Large Deformation Diffeomorphic Metric Mapping @ CIS : Manual

Usage: (default values are in parentheses) lddmm-landmark [OPTIONS] <,template_landmark_set>, <,subject_file_or_directory>, -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 (Hmap) based on the volume space file specification. Output file extension is '.xfm'. -d || --writeDXForm <,volume space file>, write out a relative volume transformation file (differential Hmap) based on the volume space file specification. Output file extension is '.dfm'. -W || --writeBackXForm <,volume space file>, write out an backwards volume transformation file (KiMap) based on the volume space file specification. Output file extension is '.xbd'. -D || --writeBackDXForm <,volume space file>, write out a backwards relative volume transformation file (differential KiMap) based on the volume space file specification. Output file extension is '.dbd'. -E || --writeVTKXForm <,volume space file>,: write out a VTK volume transformation file (Hmap) based on the volume space file specification. Output file extension is '.xfm.vtk'. -F || --writeVTKDXForm <,volume space file>,: write out a VTK difference transformation file (differential Hmap) based on the volume space file specification. Output file extension is '.dfm.vtk'. -G || --writeVTKBackXForm <,volume space file>,: write out a VTK backwards volume transformation file (KiMap) based on the volume space file specification. Output file extension is '.xbd.vtk'. -H || --writeBackVTKDXForm <,volume space file>,: write out a VTK backwards difference transformation file (differential KiMap) based on the volume space file specification. Output file extension is '.dbd.vtk'. -p || --pointXForm <,point set file>, flow the points in the file according to lddmm output. -A || --applyDeformation <,vtk or Analyze image file>,: create a volume transformation and apply it to a volume. -B || --swappedVolume: (for use with -A option) indicates swapped voxel order of image file. -C || --nearestNeighborInterpolation: (for use with -A option) use Nearest Neighbor Interpolation (vs. Trilinear). Normally used for binary images. -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. The base name of all the output files will be the concatenation of the template and target file specs and an appended extension. Each output file will have a different extension: Source.


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