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

# cmtk-jidb(1)

Fix interleaved motion using joint iterative deblurring

## NAME

jidb - Fix interleaved motion using joint iterative deblurring

## SYNOPSIS

jidb \[options\] inImage outImage

## DESCRIPTION

This tool splits an interleaved input image into the pass images, co-registers them, and reconstructs a motion-corrected image

## 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).

### Interleaving Options

- **--interleave-axis**

  Define interleave axis: this is the through-slice direction of the acquisition. Supported values: "guess-from-input", "axial", "sagittal", "coronal", "interleave-x", "interleave-y", "interleave-z", where the default is "guess-from-input", or use one of the following:

  - **--guess-from-input**

    Guess from input image **\[This is the default\]**

  - **--axial**, **-a**

    Interleaved axial images

  - **--sagittal**, **-s**

    Interleaved sagittal images

  - **--coronal**, **-c**

    Interleaved coronal images

  - **--interleave-x**, **-x**

    Interleaved along x axis

  - **--interleave-y**, **-y**

    Interleaved along y axis

  - **--interleave-z**, **-z**

    Interleaved along z axis

- **--passes** *\<integer\>*, **-p** *\<integer\>*

  Number of interleaved passes **\[Default: 2\]**

- **--pass-weight** *\<string\>*, **-W** *\<string\>*

  Set contribution weight for a pass in the form 'pass:weight'

### Motion Correction / Registration Options

- **--reference-image** *\<image-path\>*, **-R** *\<image-path\>*

  Use a separate high-resolution reference image for registration **\[Default: NONE\]**

- **--registration-metric**

  Registration metric for motion estimation by image-to-image registration. Supported values: "nmi", "mi", "cr", "msd", "cc", where the default is "msd", or use one of the following:

  - **--nmi**

    Use Normalized Mutual Information for pass-to-refereence registration

  - **--mi**

    Use standard Mutual Information for pass-to-refereence registration

  - **--cr**

    Use Correlation Ratio for pass-to-refereence registration

  - **--msd**

    Use Mean Squared Differences for pass-to-refereence registration **\[This is the default\]**

  - **--cc**

    Use Cross-Correlation for pass-to-refereence registration

- **--import-xforms-path** *\<path\>*

  Path of file from which to import transformations between passes. **\[Default: NONE\]**

- **--export-xforms-path** *\<path\>*

  Path of file to which to export transformations between passes. **\[Default: NONE\]**

### Volume Injection Options

- **--injection-kernel-sigma** *\<double\>*, **-S** *\<double\>*

  Standard deviation of Gaussian kernel for volume injection **\[Default: 1\]**

- **--injection-kernel-radius** *\<integer\>*, **-r** *\<integer\>*

  Truncation radius of injection kernel **\[Default: 4\]**

### Deblurring Options

- **--psf**

  Kernel for the inverse interpolation reconstruction Supported values: "box", "gaussian", or use one of the following:

  - **--box**

    Box-shaped PSF

  - **--gaussian**

    Gaussian-shaped PSF

- **--psf-scale** *\<double\>*

  Set global scale factor for point spread function size, which itself is derived from the input image. **\[Default: 1\]**

### Optimization Options

- **--fourth-order-error**, **-f**

  Use fourth-order (rather than second-order) error for optimization.

- **--num-iterations** *\<integer\>*, **-n** *\<integer\>*

  Maximum number of inverse interpolation iterations **\[Default: 20\]**

- **--no-truncation**, **-T**

  Turn off regional intensity truncatrion

- **--l-norm-weight** *\<double\>*

  Set constraint weight for Tikhonov-type L-Norm regularization (0 disables constraint) **\[Default: 0\]**

### Output Options

- **--write-injected-image** *\<image-path\>*

  Write initial volume injection image to path **\[Default: NONE\]**

- **--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.