warp_setting=registration_setting)
simpleGlobal_alignment_spec = dict(stack_m=brain_m_spec,
stack_f=brain_f_spec,
warp_setting=0)
aligner_parameters = generate_aligner_parameters_v2(
alignment_spec=alignment_spec,
structures_m=structures_m,
fixed_structures_are_sided=True,
fixed_surroundings_have_positive_value=
fixed_surroundings_have_positive_value,
fixed_use_surround=fixed_use_surround)
aligner = Aligner(aligner_parameters['volume_fixed'],
aligner_parameters['volume_moving'],
labelIndexMap_m2f=aligner_parameters['label_mapping_m2f'])
aligner.compute_gradient(smooth_first=True)
aligner.set_label_weights(label_weights=aligner_parameters['label_weights_m'])
################################
if use_simple_global:
T_atlas_wrt_canonicalAtlasSpace_subject_wrt_wholebrain_atlasResol = bp.unpack_ndarray_file(
'/home/yuncong/' + brain_f_spec['name'] +
'_T_atlas_wrt_canonicalAtlasSpace_subject_wrt_wholebrain_atlasResol.bp'
)
aligner.set_initial_transform(
T_atlas_wrt_canonicalAtlasSpace_subject_wrt_wholebrain_atlasResol)
aligner.set_centroid(centroid_m='structure_centroid',
fixed_use_surround = False
else:
raise
alignment_spec = dict(stack_m=brain_m_spec, stack_f=brain_f_spec, warp_setting=registration_setting)
simpleGlobal_alignment_spec = dict(stack_m=brain_m_spec, stack_f=brain_f_spec, warp_setting=0)
aligner_parameters = generate_aligner_parameters_v2(alignment_spec=alignment_spec,
structures_m=structures_m,
fixed_structures_are_sided=True,
fixed_surroundings_have_positive_value=fixed_surroundings_have_positive_value,
fixed_use_surround=fixed_use_surround)
aligner = Aligner(aligner_parameters['volume_fixed'],
aligner_parameters['volume_moving'],
labelIndexMap_m2f=aligner_parameters['label_mapping_m2f'])
aligner.compute_gradient(smooth_first=True)
aligner.set_label_weights(label_weights=aligner_parameters['label_weights_m'])
################################
if use_simple_global:
T_atlas_wrt_canonicalAtlasSpace_subject_wrt_wholebrain_atlasResol = bp.unpack_ndarray_file('/home/yuncong/CSHL_simple_global_registration/' + brain_f_spec['name'] + '_T_atlas_wrt_canonicalAtlasSpace_subject_wrt_wholebrain_atlasResol.bp')
aligner.set_initial_transform(T_atlas_wrt_canonicalAtlasSpace_subject_wrt_wholebrain_atlasResol)
aligner.set_centroid(centroid_m='structure_centroid', centroid_f='centroid_m')
else:
T_atlas_wrt_canonicalAtlasSpace_subject_wrt_wholebrain_atlasResol = np.array([[1,0,0,0],[0,1,0,0],[0,0,1,0]])
aligner.set_initial_transform(T_atlas_wrt_canonicalAtlasSpace_subject_wrt_wholebrain_atlasResol)
aligner.set_centroid(centroid_m='structure_centroid', centroid_f='structure_centroid')