volume_injection(1) Volume injection


volume_injection [options] refImage xform0 inImage0 [xform1 inImage1 ...]


Reconstruction a high-resolution volume from multiple co-registered (low-resolution) images using forward volume injection


Global Toolkit Options (these are shared by all CMTK tools)

Write list of basic command line options to standard output.
Write complete list of basic and advanced command line options to standard output.
Write list of command line options to standard output in MediaWiki markup.
Write man page source in 'nroff' markup to standard output.
Write toolkit version to standard output.
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

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]


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.