-f: mandatory argument for elastix with the file name of the fixed image.
example: -f fixedImage.mhd

-m: mandatory argument for elastix with the file name of the moving image.
example: -m movingImage.mhd

-out: mandatory argument for both elastix and transformix with the name of the directory that is going to contain everything that elastix or tranformix returns as output.
example: -out outputdirectory

-p: mandatory argument for elastix with the name of the parameter file.
example: -p parameters.txt
Multiple parameter files are allowed. It means that multiple registrations are runned in sequence, with the output of some registration as input to the next.

-fMask: Optional argument for elastix with the file name of a mask for the fixed image. The mask image should contain of zeros and ones, zeros indicating pixels that are not used for the registration.
example: -fMask fixedmask.mhd

-mMask: Optional argument for elastix with the file name of a mask for the moving image. The mask image should contain of zeros and ones, zeros indicating pixels that are not used for the registration.
example: -mMask movingmask.mhd

-tp: mandatory argument for transformix with the name of the transform parameter file.
example: -tp TransformParameters.txt
In one such a transform parameter file a reference can be used to another transform parameter file, which is then used as an initial transform.

-priority: optional argument for both elastix and transformix to specify the priority setting of this process. Choose one from {belownormal, high}.
example: -priority high
This argument is only valid for running under Windows. For Linux, run elastix with "nice".

-threads: optional argument for both elastix and transformix to specify the maximum number of threads used by this process. Default: no maximum.
example: -threads 2

-in: optional argument for transformix with the file name of an input image.
example: -in inputImage.mhd
If this option is skipped, a deformation field of the transform will be generated.

Class elastix::SplineKernelTransform< TElastix >

-fp: a file specifying a set of points that will serve as fixed image landmarks.
example: -fp fixedImagePoints.txt
The fixedImagePoints.txt file should be structured: first line should be "index" or "point", depending if the user supplies voxel indices or real world coordinates. The second line should be the number of points that should be transformed. The third and following lines give the indices or points. The same structure thus as used for transformix.

-mp: an optional file specifying a set of points that will serve as moving image landmarks, used to initialize the transformation.
example: -mp movingImagePoints.txt
The movingImagePoints.txt should be structured like the fixedImagePoints.txt. The moving landmarks should be corresponding to the fixed landmarks. If no file is provided, the transformation is initialized to be the identity, i.e. the moving landmarks are chosen identical to the fixed landmarks.

Class elastix::TransformBase< TElastix >

-t0: optional argument for elastix for specifying an initial transform parameter file.
example: -t0 TransformParameters.txt

-def: optional argument for transformix for specifying a set of points that have to be transformed.
example: -def inputPoints.txt
The inputPoints.txt file should be structured: first line should be "index" or "point", depending if the user supplies voxel indices or real world coordinates. The second line should be the number of points that should be transformed. The third and following lines give the indices or points.
It is also possible to deform all points, thereby generating a deformation field image. This is done by:
example: -def all

Global PrintHelp (void)

–help: optional argument for elastix and transformix to call the help.
example: elastix –help
example: transformix –help

–version: optional argument for elastix and transformix to call version information.
example: elastix –version
example: transformix –version