Provided by: cmtk_3.3.1p2+dfsg-2build1_amd64
epiunwarp - Unwarp Echo Planar Images
epiunwarp InputImage1 InputImage2 OutputImage1 OutputImage2 OutputDField OutputDFieldRev
Correct B0 field inhomogeneity-induced distortion in Echo Planar Images (e.g., diffusion- weighted images) using two images acquired with opposing phase encoding directions.
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 Image Parameters --phase-encode 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: --phase-encode-ap, -y Anterior/posterior phase encoding (this is the most common case) [This is the default] --phase-encode-is, -z Top/bottom phase encoding (this is rare) --phase-encode-lr, -x Lateral, left/right phase encoding (this is extremely rare) --no-flip 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. Optimization Parameters --no-init-shift-com 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. --smooth-sigma-max <double> Maximum image smoothing kernel width for coarsest level of multi-scale computation. [Default: 8] --smooth-sigma-min <double> Minimum image smoothing kernel width for finest level of multi-scale computation (0 = no smoothing; original image scale). [Default: 0] --smooth-sigma-diff <double> Difference between image smoothing kernel widths between two successive levels of the multi-scale computation. [Default: 0.25] --smoothness-constraint-weight <double> Weight factor for the second-order smoothness constraint term in the unwarping cost function. [Default: 0] --folding-constraint-weight <double> Weight factor for the folding-prevention constraint term in the unwarping cost function. [Default: 0] --iterations <integer>, -i <integer> Number of L-BFGS optimization iterations (per multi-scale level). [Default: 10] Output Options --write-jacobian-fwd <string> Write Jacobian intensity correction map for forward image. [Default: NONE] --write-jacobian-rev <string> Write Jacobian intensity correction map for reverse-encoded image. [Default: NONE]
Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko
Report bugs at http://nitrc.org/projects/cmtk/
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.