film - Fix interleaved motion using inverse interpolation
film InputImage OutputImage
This tool splits an interleaved input image into the pass images, co- registers them, and reconstructs a motion-corrected image
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. --xml Write command line syntax specification in XML markup (for Slicer integration). --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 --padding-value <double> Set padding value for input image. Pixels with this value will be ignored. [Default: disabled] 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] Initial Volume Injection Options --injection-kernel-sigma <double>, -S <double> Standard deviation of Gaussian kernel for volume injection in multiples of pixel size in each direction. [Default: 0.5] --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] Inverse Interpolation 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) --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] Reconstruction Regularization Options --l-norm-weight <double> Set constraint weight for Tikhonov-type L-Norm regularization (0 disables constraint) [Default: 0] --no-truncation, -T Turn off regional intensity truncatrion 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]
Torsten Rohlfing, with contributions from Michael P. Hasak, Greg Jefferis, Calvin R. Maurer, Daniel B. Russakoff, and Yaroslav Halchenko
http://www.fsf.org/licensing/licenses/gpl.html
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.
Personal Opportunity - Free software gives you access to billions of dollars of software at no cost. Use this software for your business, personal use or to develop a profitable skill. Access to source code provides access to a level of capabilities/information that companies protect though copyrights. Open source is a core component of the Internet and it is available to you. Leverage the billions of dollars in resources and capabilities to build a career, establish a business or change the world. The potential is endless for those who understand the opportunity.
Business Opportunity - Goldman Sachs, IBM and countless large corporations are leveraging open source to reduce costs, develop products and increase their bottom lines. Learn what these companies know about open source and how open source can give you the advantage.
Free Software provides computer programs and capabilities at no cost but more importantly, it provides the freedom to run, edit, contribute to, and share the software. The importance of free software is a matter of access, not price. Software at no cost is a benefit but ownership rights to the software and source code is far more significant.
Free Office Software - The Libre Office suite provides top desktop productivity tools for free. This includes, a word processor, spreadsheet, presentation engine, drawing and flowcharting, database and math applications. Libre Office is available for Linux or Windows.
The Free Books Library is a collection of thousands of the most popular public domain books in an online readable format. The collection includes great classical literature and more recent works where the U.S. copyright has expired. These books are yours to read and use without restrictions.
Source Code - Want to change a program or know how it works? Open Source provides the source code for its programs so that anyone can use, modify or learn how to write those programs themselves. Visit the GNU source code repositories to download the source.
Study at Harvard, Stanford or MIT - Open edX provides free online courses from Harvard, MIT, Columbia, UC Berkeley and other top Universities. Hundreds of courses for almost all major subjects and course levels. Open edx also offers some paid courses and selected certifications.
Linux Manual Pages - A man or manual page is a form of software documentation found on Linux/Unix operating systems. Topics covered include computer programs (including library and system calls), formal standards and conventions, and even abstract concepts.