Provided by: cmtk_3.3.1p2+dfsg-2build1_amd64
volume_reconstruction - Volume reconstruction
volume_reconstruction [options] refImage xform0 inImage0 [xform1 inImage1 ...]
Iterative volume reconstruction from co-registered images using inverse interpolation or joint deblurring
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
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.