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

-loglevel set the log level to "off", "error", "warning", or "info" (default),

-priority set the process priority to high, abovenormal, normal (default),

belownormal, or idle (Windows only option)

-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, run elastix, and inspect the output file "TransformParameters.0.txt".

Need further help? Please check:

* the elastix website: https://elastix.dev * the source code repository site: https://github.com/SuperElastix/elastix * the discussion forum: https://groups.google.com/g/elastix-imageregistration