antsApplyTransformsToPoints - part of ANTS registration suite
- 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
82.5,116.5,0,0,1,this is the breast 137.5,35.5,0,0,2,this
- is the beak
- [chicken3to4.mat ,1 ]
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
**** 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
- Note: To write a mha
- file, you must also pass an mha file as input.
- This option forces the points to be treated as a
- 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
pass in a 2D mha (meta format) binary image file.
- One can output the warped points to a csv file.
- -t, --transform transformFileName
- 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
- Print the help menu (short version). <VALUES>: 0
- Print the help menu. <VALUES>: 1, 0