transformix(1) apply geometric transform to an image


transformix mandatory-args [optional-args]


transformix applies a transform on an input image and/or generates a deformation field. The transform is specified in the transform-parameter file.


Call transformix from the command line with mandatory arguments:
-out output directory
-tp transform-parameter file, only 1

Optional extra commands:

-in input image to deform
-def file containing input-image points
the point are transformed according to the specified transform-parameter file use "-def all" to transform all points from the input-image, which effectively generates a deformation field.

-jac use "-jac all" to generate an image with the determinant of the spatial Jacobian
-jacmat use "-jacmat all" to generate an image with the spatial Jacobian matrix at each voxel
-priority set the process priority to high or belownormal (Windows only)
-threads set the maximum number of threads of transformix
At least one of the options "-in", "-def", "-jac", or "-jacmat" should be given.

The transform-parameter file must contain all the information necessary for transformix to run properly. That includes which transform to use, with which parameters, etc. For a usable transform-parameter file, see the output of elastix.