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Software @ CIS : lddmm-landmark : Manualmanual | faq | input formats | validation | credits | changelog | feedbacklddmm-landmark: Match template landmarks to target landmarks. Usage: (default values are in parentheses) lddmm-landmark [OPTIONS] <template_landmark_set> <subject_file_or_directory> OPTIONS -X || --vtk-xml: input files are in vtk landmark format -l || --lambda <lambda> (def = 100.000000) -s || --sigma <sigma> (def = 0.250000) -o || --optimizationType <opt (a=auto, g=gradient descent, n=Newton's method, def = n)> -t || --timeSteps <timeSteps> (def = 10) -r || --maxIterations <maxIterations> (def = 20) -j || --trajectories: write out all the trajectory values into a .trj file. -m || --momentums: write out all the momentum values into a .mom file. -c || --costsAndErrors: write out cost (.lci) and error (.lei) values by iteration into files. -w || --writeXForm <volume space file> write out an absolute volume transformation file (Kimap) based on the volume space file specification. -d || --writeDXForm <volume space file> write out a relative volume transformation file based on the volume space file specification. -p || --pointXForm <point set file> flow the points in the file according to lddmm output. -A || --applyDeformation <vtk format image file>: create a volume transformation and apply it to a volume. -i || --initialCost: produce only the initial cost values. -v || --version : display the version. -h || --help : display this message. -a || --all-info : print out data provenance information. -x || --all-info-xml : print out data provenance information in an xml format. Input Files: Accepted input file formats are described here. Optional Input:
The base name of all the output files will be the concatenation of the template and target file specs, minus their extensions. Each output file will have a different extension: .abs - The metric distance file. .les - The metric distance file with covariance (if any). .dft - The deformed template. .dft.lmk - The deformed template in standard lmk format. .imo - The initial momentums. .tfl - Contains the names of all the target files the template is compared against. .lcs - the initial value of the cost function. .trj - optional (-a): the trajectories at each time point. .mom - optional (-m): the momentum values over time. .lei - optional (-c): the values of the distance between the deformed template and the target at each iteration of the solution. .lci - optional (-c): the values of the cost function at each iteration of the solution. .xfm - optional (-w): A binary file consisting of a volume with the absolute transformation vector (x, y, z, in 32 bit float) at each voxel. The volume properties are based on the Volume Space Specification described above. Also known as the Kimap of the transformation. .dfm - optional (-d): A binary file consisting of a volume with the relative transformation vector (x, y, z, in 32 bit float) at each voxel. The volume properties are based on the Volume Space Specification described above. Equal to the Kimap - absolute position of each voxel. The filename of the output file produced when the Point Transformation option is invoked will be "Flowed" appended by the Point Transformation File name described above. The format of this file will be the LDDMM-Similitude File Format described here.
Last Modified: Monday, 22-Jun-2009 11:02:43 EDT |
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