---
name: "cmtk-volume_reconstruction"
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_reconstruction"
---

# cmtk-volume\_reconstruction(1)

Volume reconstruction

## NAME

volume\_reconstruction - Volume reconstruction

## SYNOPSIS

volume\_reconstruction \[options\] refImage xform0 inImage0 \[xform1 inImage1 ...\]

## DESCRIPTION

Iterative volume reconstruction from co-registered images using inverse interpolation or joint deblurring

## 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)

- **--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 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.