The following are examples of command line execution of minctracc:
1: minctracc volume.mnc target.mnc trans.xfm
This is the simplest invocation of minctracc. Here volume.mnc will be fit onto target.mnc and the transformation recovered will be returned in trans.xfm. By default, the principal axis transformation will be used to initiate the 7 parameter optimization using the cross-correlation objective function. The sampling lattice will have spacing between node by default.
2: minctracc volume.mnc target.mnc trans.xfm -est_center -est_translation
If the principal axes transformation cannot give a good starting guess because it cannot estimate the rotation angles (due to partial volume effects, or otherwise...), we can eliminate them from the starting guess by using the -est_center -est_translation flags. In this way, only the center of rotation and the translation necessary to align two volumes will be used to start the optimization.
3:
minctracc volume.mnc target.mnc start.xfm -est_center -lsq6 -step 8 8 8
minctracc volume.mnc target.mnc trans.xfm -est_center -lsq9 \
-transformation start.xfm
Suppose that minctracc had already been used to to get start.xfm. This transformation can be used as a starting point for a new optimization where the number of optimization parameters is increased (as above), or the spacing between nodes decreased (also as above, since we start with spacing of 8 8 8, and the second uses a default spacing of 4 4 4).