ants registration parameters

anstreg.sh

antsRegistration --float --collapse-linear-transforms-to-fixed-image-header 0 --collapse-output-transforms 1 --dimensionality 3 --initial-moving-transform [ $FIXED, $MOVING, 1 ] --interpolation Linear --output [ output_, output_warped_image.nii.gz ] --transform Rigid[ 0.1 ] --metric Mattes[ $FIXED, $MOVING, 1, 32, Regular, 0.3 ] --convergence [ 10000x111110x11110, 1e-08, 20 ] --smoothing-sigmas 4.0x2.0x1.0vox --shrink-factors 3x2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 0 --transform Affine[ 0.1 ] --metric Mattes[ $FIXED, $MOVING, 1, 32, Regular, 0.3 ] --convergence [ 10000x111110x11110, 1e-08, 20 ] --smoothing-sigmas 4.0x2.0x1.0vox --shrink-factors 3x2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 0 --transform SyN[ 0.2, 3.0, 0.0 ] --metric Mattes[ $FIXED, $MOVING, 0.5, 32 ] --metric CC[ $FIXED, $MOVING, 0.5, 4 ] --convergence [ 100x50x30, -0.01, 5 ] --smoothing-sigmas 1.0x0.5x0.0vox --shrink-factors 4x2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.005, 0.995 ]  --write-composite-transform 1

antsreg.py

reg.inputs.transforms = ['Rigid', 'Affine', 'SyN']
reg.inputs.transform_parameters = [(0.1,), (0.1,), (0.2, 3.0, 0.0)]
reg.inputs.number_of_iterations = ([[10000, 111110, 11110]] * 2 + [[100, 50, 30]])
reg.inputs.dimension = 3
reg.inputs.write_composite_transform = True
reg.inputs.collapse_output_transforms = True
reg.inputs.initial_moving_transform_com = True
reg.inputs.metric = ['Mattes'] * 2 + [['Mattes', 'CC']]
reg.inputs.metric_weight = [1] * 2 + [[0.5, 0.5]]
reg.inputs.radius_or_number_of_bins = [32] * 2 + [[32, 4]]
reg.inputs.sampling_strategy = ['Regular'] * 2 + [[None, None]]
reg.inputs.sampling_percentage = [0.3] * 2 + [[None, None]]
reg.inputs.convergence_threshold = [1.e-8] * 2 + [-0.01]
reg.inputs.convergence_window_size = [20] * 2 + [5]
reg.inputs.smoothing_sigmas = [[4, 2, 1]] * 2 + [[1, 0.5, 0]]
reg.inputs.sigma_units = ['vox'] * 3
reg.inputs.shrink_factors = [[3, 2, 1]]*2 + [[4, 2, 1]]
reg.inputs.use_estimate_learning_rate_once = [True] * 3
reg.inputs.use_histogram_matching = [False] * 2 + [True]
reg.inputs.winsorize_lower_quantile = 0.005
reg.inputs.winsorize_upper_quantile = 0.995
reg.inputs.args = '--float'