NAME

       antsApplyTransformsToPoints - part of ANTS registration suite

DESCRIPTION

   COMMAND:
              antsApplyTransformsToPoints

              antsApplyTransformsToPoints,  applied to an input image, transforms it according to
              a reference image and a transform (or a set of transforms). reads  in  a  csv  file
              with  the  first D columns defining the spatial location where the spatial location
              is defined in physical coordinates. the csv file should have a header row. here  is
              an example

       cat chicken-3.csv

              x,y,z,t,label,comment

       82.5,116.5,0,0,1,this is the breast 137.5,35.5,0,0,2,this

              is the beak

       antsApplyTransformsToPoints -d 2 -i chicken-3.csv -o test.csv -t

              [chicken3to4.mat ,1 ]

       cat test.csv

       x,y,z,t,label,comment                          10.8945447481644,162.082675013049,0,0,1,nan
       7.5367085472988,52.099713111629,0,0,2,nan the nan appears in the last column until the ITK
       CSV I/O can handle mixed numeric /

              string types. if your input is fully numeric, all is well.

       **** We now can also

              read / write .mha files.

       This is a simple binary format (Meta format - look it

              up!) that is much faster to read/write than csv format.

              Note: To write a mha

              file, you must also pass an mha file as input.

   OPTIONS:
       -d, --dimensionality 2/3

              This option forces the points to be treated as a specified-dimensionality.

       -p, --precision 0/1

              use-double-precision

       -f, --forantsr 0/1

              set true for ANTsR IO

       -i, --input inputFileName

              Currently,  the  only  input supported is a csv file with columns including x,y,z,t
              (all 4) column headers. if you dont have 4D data, still supply 4D filling in  extra
              places  with  zero.  The  points  should  be  defined in physical space. Points are
              transformed in the OPPOSITE direction of images,  therefore  you  should  pass  the
              inverse  of  what  is  needed  to  warp  the  images.  Eg if the image is warped by
              Affine.mat, you should pass the inverse of Affine.mat to transform  points  defined
              in  the  same  space as the image. If in doubt how to convert coordinates from your
              files to the space required by antsApplyTransformsToPoints try  creating/drawing  a
              simple  label  volume  with  only one voxel set to 1 and all others set to 0. Write
              down the voxel coordinates.  Then  use  ImageMaths  LabelStats  to  find  out  what
              coordinates for this voxel antsApplyTransformsToPoints is expecting. ITK uses a LPS
              coordinate                               system.                                See
              http://sourceforge.net/p/advants/discussion/840261/thread/2a1e9307/ ***Or pass in a
              2D mha (meta format) binary image file.

       -o, --output warpedOutputFileName

              One can output the warped points to a csv file.

       -t, --transform transformFileName
              [transformFileName,useInverse]

              Several transform options are supported including all  those  defined  in  the  ITK
              library  in  addition  to  a  deformation  field  transform.  The  ordering  of the
              transformations follows the ordering specified on the  command  line.  An  identity
              transform  is  pushed onto the transformation stack. Each new transform encountered
              on the command line is also pushed onto the transformation stack.   Then,  to  warp
              the  input object, each point comprising the input object is warped first according
              to the last transform pushed  onto  the  stack  followed  by  the  second  to  last
              transform,  etc.  until  the  last  transform  encountered  which  is  the identity
              transform. Also, it should be noted that the inverse transform can be  accommodated
              with  the  usual  caveat  that  such  an  inverse  must be defined by the specified
              transform class

       -h

              Print the help menu (short version).  <VALUES>: 0

       --help

              Print the help menu.  <VALUES>: 1, 0