ANTSAPPLYTRANSFORMSTOPOINTS(1) User Commands ANTSAPPLYTRANSFORMSTOPOINTS(1)
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
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 ]
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.
-d, --dimensionality 2/3
This option forces the points to be treated as a specified-dimensionality.
-p, --precision 0/1
-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 trans‐
formed 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 coordi‐
nates. 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
Several transform options are supported including all those defined in the ITK
library in addition to a deformation field transform. The ordering of the transfor‐
mations follows the ordering specified on the command line. An identity transform
is pushed onto the transformation stack. Each new transform encountered on the com‐
mand 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
antsApplyTransformsToPoints 2.2.0 August 2017 ANTSAPPLYTRANSFORMSTOPOINTS(1)