Translation

The first stage brought significant improvements:

pairwise_stage: {

  warper: translation

  warp_penalty_fn: zero { }

  region_picker: all { }

  levels: 1 2

  optimisation_method: simplex

  param_tol: 0.001

  use_exhaustive_search:  false

  n_per_dim: 5

  optimise_many_warps:  false

}

The next stage made very little improvement which is subjective.The only difference was that of levels to:

levels: 0 1

The next stage was identical to its predecessor and it appeared to align one side of the brain at the expense of another. The overall conclusion is that the first stage only (was default) should suffice. Going to a finer resolution does not result in much better results of translation.