---
name: "cmtk-volume_injection"
section: "1"
platform: "linux"
package: "cmtk"
version: "3.3.1p2+dfsg-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/cmtk-volume_injection"
---

# cmtk-volume\_injection(1)

Volume injection

## 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

http://www.fsf.org/licensing/licenses/gpl.html

## 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.