initial transformation:
12 numbers specifying the initial transformation before optimization. The first 3 parameters specify the angles around the z-, the rotated x- and the double-rotated z-axis, parameters 4-6 specify the translation along the x-, y- and z-axis, parameters 7-9 specify the scale along the x-, y- and z-axis, the remaining parameters 10-15 specify the shearing.

tolerance:
The lower the value for tolerance, the longer the optimization will take, resulting in an improved result.

coarse level:
Optimization is performed in a multi-resolution approach. A coarse level of 3 means that the images are resampled 3 times (by a factor of 2), so the image size is 1/8th of the original image in each dimension, for the first optimization round.

fine level:
The final optimization is performed on this level. A value of 1 means that the final optimization is performed on half the original resolution.

Template:
The reference image to which the model image is aligned.

Model:
The image that is going to be transformed to match the template.

out-of-bounds value:
Should be set to the estimated background value in the images.

bounding box:
6 numbers specifying the offset (x, y and z) and the extent (w, h and d) of an optional bounding box. If set, optimization will only consider this region (in the template image).

Rotation:

Translation:

Scaling:

Shearing:
Only selected parameters are optimized.

Presets:
Some presets for convenience. Selecting “Affine” will select all check boxes above, “Rigid” will select only rotation and translation parameters, etc.