.TH jidb "1" "Jan 25 2019" "CMTK 3.3.1p1" "The Computational Morphometry Toolkit"
.SH NAME
jidb \- Fix interleaved motion using joint iterative deblurring
.SH SYNOPSIS
jidb [options] inImage outImage
.SH DESCRIPTION
This tool splits an interleaved input image into the pass images, co-registers them, and reconstructs a motion-corrected image
.SH OPTIONS
.SS Global Toolkit Options (these are shared by all CMTK tools)
.TP 5
\fB\-\-help\fR
Write list of basic command line options to standard output.
.TP 5
\fB\-\-help-all\fR
Write complete list of basic and advanced command line options to standard output.
.TP 5
\fB\-\-wiki\fR
Write list of command line options to standard output in MediaWiki markup.
.TP 5
\fB\-\-man\fR
Write man page source in 'nroff' markup to standard output.
.TP 5
\fB\-\-version\fR
Write toolkit version to standard output.
.TP 5
\fB\-\-echo\fR
Write the current command line to standard output.
.TP 5
\fB\-\-verbose-level\fR \fI<integer>\fR
Set verbosity level.
.TP 5
\fB\-\-verbose\fR, \fB\-v\fR
Increment verbosity level by 1 (deprecated; supported for backward compatibility).
.TP 5
\fB\-\-threads\fR \fI<integer>\fR
Set maximum number of parallel threads (for POSIX threads and OpenMP).
.SS Interleaving Options
.TP 5
\fB\-\-interleave-axis\fR
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:
.RS 5
.TP 5
\fB\-\-guess-from-input\fR
Guess from input image
\fB[This is the default]\fR
.TP 5
\fB\-\-axial\fR, \fB\-a\fR
Interleaved axial images
.TP 5
\fB\-\-sagittal\fR, \fB\-s\fR
Interleaved sagittal images
.TP 5
\fB\-\-coronal\fR, \fB\-c\fR
Interleaved coronal images
.TP 5
\fB\-\-interleave-x\fR, \fB\-x\fR
Interleaved along x axis
.TP 5
\fB\-\-interleave-y\fR, \fB\-y\fR
Interleaved along y axis
.TP 5
\fB\-\-interleave-z\fR, \fB\-z\fR
Interleaved along z axis
.RE
.TP 5
\fB\-\-passes\fR \fI<integer>\fR, \fB\-p\fR \fI<integer>\fR
Number of interleaved passes
.B [Default: 2]
.TP 5
\fB\-\-pass-weight\fR \fI<string>\fR, \fB\-W\fR \fI<string>\fR
Set contribution weight for a pass in the form 'pass:weight'
.SS Motion Correction / Registration Options
.TP 5
\fB\-\-reference-image\fR \fI<image-path>\fR, \fB\-R\fR \fI<image-path>\fR
Use a separate high-resolution reference image for registration
.B [Default: NONE]
.TP 5
\fB\-\-registration-metric\fR
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:
.RS 5
.TP 5
\fB\-\-nmi\fR
Use Normalized Mutual Information for pass-to-refereence registration
.TP 5
\fB\-\-mi\fR
Use standard Mutual Information for pass-to-refereence registration
.TP 5
\fB\-\-cr\fR
Use Correlation Ratio for pass-to-refereence registration
.TP 5
\fB\-\-msd\fR
Use Mean Squared Differences for pass-to-refereence registration
\fB[This is the default]\fR
.TP 5
\fB\-\-cc\fR
Use Cross-Correlation for pass-to-refereence registration
.RE
.TP 5
\fB\-\-import-xforms-path\fR \fI<path>\fR
Path of file from which to import transformations between passes.
.B [Default: NONE]
.TP 5
\fB\-\-export-xforms-path\fR \fI<path>\fR
Path of file to which to export transformations between passes.
.B [Default: NONE]
.SS Volume Injection Options
.TP 5
\fB\-\-injection-kernel-sigma\fR \fI<double>\fR, \fB\-S\fR \fI<double>\fR
Standard deviation of Gaussian kernel for volume injection
.B [Default: 1]
.TP 5
\fB\-\-injection-kernel-radius\fR \fI<integer>\fR, \fB\-r\fR \fI<integer>\fR
Truncation radius of injection kernel
.B [Default: 4]
.SS Deblurring Options
.TP 5
\fB\-\-psf\fR
Kernel for the inverse interpolation reconstruction
Supported values: "box", "gaussian", or use one of the following:
.RS 5
.TP 5
\fB\-\-box\fR
Box-shaped PSF
.TP 5
\fB\-\-gaussian\fR
Gaussian-shaped PSF
.RE
.TP 5
\fB\-\-psf-scale\fR \fI<double>\fR
Set global scale factor for point spread function size, which itself is derived from the input image.
.B [Default: 1]
.SS Optimization Options
.TP 5
\fB\-\-fourth-order-error\fR, \fB\-f\fR
Use fourth-order (rather than second-order) error for optimization.
.TP 5
\fB\-\-num-iterations\fR \fI<integer>\fR, \fB\-n\fR \fI<integer>\fR
Maximum number of inverse interpolation iterations
.B [Default: 20]
.TP 5
\fB\-\-no-truncation\fR, \fB\-T\fR
Turn off regional intensity truncatrion
.TP 5
\fB\-\-l-norm-weight\fR \fI<double>\fR
Set constraint weight for Tikhonov-type L-Norm regularization (0 disables constraint)
.B [Default: 0]
.SS Output Options
.TP 5
\fB\-\-write-injected-image\fR \fI<image-path>\fR
Write initial volume injection image to path
.B [Default: NONE]
.TP 5
\fB\-\-write-images-as-float\fR, \fB\-F\fR
Write output images as floating point [default: same as input]
.SH AUTHORS
Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko
.SH LICENSE
http://www.fsf.org/licensing/licenses/gpl.html
.SH BUGS
Report bugs at http://nitrc.org/projects/cmtk/
.SH 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.