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Software at CIS : lddmm-landmark : Manual

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lddmm-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 (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.

Input Files:

Accepted input file formats are described here.

Optional Input:

  • Volume Space Specification
    The -w option (write volume transformation) requires a volume space specification file with the following format:
    Img_Width   Img_Height   NumofSlices   FovX    FovY   SliceThickness

    Where:
    • Img_Width - Number of voxels in X dimension.
    • Img_Height - Number of voxels in Y dimension.
    • NumofSlices - Number of Slices (voxels in Z dimension).
    • FovX - Field of View X (Img_Width * Resolution in X).
    • FovY - Field of View Y (Img_Width * Resolution in Y).
    • SliceThickness - Slice Thickness (Resolution in Z).
  • Point Transformation File
    The -p option (write point transform) accepts as input any of the landmark file formats described in the "Input Files" section above.
  • Volume Space Specification
    The -A option accepts vtk format image data files.

Output:

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:

  • .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 vector valued volume with the absolute transformation vector (x, y, z, in 32 bit float) at each voxel. The size and resolution of the volume are based on the Volume Space Specification File described above. Also known as the Hmap 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 size and resolution of the volume are based on the Volume Space Specification File described above. Could be described as the differential Hmap of the transformation.
  • .xbd - optional (-W): A binary file consisting of a vector valued volume with the absolute reverse transformation vector (x, y, z, in 32 bit float) at each voxel. The size and resolution of the volume are based on the Volume Space Specification File described above. Also known as the KiMap of the transformation.
  • .dbd - optional (-D): A raw binary file consisting of a volume with the relative reverse transformation vector (x, y, z, in 32 bit float) at each voxel. The size and resolution of the volume are based on the Volume Space Specification File described above. Could be described as the differential KiMap of the transformation.
  • .xfm.vtk - optional (-E): A vtk formatted Hmap of the transformation. Same as -w but in vtk vector field format.
  • .dfm.vtk - optional (-F): A vtk formatted differential Hmap of the transformation. Same as -d but in vtk vector field format.
  • .xbd.vtk - optional (-G): A vtk formatted KiMap of the transformation. Same as -W but in vtk vector field format.
  • .dbd.vtk - optional (-H): A vtk formatted differential Kimap of the transformation. Same as -D but in vtk vector field format.
  • Flowed<PointFileName> - optional (-p <PointFileName>) The filename of the output file produced when the Point Transformation option is invoked will be "Flowed" appended by the Point Transformation File name specified. The format of this file will be the LDDMM-Similitude File Format described here.
  • Flowed<VolumeFileName> - optional (-A <VolumeFileName>) The filename of the output file produced when the Volume Transformation option is invoked will be "Flowed" appended by the Volume Transformation File name specified.

Last Modified: Wednesday, 23rd March, 2011 @ 11:22am

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