.TH epiunwarp "1" "Jan 25 2019" "CMTK 3.3.1p1" "The Computational Morphometry Toolkit"
.SH NAME
epiunwarp \- Unwarp Echo Planar Images
.SH SYNOPSIS
\fBepiunwarp\fR InputImage1 InputImage2 OutputImage1 OutputImage2 OutputDField OutputDFieldRev 
.SH DESCRIPTION
Correct B0 field inhomogeneity-induced distortion in Echo Planar Images (e.g., diffusion-weighted images) using two images acquired with opposing phase encoding directions.
.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 Input Image Parameters
.TP 5
\fB\-\-phase-encode\fR
Define the phase-encoded image coordinate direction.
Supported values: "phase-encode-ap", "phase-encode-is", "phase-encode-lr", where the default is "phase-encode-ap", or use one of the following:
.RS 5
.TP 5
\fB\-\-phase-encode-ap\fR, \fB\-y\fR
Anterior/posterior phase encoding (this is the most common case)
\fB[This is the default]\fR
.TP 5
\fB\-\-phase-encode-is\fR, \fB\-z\fR
Top/bottom phase encoding (this is rare)
.TP 5
\fB\-\-phase-encode-lr\fR, \fB\-x\fR
Lateral, left/right phase encoding (this is extremely rare)
.RE
.TP 5
\fB\-\-no-flip\fR
Use this switch is the reverse phase-encoded image does not need to be flipped prior to unwarping. If normal and reverse phase-encoded image display in the same gross orientation in 'triplanar', then flipping is not necessary and must be turned off using this switch.
.SS Optimization Parameters
.TP 5
\fB\-\-no-init-shift-com\fR
Disable initialization of unwarping by shifting each row to align the centers of mass of forward and reverse acquisition. Instead, use all-zero initial deformation field.
.TP 5
\fB\-\-smooth-sigma-max\fR \fI<double>\fR
Maximum image smoothing kernel width for coarsest level of multi-scale computation.
.B [Default: 8]
.TP 5
\fB\-\-smooth-sigma-min\fR \fI<double>\fR
Minimum image smoothing kernel width for finest level of multi-scale computation (0 = no smoothing; original image scale).
.B [Default: 0]
.TP 5
\fB\-\-smooth-sigma-diff\fR \fI<double>\fR
Difference between image smoothing kernel widths between two successive levels of the multi-scale computation.
.B [Default: 0.25]
.TP 5
\fB\-\-smoothness-constraint-weight\fR \fI<double>\fR
Weight factor for the second-order smoothness constraint term in the unwarping cost function.
.B [Default: 0]
.TP 5
\fB\-\-folding-constraint-weight\fR \fI<double>\fR
Weight factor for the folding-prevention constraint term in the unwarping cost function.
.B [Default: 0]
.TP 5
\fB\-\-iterations\fR \fI<integer>\fR, \fB\-i\fR \fI<integer>\fR
Number of L-BFGS optimization iterations (per multi-scale level).
.B [Default: 10]
.SS Output Options
.TP 5
\fB\-\-write-jacobian-fwd\fR \fI<string>\fR
Write Jacobian intensity correction map for forward image.
.B [Default: NONE]
.TP 5
\fB\-\-write-jacobian-rev\fR \fI<string>\fR
Write Jacobian intensity correction map for reverse-encoded image.
.B [Default: NONE]
.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.