In the OF experiments, the following file was used with variation in the objective functions used.
// GENERAL ARGUMENTS
matcher: comp_region_matcher
sampler: raw_intensity
pair_tex_objective_fn: mi { }
pair_shape_objective_fn: def_energy { } // Typical values 0.001
pair_tex_weighting: 0.5
group_tex_objective_fn: wtd_abs_diff { }
group_shape_objective_fn: def_energy { }
group_tex_weighting: 0.00005
points_selector: all { border: 1 fi_lo: 0.10 fi_hi: 0.9 fj_lo: 0.1 fj_hi: 0.9 }
pyr_builder: gaussian
warps_affect_warp_regions: false
images: {
/home/S00/schestr0/NRR/BrainExperiments/DemBrains/abra_l_auto
/home/S00/schestr0/NRR/BrainExperiments/DemBrains/bowl_i_auto
}
///////////////////////////////////////////////////////////
// TRANSLATION STAGE
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
}
///////////////////////////////////////////////////////////
// SCALING STAGE
pairwise_stage: {
warper: scale
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
}
///////////////////////////////////////////////////////////
// TRANSLATION STAGE
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
}
///////////////////////////////////////////////////////////
// SCALING STAGE
pairwise_stage: {
warper: scale
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
}
///////////////////////////////////////////////////////////
// AFFINE STAGE
pairwise_stage: {
warper: affine
warp_penalty_fn: zero { }
region_picker: all { }
levels: 2 2
optimisation_method: simplex
param_tol: 0.001
use_exhaustive_search: false
n_per_dim: 5
optimise_many_warps: false
}
pairwise_stage: {
warper: affine
warp_penalty_fn: zero { }
region_picker: all { }
levels: 1 1
optimisation_method: simplex
param_tol: 0.001
use_exhaustive_search: false
n_per_dim: 5
optimise_many_warps: false
}
///////////////////////////////////////////////////////////
// NON-RIGID STAGE
pairwise_stage: {
warper: bilin_grid { ni: 4 nj: 4 nk: 4 }
warp_penalty_fn: zero { }
region_picker: all { }
levels: 2 2
optimisation_method: downhill_search
param_tol: 0.001
use_exhaustive_search: false
n_per_dim: 5
optimise_many_warps: false
n_opt_its: 10
}
pairwise_stage: {
warper: bilin_grid { ni: 5 nj: 5 nk: 5 }
warp_penalty_fn: zero { }
region_picker: all { }
levels: 1 1
optimisation_method: downhill_search
param_tol: 0.001
use_exhaustive_search: false
n_per_dim: 5
optimise_many_warps: false
n_opt_its: 10
}