table of contents
| volume_injection(1) | The Computational Morphometry Toolkit | volume_injection(1) |
NAME¶
volume_injection - Volume injection
SYNOPSIS¶
volume_injection [options] refImage xform0 inImage0 [xform1 inImage1 ...]
DESCRIPTION¶
Reconstruction a high-resolution volume from multiple co-registered (low-resolution) images using forward volume injection
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)
- --pass-weight <string>, -W <string>
- Set contribution weight for a pass in the form 'pass:weight'
Reconstruction Grid Options¶
- --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]
- --crop <string>
- Crop reference to pixel region x0,y0,z1:x1,y1,z1
Volume Injection Options¶
- --isotropic-injection
- Use isotropic volume injection [default: scaled with pass image pixel size per dimension]
- --injection-kernel-sigma <double>, -S <double>
- Gauss contribution [Default: 1]
- --injection-kernel-radius <integer>, -r <integer>
- VolumeInjectionRadius of affected pixel [Default: 0]
Output Options¶
- --output <string>, -o <string>
- Output image path [Default: volume_injection.nii ]
- --write-images-as-float, -F
- Write output images as floating point [default: same as input]
AUTHORS¶
Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko
LICENSE¶
BUGS¶
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.
| Nov 13 2020 | CMTK 3.3.1p1 |