SYNOPSIS
volume_reconstruction [options] refImage xform0 inImage0 [xform1 inImage1 ...]DESCRIPTION
Iterative volume reconstruction from co-registered images using inverse interpolation or joint deblurringOPTIONS
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, Daniel B. Russakoff, and Yaroslav HalchenkoBUGS
Report bugs at http://nitrc.org/projects/cmtk/ACKNOWLEDGMENTS
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.