Man pages for neuroconductor/extrantsr
Extra Functions to Build on the 'ANTsR' Package
| accessor-methods | Extract Image Attributes 'origin' from 'antsImage' or 'nifti'... |
| ants2oro | Convert Between antsImage and nifti objects |
| ants_apply_transforms-methods | Apply ANTs transforms to nifti images |
| ants_bwlabel | ANTs BWLabel Clusters of Certain Size |
| antsCopy | Copy Information of One Image to Another |
| ants.extract | Extract values from antsImage from mask |
| ants.overlay | Plot Lightbox for antsImage |
| ants_regwrite | Registration to a Template |
| applyEmptyImageDimensions-methods | Apply Subsetting from Empty Image Dimensions |
| apply_malf_regs | Apply MALF Registrations |
| apply_multi_reg-methods | Check if antsImage or read in |
| bias_correct | N3 or N4 Correct |
| bias_ss | Bias Field Correct then Skull Strip |
| brain_extract | Wrapper for ANTs brain extraction |
| c3d | Convert NeuroImage Types |
| check_ants-methods | Check if antsImage or read in |
| checkimg-methods | Force object to filename |
| check_nifti-methods | Check if nifti image or read in a nifti image |
| compose_transform_to_file | Compose Transforms from ANTsR to a composite file |
| corr_img | Neighborhood Correlation Image |
| cort_thickness | Compute cortical thickness using Kelly Kapowski (ANTsR) |
| create_moment | Create Neighborhood Momemts of an Image |
| diff_self | Flipped Difference Image |
| double_remove_neck | Remove Neck Twice from a Scan |
| emptyImageDimensionsMask-methods | Make Mask from Empty Image Dimensions |
| face_removal_mask_ants | Face Removal Mask using ANTs Registration |
| fill_2d_z | Image Mask Filler over each slice in Z-direction |
| filler | Image Mask Filler |
| finite_img-methods | Finite Image |
| fslbet_robust | Robust Skull Stripping with COG estimation and Bias... |
| group_xyz2 | Center of Gravity for Multiple Components/Areas |
| image_similarity | Compute Image Similarity Metrics |
| img_cov_matrix | Neighborhood Covariance Matrix |
| img_density_entropy | Image Entropy using density |
| img_hist_entropy | Image Entropy using histograms |
| img_split | Split an Image into Multiple Sub-Images |
| inpaint | Inpainting of images |
| jacobian_image | Image of the Determinant of the Jacobian |
| label_clusters | Label Clusters |
| label_mask | Label Connected Components |
| largest_component | Get Largest Component |
| local_quantile_img | Quantile Transform Voxel based on Neighborhood Distribution |
| makepng | Non-exported function to make png |
| malf | Multi-Atlas Label Fusion |
| malf_registration | Multi-Atlas Label Fusion Registration |
| maskEmptyImageDimensions-methods | Apply Masking from Empty Image Dimensions |
| multi_reg | Multi-Registration |
| multi_rereg | Two-Stage Multi-Registration of images |
| mutual_information | Calculates Mutual Information on nifti objects |
| my.tab | Quick Tabulation for logical vectors |
| n4_4d | Four-Dimensional Bias-Field Correction |
| neighborhood | Get Neighborhood of Voxels from an Image |
| neighborhood_index | Get Neighborhood Matrix of Indices from an Image |
| oasis | OASIS Processing Pipeline |
| oMask | Get Mask from nifti object |
| oMath | Perform iMath on nifti objects |
| oro2ants | Convert Between nifti and antsImage |
| ortho2-methods | Orthographic Display, added options |
| otropos | Run Atropos for nifti objects |
| otropos2 | Run Atropos for nifti objects |
| perona_malik | Perona-Malik Anisotropic Filter |
| pixdim-methods | Extract Image pixdim attribute |
| preprocess_mri_across | Preprocess MRI acros visits |
| preprocess_mri_within | Within Visit Registration |
| process_filenames | Process filenames to ensure nifti and consistency |
| read_transformlist | Read Transform List from ANTsR |
| reapply_malf | Reapply MALF Operation |
| reg_flip | Flip Image with Registration |
| reg_flip_img | Flip Image with Registration |
| registration | Registration Wrapper function |
| reg_whitestripe | WhiteStripe Normalization |
| reg_zscore | Z-score Normalization |
| remove_neck | Remove Neck from Image |
| reorder_neigh_indices | Reorder Voxel Neighborhood |
| reproducible_ants | Set reproducible seeds and threads for ANTsR execution |
| resample_image-methods | Resample an image |
| resample_to_target-methods | Resample an Image to a Target Image |
| robust_brain_mask | Robust Brain Mask from Template |
| scaled_neighborhood | Get Scaled Neighborhood of Voxels from an Image |
| sim | Calculate Overlap Metrics |
| smooth_image | Gaussian smooth image using ANTsR |
| smri_preproc | Standard MRI Preprocessing |
| ss_bias | Skull Strip then Bias Field Correct |
| stat_img | Create Statistics Image |
| subset_4d-methods | Subset a 4D image |
| tempants | Create temporary nii.gz file from antsImage |
| transformlist_from_outprefix | Get list of transforms that would likely be made with a... |
| within_visit_registration | Within Visit Registration |
| write_transformlist | Read Transform List from ANTsR |
| zero_pad | Zero pads an image |
| zscore_template | Create Z-score-to-Template Image |
