You need to specify at least two data volumes on the command line, the first is the source volume and second is the target volume. The third item on the command line is the name of the output transformation file, specifying where the program will store the results.
Using flags on the command line, you may specify the type of transformation to be optimized and saved, mask files to be used with the source or target volumes, a transformation file to specify the initial starting condition, the type of objective function to be minimized, the type of interpolation to use, and the definition of the sampling matrix used to measure the objective function.
Internally, the program optimizes the transformation parameters of translations, rotations, scaling(s) and possibly shear(s). These parameters are used to create a homogeneous transformation matrix that maps the data in the space of the first volume to the space of the second volume. It is this matrix that is saved in the output transformation file.
The following paragraphs describe the program in slightly more detail.