Man pages for neuroim2
Data Structures for Brain Imaging Data
| AbstractSparseNeuroVec-class | AbstractSparseNeuroVec Class |
| add_dim-methods | Add a Dimension to an Object |
| affine_utils | Affine utility functions |
| AFNIMetaInfo | Create AFNI Format Metadata Object |
| anatomical_axes | Pre-defined anatomical axes |
| annotate_orientation | Add L/R and A/P/S/I annotations (optional) |
| Arith-methods | Arithmetic Operations |
| ArrayLike3D-class | ArrayLike3D Class |
| ArrayLike4D-class | ArrayLike4D Class |
| ArrayLike5D-class | ArrayLike5D Class |
| as.array | Generic as.array Method |
| as.array-methods | Convert ClusteredNeuroVol to a base array |
| as_canonical | Reorient Image to Canonical (RAS+) Orientation |
| as-ClusteredNeuroVol-DenseNeuroVol | Convert ClusteredNeuroVol to DenseNeuroVol |
| as.dense | Convert to dense representation |
| as.dense-methods | Convert a NeuroVecSeq to a DenseNeuroVec |
| as-DenseNeuroVol-array | Convert DenseNeuroVol to array |
| as.list-methods | Convert FileBackedNeuroVec to List |
| as.logical-methods | as.logical |
| as.mask | Convert to a LogicalNeuroVol |
| as.mask-methods | Convert NeuroVol to a mask |
| as.matrix | Generic as.matrix Method |
| as.matrix-methods | convert a 'NeuroVec' to a matrix |
| as_mmap | Convert a NeuroVec to a memory-mapped representation |
| as_nifti_header | Construct a Minimal NIfTI-1 Header from a NeuroVol |
| as.numeric-methods | Convert SparseNeuroVol to numeric |
| as.raster | Generic Method for Converting Objects to Raster Format |
| as.sparse | Convert to from dense to sparse representation |
| as.sparse-methods | Convert DenseNeuroVec to sparse representation using mask |
| as.vector-methods | Convert SparseNeuroVol to a base vector |
| axcodes-methods | Get Orientation Axis Codes |
| axes-methods | Extract Image Axes |
| AxisSet1D-class | AxisSet1D |
| AxisSet2D-class | AxisSet2D |
| AxisSet3D-class | AxisSet3D Class |
| AxisSet4D-class | AxisSet4D Class |
| AxisSet5D-class | AxisSet5D Class |
| AxisSet-class | AxisSet |
| BigNeuroVec-class | BigNeuroVec Class |
| BigNeuroVec-methods | Create a Memory-Mapped Neuroimaging Vector |
| bilateral_filter | Apply a bilateral filter to a volumetric image |
| bilateral_filter_4d | Apply a 4D bilateral filter to a NeuroVec |
| BinaryReader | Create Binary Reader Object |
| BinaryReader-class | BinaryReader Class |
| BinaryWriter | Create Binary Writer Object |
| BinaryWriter-class | BinaryWriter Class |
| bounds-methods | Extract Spatial Bounds of an Image |
| centroid-methods | return the centroid of an object |
| centroids-methods | Return a matrix of centroids of an object |
| cgb_filter | Correlation-guided bilateral filtering (convenience wrapper) |
| cgb_make_graph | Build a correlation-guided bilateral (CGB) graph |
| cgb_smooth | Apply a precomputed CGB graph to volumetric data |
| cgb_smooth_loro | Leave-one-run-out smoothing helper |
| close-methods | Close a BinaryReader or BinaryWriter |
| ClusteredNeuroVec | ClusteredNeuroVec: Cluster-aware 4D neuroimaging data |
| ClusteredNeuroVec-class | ClusteredNeuroVec Class |
| ClusteredNeuroVol-class | ClusteredNeuroVol Class |
| clustered_searchlight | Create a clustered searchlight iterator |
| cluster_searchlight_series | Cluster-centroid searchlight over cluster time-series |
| ColumnReader | Create Column Reader Object |
| ColumnReader-class | ColumnReader |
| Compare-methods | Comparison Operations |
| concat-methods | Concatenate two objects in the time dimension |
| conn_comp_3D | Extract Connected Components from a 3D Binary Mask |
| conn_comp-methods | Connected components |
| coords | Extract coordinates from an object |
| coords-methods | Extract Coordinates from an IndexLookupVol Object |
| coord_to_grid-methods | convert n-dimensional real world coordinates to grid... |
| coord_to_index-methods | convert n-dimensional real world coordinates to 1D indices |
| createNIfTIHeader | Create an Empty NIfTI-1 Header List |
| cuboid_roi | Create A Cuboid Region of Interest |
| data_file_matches-methods | Generic function to test whether a file name conforms to the... |
| data_file-methods | Generic function to get the name of the data file, given a... |
| data_reader | Create a Data Reader |
| data_reader-methods | Create Data Reader for AFNI Format |
| DenseNeuroVec-class | DenseNeuroVec Class |
| DenseNeuroVol-class | DenseNeuroVol Class |
| deoblique | Deoblique a Neuroimaging Space or Volume |
| dim-methods | Get Dimensions of FileMetaInfo Object |
| dim_of-methods | Get the length of a given dimension of an object |
| downsample-methods | Downsample an Image |
| drop | Generic Drop Method |
| drop_dim-methods | Drop a Dimension from an Object |
| drop-methods | Drop a dimension |
| ecode_name | Get Extension Code Name |
| embed_kernel-methods | Generic function to position kernel in a position in image... |
| extension | Get Extension by Code |
| extensions | Get Extensions from an Object |
| extract-methods | [[ |
| extractor3d | Array-like access for 3-dimensional data structures |
| extractor4d | Array-like access for 4-dimensional data structures |
| FileBackedNeuroVec | Create a File-Backed Neuroimaging Vector |
| FileBackedNeuroVec-class | FileBackedNeuroVec Class |
| FileFormat-class | FileFormat Class |
| FileFormat-operations | File Format Operations for Neuroimaging Data |
| file_matches-methods | Generic function to test whether a file name conforms to the... |
| FileMetaInfo-class | FileMetaInfo Class |
| FileSource-class | FileSource Class |
| findAnatomy3D | Find 3D anatomical orientation from axis abbreviations |
| gaussian_blur | Gaussian Blur for Volumetric Images |
| get_afni_attribute | Get AFNI Attribute from Extension |
| grid_to_coord-methods | Generic function to convert N-dimensional grid coordinates to... |
| grid_to_grid-methods | Generic function to convert voxel coordinates in the... |
| grid_to_index-methods | Generic function to convert N-dimensional grid coordinates to... |
| guided_filter | Edge-Preserving Guided Filter for Volumetric Images |
| has_extensions | Check if Extensions are Present |
| header_file_matches-methods | Generic function to test whether a file name conforms to the... |
| header_file-methods | Generic function to get the name of the header file, given a... |
| header-methods | Access NIfTI Header Information |
| image | Generic Image Method for Creating Visual Representations |
| IndexLookupVol-class | IndexLookupVol Class |
| index_to_coord-methods | convert 1d indices to n-dimensional real world coordinates |
| index_to_grid-methods | Convert 1d indices to n-dimensional grid coordinates |
| indices | Extract indices |
| indices-methods | Get Indices from an IndexLookupVol Object |
| inverse_trans-methods | Extract inverse image coordinate transformation |
| Kernel | Create a Kernel object from a function of distance from... |
| Kernel-class | Kernel |
| labels-methods | Get Labels from ClusteredNeuroVec |
| laplace_enhance | Laplacian Enhancement Filter for Volumetric Images |
| length-methods | Get length of NeuroVec object |
| linear_access | Extract values from an array-like object using linear... |
| linear_access-methods | Linear Access Method for FileBackedNeuroVec |
| list_afni_attributes | List AFNI Attributes in Extension |
| load_data | Read data from a data source. |
| load_data-methods | Load image data from a NeuroVecSource object |
| LogicalNeuroVol-class | LogicalNeuroVol Class |
| Logic-methods | Logic Operations for Neuroimaging Volumes |
| lookup | Index Lookup operation |
| lookup-methods | Lookup Values in an IndexLookupVol Object |
| make_time_weights | Build smooth time weights from motion/outlier metrics |
| map-methods | Apply a function to an object. |
| MappedNeuroVec-class | MappedNeuroVec Class |
| MappedNeuroVecSource-class | MappedNeuroVecSource Class |
| mapToColors | Map intensity values to colors |
| map_values-methods | Map Values from One Set to Another Using a User-supplied... |
| mask-methods | Extract Mask from Neuroimaging Object |
| matricized_access-methods | Extract values from a 4D tensor using a matrix of time-space... |
| matrixToQuatern | Convert a Transformation Matrix to a Quaternion... |
| mean-methods | Temporal Mean of a NeuroVec |
| meta_info | Lightweight metadata for neuroimaging files |
| MetaInfo | Create Neuroimaging Metadata Object |
| MetaInfo-class | MetaInfo Class |
| NamedAxis-class | NamedAxis |
| ndim-methods | Extract the number of dimensions of an object |
| NeuroBucket-class | NeuroBucket |
| neuro-downsample | Downsampling Methods for Neuroimaging Objects |
| NeuroHyperVec | Constructor for NeuroHyperVec class |
| NeuroHyperVec-class | NeuroHyperVec Class |
| neuroim2-package | neuroim2: neuroimaging data structures for analysis |
| NeuroObj-class | NeuroObj Class |
| neuro-ops | Arithmetic and Comparison Operations for Neuroimaging Objects |
| neuro-resample | Resampling Methods for Neuroimaging Objects |
| NeuroSlice | NeuroSlice: 2D Neuroimaging Data Container |
| NeuroSlice-class | NeuroSlice Class |
| NeuroSpace | NeuroSpace: Spatial Reference System for Neuroimaging Data |
| NeuroSpace-class | NeuroSpace Class |
| NeuroVec-class | NeuroVec Class |
| NeuroVecSeq | NeuroVecSeq: A Container for Sequential NeuroVec Objects |
| NeuroVecSeq-class | NeuroVecSeq Class |
| NeuroVecSeq-methods | Extract Element from NeuroVecSeq |
| NeuroVecSource | NeuroVecSource |
| NeuroVecSource-class | NeuroVecSource Class |
| NeuroVol | NeuroVol: 3D Neuroimaging Volume Class |
| NeuroVol-class | NeuroVol Class |
| NeuroVolSource-class | Constructor for NeuroVolSource |
| NiftiExtension | Create a NIfTI Extension |
| NiftiExtension-class | NiftiExtension Class |
| NiftiExtensionCodes | Known NIfTI Extension Codes |
| NiftiExtensionList-class | NiftiExtensionList Class |
| NIFTIMetaInfo | Create NIFTI Format Metadata Object |
| None | Pre-defined null axis |
| normalize_mask | Normalize a mask to a logical array |
| not-methods | Logical Negation for Neuroimaging Volumes |
| NullAxis | Pre-defined null axis set |
| num_clusters-methods | Number of Clusters |
| numericOrMatrix-class | numericOrMatrix Union |
| OrientationList2D | Pre-defined 2D orientation configurations |
| OrientationList3D | Pre-defined 3D orientation configurations |
| orientation_utils | Orientation utility functions |
| origin-methods | Extract Image Origin |
| parse_afni_extension | Parse AFNI Extension |
| parse_extension | Parse NIfTI Extension Data |
| partition-methods | Partition an image into a set of disjoint clusters |
| patch_set | Generate a set of coordinate "patches" of fixed size from an... |
| patch_set-methods | Create a patch set from a NeuroVol object |
| perm_mat-methods | Extract permutation matrix associated with an image |
| plot-methods | Plot a NeuroSlice |
| plot_montage | Plot a montage of axial (or any-plane) slices using facetting |
| plot_ortho | Orthogonal three-plane view with optional crosshairs |
| plot_overlay | Composite an overlay map on a structural background |
| prepare_confounds | Prepare weighted nuisance projectors for each run |
| quaternToMatrix | Convert Quaternion Parameters to a Transformation Matrix |
| random_searchlight | Create a spherical random searchlight iterator |
| read_columns-methods | Read a set of column vector from an input source (e.g.... |
| read_elements-methods | Read a sequence of elements from an input source |
| read_header | read header information of an image file |
| read_hyper_vec | Read a 5D image as a NeuroHyperVec |
| read_image | read_image |
| read_meta_info-methods | Generic function to read image meta info given a file |
| read_vec | read_vec |
| read_vol | Load a single 3D image volume from a file |
| read_vol_list | read_vol_list |
| reorient-methods | Remap the grid-to-world coordinates mapping of an image. |
| resampled_searchlight | Create a resampled searchlight iterator |
| resample-methods | Resample an Image to Match the Space of Another Image |
| resample_to | Resample an image with readable method names |
| resolve_cmap | Neuroimaging color palettes and helpers |
| ROI-class | ROI |
| ROICoords | Create ROI Coordinates Object |
| ROICoords-class | ROICoords |
| ROIVec | Create an instance of class 'ROIVec' |
| ROIVec-class | ROIVec |
| ROIVecWindow-class | ROIVecWindow |
| ROIVol | Create ROI Volume Object |
| ROIVol-class | ROIVol |
| ROIVolWindow-class | ROIVolWindow |
| scale | Generic Scale Method |
| scale_fill_neuro | A ggplot2 fill scale with neuroimaging-friendly defaults |
| scale_series-methods | Generic functions to scale (center and/or normalize by... |
| searchlight | Create an exhaustive searchlight iterator |
| searchlight_coords | Create an exhaustive searchlight iterator for voxel... |
| searchlight-methods | Searchlight Analysis Methods |
| searchlight_shape_functions | Convenience shape generators for 'resampled_searchlight()' |
| series-methods | Extract one or more series from object |
| series_roi | Extract time series from specific voxel coordinates and... |
| show-helpers | Internal helpers for consistent show() formatting |
| show-methods | Show method for NamedAxis objects |
| simulate_fmri | Simulate fMRI Data |
| slice-methods | Extract image slice |
| slices-methods | Extract an ordered series of 2D slices from a 3D or 4D object |
| space-methods | Extract Geometric Properties of an Image |
| space_utils | Space utility functions |
| spacing-methods | Extract Voxel Dimensions of an Image |
| SparseNeuroVec-class | SparseNeuroVec Class |
| SparseNeuroVec-methods | [[ |
| SparseNeuroVecSource-class | SparseNeuroVecSource Class |
| SparseNeuroVol-array | Convert SparseNeuroVol to array |
| SparseNeuroVol-class | SparseNeuroVol Class |
| SparseNeuroVol-numeric | Convert SparseNeuroVol to numeric |
| spatial-filter | Spatial Filtering Methods for Neuroimaging Data |
| spherical_roi | Create a Spherical Region of Interest |
| spherical_roi_set | Create Multiple Spherical Regions of Interest |
| split_blocks-methods | Cut a vector-valued object into a list of sub-blocks |
| split_clusters-methods | Cut an object into a list of spatial or spatiotemporal... |
| split_fill-methods | Fill Disjoint Sets of Values with the Output of a Function |
| split_reduce-methods | Summarize Subsets of an Object by Splitting by Row and... |
| split_scale-methods | Center and/or Scale Row-subsets of a Matrix or Matrix-like... |
| square_roi | Create a square region of interest |
| strip_extension-methods | Generic function to strip extension from file name, given a... |
| sub_clusters | Select a Subset of Clusters |
| sub_vector-methods | Generic function to extract a sub-vector from a 'NeuroVec'... |
| Summary-methods | Summary Methods for Neuroimaging Objects |
| summary-neuro-methods | Summary of Neuroimaging Objects |
| temporal_access-methods | Extract full sparse rows across time. |
| theme_neuro | A minimal, publication-friendly theme for image slices |
| TIME | Time axis |
| TimeAxis | Time axis set |
| trans-methods | Extract image coordinate transformation |
| values-methods | Extract Data Values of an Object |
| vec_from_vols | Create NeuroVec from list of NeuroVol objects |
| vectors-methods | Extract an ordered list of 1D vectors. |
| vols-methods | Extract an ordered series of 3D volumes. |
| volume_labels-methods | Get per-volume labels for a 'NeuroVec'. |
| voxels-methods | extract voxel coordinates |
| which_dim-methods | Find Dimensions of a Given Axis |
| write_elements-methods | Write a sequence of elements from an input source |
| write_vec-methods | Write a 4d image vector to disk |
| write_vol-methods | Write a 3d image volume to disk |
