Man pages for bbuchsbaum/neuroim2
Data Structures and IO for Neuroimaging Data with an Emphasis on Functional Magnetic Resonance Imaging (FMRI)
| AbstractSparseNeuroVec-class | AbstractSparseNeuroVec Class |
| add_dim-methods | Add a Dimension to an Object |
| AFNIMetaInfo | Create AFNI Format Metadata Object |
| anatomical_axes | Pre-defined anatomical axes |
| Arith-methods | Perform arithmetic operations between two SparseNeuroVol... |
| Arith-NeuroVec-NeuroVol-method | Arithmetic Operations for NeuroVec and NeuroVol |
| Arith-NeuroVol-NeuroVec-method | Arithmetic Operations for NeuroVol and NeuroVec |
| Arith-ROIVol-ROIVol-method | This function performs arithmetic operations on two ROIVol... |
| as | conversion from 'NeuroVol' to 'LogicalNeuroVol' |
| as.dense | Convert to dense representation |
| as.dense-methods | Coerce ROIVol to DenseNeuroVol using as.dense method |
| 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-methods | convert a 'NeuroVec' to a matrix |
| as.numeric-methods | Convert SparseNeuroVol to numeric |
| as.sparse | Convert to from dense to sparse representation |
| as.sparse-methods | Convert DenseNeuroVec to sparse representation using mask |
| axes-methods | Extract Image Axes |
| AxisSet1D | Create a one-dimensional axis set |
| AxisSet1D-class | AxisSet1D |
| AxisSet2D | Create a two-dimensional axis set |
| AxisSet2D-class | AxisSet2D |
| AxisSet3D | Create a three-dimensional axis set |
| AxisSet3D-class | AxisSet3D Class |
| AxisSet4D-class | AxisSet4D Class |
| AxisSet5D-class | AxisSet5D Class |
| AxisSet-class | AxisSet |
| BigNeuroVec-class | BigNeuroVec Class |
| bilateral_filter | Apply a bilateral filter to a volumetric image |
| BinaryReader | Create Binary Reader Object |
| BinaryReader-class | BinaryReader Class |
| BinaryWriter | Create Binary Writer Object |
| BinaryWriter-class | BinaryWriter Class |
| bootstrap_searchlight | Create a bootstrap spherical searchlight iterator |
| 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 |
| close-methods | Close a BinaryReader or BinaryWriter |
| ClusteredNeuroVol-class | ClusteredNeuroVol Class |
| clustered_searchlight | Create a clustered searchlight iterator |
| ColumnReader | Create Column Reader Object |
| ColumnReader-class | ColumnReader |
| Compare-methods | Compare a SparseNeuroVol object with a numeric value |
| 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 |
| 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 |
| DenseNeuroVec-class | DenseNeuroVec Class |
| DenseNeuroVol-class | DenseNeuroVol Class |
| dim-FileMetaInfo-method | Get Dimensions of FileMetaInfo Object |
| dim-methods | dim of 'NeuroObj' object |
| dim-NeuroSpace-method | dim |
| dim_of-methods | Get the length of a given dimension of an object |
| dot-getAxis | Get anatomical axis from direction vector |
| dot-read_mmap | Read Data Using Memory Mapping |
| drop_dim-AxisSet2D-missing-method | Drop dimension from axis set |
| drop_dim-AxisSet2D-numeric-method | Drop dimension from axis set |
| drop_dim-AxisSet3D-missing-method | Drop dimension from axis set |
| drop_dim-AxisSet3D-numeric-method | Drop dimension from axis set |
| drop_dim-methods | Drop a Dimension from an Object |
| drop-NeuroVec-method | drop |
| embed_kernel-methods | Generic function to position kernel in a postion in image... |
| 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 |
| grid_to_coord-methods | Generic function to convert N-dimensional grid coordinate... |
| grid_to_grid-methods | Generic function to convert voxel coordinates in the... |
| grid_to_index-methods | Generic function to convert N-dimensional grid coordinate to... |
| guided_filter | Edge-Preserving Guided Filter for Volumetric Images |
| 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... |
| 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 |
| initialize-IndexLookupVol-method | Initialize 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 |
| laplace_enhance | Laplacian Enhancement Filter for Volumetric Images |
| length-NeuroVec-method | Get the length of a NeuroVec object |
| linear_access | Extract values from an array-like object using linear... |
| linear_access-FileBackedNeuroVec-numeric-method | Linear Access Method for FileBackedNeuroVec |
| linear_access-methods | Linear Access to NeuroVecSeq Data |
| linear_access-NeuroHyperVec-ANY-method | Linear access method for NeuroHyperVec |
| load_data | Load data from a data source. |
| LogicalNeuroVol-class | LogicalNeuroVol Class |
| lookup | Index Lookup operation |
| lookup-methods | Lookup Values in an IndexLookupVol Object |
| map-methods | Apply a function to an object. |
| MappedNeuroVec-class | MappedNeuroVec Class |
| MappedNeuroVecSource-class | MappedNeuroVecSource Class |
| map_values-methods | Map Values from One Set to Another Using a User-supplied... |
| matchAnatomy2D | Find matching 2D anatomical orientation |
| matchAnatomy3D | Find matching 3D anatomical orientation |
| matchAxis | Match anatomical axis abbreviation to full axis object |
| matricized_access-methods | Extract values from a matricized (x,y,z) of a 4D tensor using... |
| MetaInfo | Create Neuroimaging Metadata Object |
| MetaInfo-class | MetaInfo Class |
| NamedAxis-class | NamedAxis |
| ndim-AxisSet-method | Get number of dimensions in axis set |
| ndim-methods | Extract the number of dimensions of an object |
| NeuroBucket-class | NeuroBucket |
| NeuroHyperVec | Constructor for NeuroHyperVec class |
| NeuroHyperVec-class | NeuroHyperVec Class |
| neuroim2-package | neuroim2: neuroimaging data structures for analysis |
| NeuroObj-class | NeuroObj Class |
| 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 |
| NeuroVol | Construct a NeuroVol object |
| NeuroVol-class | NeuroVol Class |
| NeuroVolSource-class | Constructor for NeuroVolSource |
| niftiDim | Extract NIFTI Dimensions |
| NIFTIMetaInfo | Create NIFTI Format Metadata Object |
| None | Pre-defined null axis |
| NullAxis | Pre-defined null axis set |
| num_clusters | Number of Clusters |
| num_clusters-methods | Number of Clusters |
| OrientationList2D | Pre-defined 2D orientation configurations |
| OrientationList3D | Pre-defined 3D orientation configurations |
| origin-methods | Extract Image Origin |
| 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-AxisSet2D-method | Get permutation matrix from axis set |
| perm_mat-AxisSet3D-method | Get permutation matrix from axis set |
| perm_mat-methods | Extract permutation matrix associated with an image |
| perm_mat-NeuroSpace-method | Get permutation matrix from axis set |
| plot-methods | Visualize 2D Neuroimaging Slice |
| print_-AxisSet2D-method | Print method for AxisSet2D objects |
| print_-AxisSet3D-method | Print method for AxisSet3D objects |
| print_-NamedAxis-method | Print method for NamedAxis objects |
| 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-BinaryReader-numeric-method | Read Elements from Binary Reader |
| read_elements-methods | Read a sequence of elements from an input source |
| read_header | read header information of an image file |
| read_mapped_data | Read Mapped Data from 4D Image |
| read_mapped_series | Read Mapped Series from 4D Image |
| read_mapped_vols | Read Mapped Volumes from 4D Image |
| read_meta_info-methods | Generic function to read image meta info given a file and a... |
| read_vec | read_vec |
| read_vol | Load an image volume from a file |
| read_vol_list | read_vol_list |
| render-methods | Render an image to create a drawable image. |
| render_slice-methods | Render a slice at z coordinate |
| reorient-methods | Remap the grid-to-world coordinates mapping of an image. |
| resample-methods | Resample an Image to Match the Space of Another Image |
| resample-NeuroVol-NeuroSpace-method | Resample a NeuroVol object to match a NeuroSpace object |
| resample-NeuroVol-NeuroVol-method | Resample a NeuroVol object |
| ROI-class | ROI |
| ROICoords-class | ROICoords |
| ROIVec | Create an instance of class 'ROIVec' |
| ROIVec-class | ROIVec |
| ROIVecWindow-class | ROIVecWindow |
| ROIVol | Create an instance of class 'ROIVol' |
| ROIVol-class | ROIVol |
| ROIVolWindow-class | ROIVolWindow |
| 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... |
| series-methods | Extract one or more series from object and return as ROI... |
| series-NeuroHyperVec-ANY-method | Series method for NeuroHyperVec |
| series_reader | Create Series Reader for 4D Image |
| show-AxisSet1D-method | Show method for AxisSet1D objects |
| show-AxisSet2D-method | Show method for AxisSet2D objects |
| show-AxisSet3D-method | Show method for AxisSet3D objects |
| show-AxisSet4D-method | Show method for AxisSet4D objects |
| show-ClusteredNeuroVol-method | Display ClusteredNeuroVol Information |
| show-FileMetaInfo-method | show a 'FileMetaInfo' |
| show-MappedNeuroVec-method | Show Method for MappedNeuroVec Objects |
| show-NamedAxis-method | Show method for NamedAxis objects |
| show-NeuroHyperVec-method | Show NeuroHyperVec Object |
| show-NeuroSlice-method | Print NeuroSlice Object Details |
| show-NeuroSpace-method | Display NeuroSpace Object Details |
| show-NeuroVec-method | show a NeuroVec object |
| show-NeuroVecSource-method | show a NeuroVecSource object |
| show-NeuroVol-method | show a 'NeuroVol' |
| show-ROIVec-method | show an 'ROIVec' |
| show-ROIVol-method | show an 'ROIVol' |
| show-SparseNeuroVec-method | show a 'SparseNeuroVec' |
| show-SparseNeuroVol-method | show a 'SparseNeuroVol' |
| 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 |
| 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 |
| 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-AbstractSparseNeuroVec-numeric-numeric-ANY-method | Extractor Method for AbstractSparseNeuroVec |
| sub-NeuroHyperVec-ANY-ANY-ANY-method | [ method for NeuroHyperVec |
| sub-sub-NeuroVec-numeric-method | [[ |
| sub_vector-methods | Generic function to extract a sub-vector from a 'NeuroVec'... |
| Summary-DenseNeuroVol-method | Summary of DenseNeuroVol |
| Summary-SparseNeuroVec-method | Summary of SparseNeuroVec |
| Summary-SparseNeuroVol-method | Summary of SparseNeuroVol |
| TIME | Time axis |
| TimeAxis | Time axis set |
| trans-methods | Extract image coordinate transformation |
| values-methods | Extract Data Values of an Object |
| vectors-methods | Extract an ordered list of 1D vectors. |
| vols-methods | Extract an ordered series of 3D volumes. |
| vol_subset-methods | subset an 'ROIVol' |
| voxels-methods | extract voxel coordinates |
| which_dim-methods | Find Dimensions of a Given Axis |
| write_elements-BinaryWriter-numeric-method | Write Elements to Binary Writer |
| 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 |
