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Software at CIS : lddmm-volume : Tutorial

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Overview

This tutorial will contain the basic architecture of the software. Currently we have the data flow in the LDDMM software along with some sample output visualized using Matlab 6. This section also contains the format of the files in the output and the description of all the files. This is espcially valueable for BIRN partners using the LDDMM through the BIRN Portal. This output generated by LDDMM to be viewed with VTK visualizaion applications. Click here for more information.

The following diagram is a basic overview of the software's dataflow:

Output Files

The following is the list of the files that the LDDMM software currently produces.
Notes
  1. ~ implies the number of timesteps LDDMM is ran over. For example File~.vtk at 5 timesteps means the output will be File1.vtk, File2.vtk, File3.vtk, File4.vtk, and File5.vtk.
  2. Data files in the Z direction will only appear when the input data is in 3 dimensions.
  • VTK Output
    1. MoviedefAtlas~.vtk These files contain the vtk data of the deformed
    atlas or the atlas image composed with the inverse diffeomorphism
    over each timestep.
    2. MoviedefPatient~.vtk These files contain the vtk data of the deformed
    patient or the patient image composed with the diffeomorphism
    over each timestep
    3. MovieHxmap~.vtk
    MovieHymap~.vtk
    MovieHzmap~.vtk
         		VTK data of the inverse diffeomorphism
    over each timestep in each direction.
    4. MovieKixmap~.vtk
    MovieKiymap~.vtk
    MovieKizmap~.vtk
    		 VTK data of the diffeomorphism
    over each timestep in each direction.
    5. MovieVelocityX~.vtk
    MovieVelocityY~.vtk
    MovieVelocityZ~.vtk
    		 Velocity at each timestep in each direction



Sample I/O Data

Click here to download the input data used (monkey brain 80x80x1) and click here to download the output data. Please be sure to credit the Lab of Dr. David Van Essen of Washington University for the input data and the LDDMM software group for the output data.

The following are some of visualizations of the output generated by LDDMM on the monkey brain data.




compareIO.eps



IOerror.eps



HGridPlot.eps.



KiGridPlot.eps


VTK

For more information on file formats in VTK please refer to this document.

Last Modified: Thursday, 30th May, 2013 @ 09:30am

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