svn co https://svn.janelia.org/penglab/projects/vaa3d_tools/released_plugins/v3d_plugins/principalskeleton_detection

   Usage : v3d -x principal_skeleton -f detect -i <inimg_file> <iniskele_file> <domain_file> 
               -o <deformskele_file> <cubicswc_file> -p <channel> <stop_thresh>

    inimg_file         name of input image file
    iniskele_file      name of input initial skeleton file (.marker)
    domain_file        name of input domain definition file (.domain)
    deformskele_file   name of output deformed skeleton control points in a marker file (.marker)
    cubicswc_file      name of output cubic-spline smoothed skeleton swc file (.swc)
    channel            the input channel value, default 2 and start from 0
    stop_thresh        stop threshold, default 0.01

   e.g. v3d -x principal_skeleton -f detect -i input.raw iniskele_file.marker domain_file.domain 
            -o deformskele.marker cubicswc.swc -p 2 0.01

   Usage : v3d -x principal_skeleton -f warp -i <subimg_file> <submak_file> <tarimg_file> <tarmak_file> 
                  <domain_file> -o <outimg_file>

    subimg_file     file name of subject image
    submak_file     file name of subject skeleton (.marker)
    tarimg_file     file name of target image
    tarmak_file     file name of target skeleton (.marker)
    domain_file     file name of domain definition (.domain)

  e.g. v3d -x principal_skeleton -f warp -i subimg.raw submak.marker tarimg.raw 
              tarmak.marker domain_file.domain -o outimg.raw