ants package

Subpackages

• ants.contrib package
  • Subpackages
    • ants.contrib.bids package
      • Submodules
      • ants.contrib.bids.cohort module
      • Module contents
    • ants.contrib.sampling package
      • Submodules
      • ants.contrib.sampling.affine2d module
        • RandomRotate2D
          • RandomRotate2D.transform()
        • RandomShear2D
          • RandomShear2D.transform()
        • RandomTranslate2D
          • RandomTranslate2D.transform()
        • RandomZoom2D
          • RandomZoom2D.transform()
        • Rotate2D
          • Rotate2D.transform()
        • Shear2D
          • Shear2D.transform()
        • Translate2D
          • Translate2D.transform()
        • Zoom2D
          • Zoom2D.transform()
      • ants.contrib.sampling.affine3d module
        • Affine3D
          • Affine3D.transform()
        • RandomRotate3D
          • RandomRotate3D.transform()
        • RandomShear3D
          • RandomShear3D.transform()
        • RandomTranslate3D
          • RandomTranslate3D.transform()
        • RandomZoom3D
          • RandomZoom3D.transform()
        • Rotate3D
          • Rotate3D.transform()
        • Shear3D
          • Shear3D.transform()
        • Translate3D
          • Translate3D.transform()
        • Zoom3D
          • Zoom3D.transform()
      • ants.contrib.sampling.transforms module
        • List of Transformations:
        • BlurIntensity
          • BlurIntensity.transform()
        • CastIntensity
          • CastIntensity.transform()
        • FlipImage
          • FlipImage.transform()
        • LocallyBlurIntensity
          • LocallyBlurIntensity.transform()
        • MultiResolutionImage
          • MultiResolutionImage.transform()
        • NormalizeIntensity
          • NormalizeIntensity.transform()
        • RescaleIntensity
          • RescaleIntensity.transform()
        • ScaleImage
          • ScaleImage.transform()
        • ShiftScaleIntensity
          • ShiftScaleIntensity.transform()
        • SigmoidIntensity
          • SigmoidIntensity.transform()
        • TranslateImage
          • TranslateImage.transform()
      • Module contents
    • ants.contrib.sklearn_interface package
      • Submodules
      • ants.contrib.sklearn_interface.sklearn_registration module
        • RigidRegistration
          • RigidRegistration.fit()
          • RigidRegistration.inverse_transform()
          • RigidRegistration.transform()
      • Module contents
  • Module contents
• ants.core package
  • Submodules
  • ants.core.ants_image module
    • ANTsImage
      • ANTsImage.abp_n4()
      • ANTsImage.abs()
      • ANTsImage.add_noise_to_image()
      • ANTsImage.anti_alias()
      • ANTsImage.apply()
      • ANTsImage.argmax()
      • ANTsImage.argmin()
      • ANTsImage.argrange()
      • ANTsImage.as_label_image()
      • ANTsImage.astype()
      • ANTsImage.clone()
      • ANTsImage.convolve_image()
      • ANTsImage.copy()
      • ANTsImage.create_tiled_mosaic()
      • ANTsImage.create_warped_grid()
      • ANTsImage.crop_image()
      • ANTsImage.crop_indices()
      • ANTsImage.decrop_image()
      • ANTsImage.denoise_image()
      • ANTsImage.direction
      • ANTsImage.flatten()
      • ANTsImage.functional_lung_segmentation()
      • ANTsImage.fuzzy_spatial_cmeans_segmentation()
      • ANTsImage.get_average_of_timeseries()
      • ANTsImage.get_center_of_mass()
      • ANTsImage.get_centroids()
      • ANTsImage.get_mask()
      • ANTsImage.get_neighborhood_at_voxel()
      • ANTsImage.get_neighborhood_in_mask()
      • ANTsImage.get_orientation()
      • ANTsImage.get_pointer_string()
      • ANTsImage.histogram_equalize_image()
      • ANTsImage.iMath()
      • ANTsImage.iMath_GC()
      • ANTsImage.iMath_GD()
      • ANTsImage.iMath_GE()
      • ANTsImage.iMath_GO()
      • ANTsImage.iMath_MC()
      • ANTsImage.iMath_MD()
      • ANTsImage.iMath_ME()
      • ANTsImage.iMath_MO()
      • ANTsImage.iMath_canny()
      • ANTsImage.iMath_fill_holes()
      • ANTsImage.iMath_get_largest_component()
      • ANTsImage.iMath_grad()
      • ANTsImage.iMath_histogram_equalization()
      • ANTsImage.iMath_laplacian()
      • ANTsImage.iMath_maurer_distance()
      • ANTsImage.iMath_normalize()
      • ANTsImage.iMath_pad()
      • ANTsImage.iMath_perona_malik()
      • ANTsImage.iMath_propagate_labels_through_mask()
      • ANTsImage.iMath_sharpen()
      • ANTsImage.iMath_truncate_intensity()
      • ANTsImage.image_math()
      • ANTsImage.image_to_cluster_images()
      • ANTsImage.kmeans_segmentation()
      • ANTsImage.label_clusters()
      • ANTsImage.label_image_centroids()
      • ANTsImage.label_stats()
      • ANTsImage.labels_to_matrix()
      • ANTsImage.list_to_ndimage()
      • ANTsImage.mask_image()
      • ANTsImage.max()
      • ANTsImage.mean()
      • ANTsImage.median()
      • ANTsImage.min()
      • ANTsImage.morphology()
      • ANTsImage.motion_correction()
      • ANTsImage.movie()
      • ANTsImage.multi_label_morphology()
      • ANTsImage.n3_bias_field_correction()
      • ANTsImage.n3_bias_field_correction2()
      • ANTsImage.n4_bias_field_correction()
      • ANTsImage.ndimage_to_list()
      • ANTsImage.new_image_like()
      • ANTsImage.nonzero()
      • ANTsImage.numpy()
      • ANTsImage.orientation
      • ANTsImage.origin
      • ANTsImage.otsu_segmentation()
      • ANTsImage.pad_image()
      • ANTsImage.plot()
      • ANTsImage.plot_hist()
      • ANTsImage.plot_ortho()
      • ANTsImage.prior_based_segmentation()
      • ANTsImage.quantile()
      • ANTsImage.range()
      • ANTsImage.reflect_image()
      • ANTsImage.reorient_image2()
      • ANTsImage.resample_image()
      • ANTsImage.resample_image_to_target()
      • ANTsImage.rgb_to_vector()
      • ANTsImage.scalar_to_rgb()
      • ANTsImage.set_direction()
      • ANTsImage.set_origin()
      • ANTsImage.set_spacing()
      • ANTsImage.slice_image()
      • ANTsImage.smooth_image()
      • ANTsImage.spacing
      • ANTsImage.split_channels()
      • ANTsImage.std()
      • ANTsImage.sum()
      • ANTsImage.symmetrize_image()
      • ANTsImage.threshold_image()
      • ANTsImage.to_file()
      • ANTsImage.to_filename()
      • ANTsImage.to_nibabel()
      • ANTsImage.unique()
      • ANTsImage.vector_to_rgb()
      • ANTsImage.view()
      • ANTsImage.weingarten_image_curvature()
    • LabelImage
      • LabelImage.generate_data()
      • LabelImage.items()
      • LabelImage.keys()
      • LabelImage.metakeys()
      • LabelImage.n_values()
      • LabelImage.parentkey()
      • LabelImage.uniquekeys()
      • LabelImage.values()
    • allclose()
    • copy_image_info()
    • get_direction()
    • get_origin()
    • get_spacing()
    • image_physical_space_consistency()
    • image_type_cast()
    • set_direction()
    • set_origin()
    • set_spacing()
  • ants.core.ants_image_io module
    • dicom_read()
    • from_numpy()
    • image_clone()
    • image_header_info()
    • image_list_to_matrix()
    • image_read()
    • image_write()
    • images_from_matrix()
    • images_to_matrix()
    • make_image()
    • matrix_from_images()
    • matrix_to_images()
    • matrix_to_timeseries()
    • timeseries_to_matrix()
  • ants.core.ants_metric module
  • ants.core.ants_metric_io module
    • create_ants_metric()
    • new_ants_metric()
    • supported_metrics()
  • ants.core.ants_transform module
    • ANTsTransform
      • ANTsTransform.apply()
      • ANTsTransform.apply_to_image()
      • ANTsTransform.apply_to_point()
      • ANTsTransform.apply_to_vector()
      • ANTsTransform.fixed_parameters
      • ANTsTransform.invert()
      • ANTsTransform.parameters
      • ANTsTransform.set_fixed_parameters()
      • ANTsTransform.set_parameters()
    • apply_ants_transform()
    • apply_ants_transform_to_image()
    • apply_ants_transform_to_point()
    • apply_ants_transform_to_vector()
    • compose_ants_transforms()
    • get_ants_transform_fixed_parameters()
    • get_ants_transform_parameters()
    • invert_ants_transform()
    • set_ants_transform_fixed_parameters()
    • set_ants_transform_parameters()
    • transform_index_to_physical_point()
    • transform_physical_point_to_index()
  • ants.core.ants_transform_io module
    • create_ants_transform()
    • new_ants_transform()
    • read_transform()
    • transform_from_displacement_field()
    • transform_to_displacement_field()
    • write_transform()
  • Module contents
• ants.learn package
  • Submodules
  • ants.learn.decomposition module
    • eig_seg()
    • initialize_eigenanatomy()
    • sparse_decom2()
  • Module contents
• ants.lib package
  • Module contents
• ants.registration package
  • Submodules
  • ants.registration.affine_initializer module
    • affine_initializer()
  • ants.registration.apply_transforms module
    • apply_transforms()
    • apply_transforms_to_points()
  • ants.registration.build_template module
    • build_template()
  • ants.registration.create_jacobian_determinant_image module
    • create_jacobian_determinant_image()
    • deformation_gradient()
  • ants.registration.create_warped_grid module
    • create_warped_grid()
  • ants.registration.fsl2antstransform module
    • fsl2antstransform()
  • ants.registration.interface module
    • motion_correction()
    • registration()
  • ants.registration.make_points_image module
    • make_points_image()
  • ants.registration.metrics module
    • image_mutual_information()
  • ants.registration.reflect_image module
    • reflect_image()
  • ants.registration.reorient_image module
    • get_center_of_mass()
    • get_orientation()
    • get_possible_orientations()
    • reorient_image2()
  • ants.registration.resample_image module
    • resample_image()
    • resample_image_to_target()
  • ants.registration.symmetrize_image module
    • symmetrize_image()
  • Module contents
• ants.segmentation package
  • Submodules
  • ants.segmentation.anti_alias module
    • anti_alias()
  • ants.segmentation.atropos module
    • atropos()
  • ants.segmentation.joint_label_fusion module
    • joint_label_fusion()
    • local_joint_label_fusion()
  • ants.segmentation.kelly_kapowski module
    • kelly_kapowski()
  • ants.segmentation.kmeans module
    • kmeans_segmentation()
  • ants.segmentation.label_geometry_measures module
    • label_geometry_measures()
  • ants.segmentation.otsu module
    • otsu_segmentation()
  • ants.segmentation.prior_based_segmentation module
    • prior_based_segmentation()
  • Module contents
• ants.utils package
  • Submodules
  • ants.utils.bias_correction module
    • abp_n4()
    • n3_bias_field_correction()
    • n3_bias_field_correction2()
    • n4_bias_field_correction()
  • ants.utils.channels module
    • merge_channels()
    • split_channels()
  • ants.utils.convert_nibabel module
    • from_nibabel()
    • nifti_to_ants()
    • to_nibabel()
  • ants.utils.crop_image module
    • crop_image()
    • crop_indices()
    • decrop_image()
  • ants.utils.denoise_image module
    • denoise_image()
  • ants.utils.get_ants_data module
    • get_ants_data()
    • get_data()
  • ants.utils.get_centroids module
    • get_centroids()
  • ants.utils.get_mask module
    • get_mask()
  • ants.utils.get_neighborhood module
    • get_neighborhood_at_voxel()
    • get_neighborhood_in_mask()
  • ants.utils.iMath module
    • iMath()
    • iMath_GC()
    • iMath_GD()
    • iMath_GE()
    • iMath_GO()
    • iMath_MC()
    • iMath_MD()
    • iMath_ME()
    • iMath_MO()
    • iMath_canny()
    • iMath_fill_holes()
    • iMath_get_largest_component()
    • iMath_grad()
    • iMath_histogram_equalization()
    • iMath_laplacian()
    • iMath_maurer_distance()
    • iMath_normalize()
    • iMath_pad()
    • iMath_perona_malik()
    • iMath_propagate_labels_through_mask()
    • iMath_sharpen()
    • iMath_truncate_intensity()
    • image_math()
    • multiply_images()
  • ants.utils.image_similarity module
    • image_similarity()
  • ants.utils.image_to_cluster_images module
    • image_to_cluster_images()
  • ants.utils.impute module
    • impute()
  • ants.utils.invariant_image_similarity module
    • convolve_image()
    • invariant_image_similarity()
  • ants.utils.label_clusters module
    • label_clusters()
  • ants.utils.label_image_centroids module
    • label_image_centroids()
  • ants.utils.label_stats module
    • label_stats()
  • ants.utils.labels_to_matrix module
    • labels_to_matrix()
  • ants.utils.mask_image module
    • mask_image()
  • ants.utils.mni2tal module
    • mni2tal()
  • ants.utils.morphology module
    • morphology()
  • ants.utils.multi_label_morphology module
    • multi_label_morphology()
  • ants.utils.ndimage_to_list module
    • list_to_ndimage()
    • ndimage_to_list()
  • ants.utils.pad_image module
    • pad_image()
  • ants.utils.process_args module
    • get_lib_fn()
    • get_pointer_string()
    • short_ptype()
  • ants.utils.quantile module
    • bandpass_filter_matrix()
    • compcor()
    • get_average_of_timeseries()
    • ilr()
    • quantile()
    • rank_intensity()
    • regress_components()
    • regress_poly()
  • ants.utils.scalar_rgb_vector module
    • rgb_to_vector()
    • scalar_to_rgb()
    • vector_to_rgb()
  • ants.utils.slice_image module
    • slice_image()
  • ants.utils.smooth_image module
    • smooth_image()
  • ants.utils.threshold_image module
    • threshold_image()
  • ants.utils.weingarten_image_curvature module
    • weingarten_image_curvature()
  • Module contents
• ants.viz package
  • Submodules
  • ants.viz.create_tiled_mosaic module
    • create_tiled_mosaic()
  • ants.viz.plot module
    • plot()
  • ants.viz.render_surface_function module
  • ants.viz.surface module
  • ants.viz.volume module
  • Module contents

Submodules

ants.version module

Module contents