There are two basic methods to get an initial transformation to start the optimization process. The first, by default, uses the principal axes transformation (PAT) as the starting transformation. For the second method, the user specifies a .xfm file that contains a linear transformation, mapping points of volume one (source) into volume two (target).
The program extracts the transformation parameters from either transformation matrix (PAT or user input) and optimizes these parameters when trying to find the best transformation.
When the PAT is used, the center of rotation and scaling is automatically estimated from the center of gravity of the source data set. When the user specifies a transformation matrix, the default center is 0,0,0. The user can can change this in two ways: 1) the -center cx cy cz option permits direct input of the center to be used, 2) the -est_center option tells the program to calculate and use the center of gravity of the source volume. Note that it is a good idea to have a reasonable guess for the center of rotation and scaling since it makes the parameters more orthogonal to each other (e.g. a small change in rotation will not grossly affect the translations). Note that you can use -est_center to have the program estimate the center of gravity.
From minctracc -help:
Initial transformation information. -transformation: Initial world transformation. (Default = identity). -est_center: use center estimated from Principal axis transformation. -est_scales: use scales estimated from Principal axis transformation. -est_rotations: use rotations estimated from Principal axis transformation. -est_translations: use translations estimated from Principal axis transformation. -center: Force center of rotation and scale. Default value: 0 0 0
One can also use only part of the PAT parameters by specifying -est_center, -est_scales, -est_rotations or -est_translations. Often we have found that when the principal axis are difficult to determine (as in cases of data sets with few slices) that the center and translation are the only reliable information that can be determined. So the parameters -est_center -est_translations are used to specify the initial starting position.