Create template
I am learning to use Dartel for registration. By default, in batch module, Dartel (create template) runs 6 iterations to estimate the final template.
It runs six outer iterations (generating a series of six templates), but each of these does three inner iterations.
1) Except the non-linear deformation, does it also run affine transformation in each of the iteration?
No, it just does the nonlinear warping. It assumes that the "imported" rc1, rc2 etc images (generated by the segmentation) have been approximately aligned to MNI space with the closest rigid body transform. Within each header of the rc images is an additional matrix, which relates the positioning of the imported image with that of the original data.
For those on the list using the longitudinal toolbox of SPM12, you should note that rigid-body and non-linear registration (as well as bias correction) are combined into the same procedure.
2) Does it use the registration results of each subject from to previous iteration as the input images, and register them to the averaged template in each iteration?
At each iteration, it takes the previous estimate of the deformations, and refines them by matching the images and current template together slightly more accurately. Then the template is re-generated from the (Jacobian weighted) average of the original rc* images.
Best regards,
-John