Merge pull request #554 from satra/fix/ants

Fix/ants

Author: chrisgorgo

examples/smri_ants_registration.py

@@ -54,26 +54,31 @@
 """
 
 reg = Registration()
-reg.inputs.fixed_image =  [input_images[0], input_images[0] ]
-reg.inputs.moving_image = [input_images[1], input_images[1] ]
-reg.inputs.transforms = ['Affine', 'SyN']
-reg.inputs.transform_parameters = [(2.0,), (0.25, 3.0, 0.0)]
-reg.inputs.number_of_iterations = [[1500, 200], [100, 50, 30]]
-reg.inputs.dimension = 3
-reg.inputs.write_composite_transform = True
-reg.inputs.metric = ['Mattes']*2
-reg.inputs.metric_weight = [1]*2 # Default (value ignored currently by ANTs)
-reg.inputs.radius_or_number_of_bins = [32]*2
-reg.inputs.sampling_strategy = ['Random', None]
-reg.inputs.sampling_percentage = [0.05, None]
-reg.inputs.convergence_threshold = [1.e-8, 1.e-9]
-reg.inputs.convergence_window_size = [20]*2
-reg.inputs.smoothing_sigmas = [[1,0], [2,1,0]]
-reg.inputs.shrink_factors = [[2,1], [3,2,1]]
-reg.inputs.use_estimate_learning_rate_once = [True, True]
-reg.inputs.use_histogram_matching = [True, True] # This is the default
+reg.inputs.fixed_image =  input_images[0]
+reg.inputs.moving_image = input_images[1]
 reg.inputs.output_transform_prefix = 'thisTransform'
 reg.inputs.output_warped_image = 'INTERNAL_WARPED.nii.gz'
+
+reg.inputs.transforms = ['Translation', 'Rigid', 'Affine', 'SyN']
+reg.inputs.transform_parameters = [(0.1,), (0.1,), (0.1,), (0.3, 3.0, 0.0)]
+reg.inputs.number_of_iterations = [[10000, 0, 0], [10000, 0, 0], [10000, 0, 0], [10, 0, 0]]
+reg.inputs.dimension = 3
+reg.inputs.write_composite_transform = True
+reg.inputs.collapse_output_transforms = True
+reg.inputs.metric = ['Mattes']*4
+reg.inputs.metric_weight = [1]*4 # Default (value ignored currently by ANTs)
+reg.inputs.radius_or_number_of_bins = [32]*4
+reg.inputs.sampling_strategy = ['Regular']*3 + [None]
+reg.inputs.sampling_percentage = [0.1]*3 + [None]
+reg.inputs.convergence_threshold = [1.e-8]*4
+reg.inputs.convergence_window_size = [20]*4
+reg.inputs.smoothing_sigmas = [[4,2,1]]*3 + [[2,1,0]]
+reg.inputs.sigma_units = ['vox']*4
+reg.inputs.shrink_factors = [[6,4,2]]*3 + [[4,2,1]]
+reg.inputs.use_estimate_learning_rate_once = [True, True, True, True]
+reg.inputs.use_histogram_matching = [False]*3 + [True] # This is the default
+reg.inputs.initial_moving_transform_com = True
+reg.inputs.output_warped_image = True
 reg.cmdline