM error. [Default: NONE] --write-images-as-float, -F Write output images as floating point 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 volume_reconstruction(1)