Man pages for bbuchsbaum/neuroim2
Data Structures and IO for Neuroimaging Data with an Emphasis on Functional Magnetic Resonance Imaging (FMRI)
| AbstractSparseNeuroVec-class | AbstractSparseNeuroVec |
| add_dim-methods | Add a Dimension to an Object |
| Arith-methods | Perform arithmetic operations between two SparseNeuroVol... |
| Arith-NeuroVec-NeuroVol-method | Arithmetic Operations for NeuroVec and NeuroVol |
| 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 | as.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-class | AxisSet1D |
| AxisSet2D-class | AxisSet2D |
| AxisSet3D-class | AxisSet3D |
| AxisSet4D-class | AxisSet4D |
| AxisSet5D-class | AxisSet5D |
| AxisSet-class | AxisSet |
| BigNeuroVec-class | BigNeuroVec |
| bilateral_filter | Apply a bilateral filter to a volumetric image |
| BinaryReader | BinaryReader |
| BinaryReader-class | BinaryReader |
| BinaryWriter-class | BinaryWriter |
| bootstrap_searchlight | Create a spherical searchlight iterator that samples regions... |
| 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 |
| ClusteredNeuroVol-class | ClusteredNeuroVol Class |
| ColumnReader | ColumnReader |
| 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 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-methods | Generic function to create data reader |
| DenseNeuroVec-class | DenseNeuroVec |
| DenseNeuroVec-H5NeuroVec | Convert DenseNeuroVec to H5NeuroVec |
| DenseNeuroVol-class | DenseNeuroVol |
| DenseNeuroVol-H5NeuroVol | Convert DenseNeuroVol to H5NeuroVol |
| dim-FileMetaInfo-method | dim of 'FileMetaInfo' |
| dim-methods | dim of 'NeuroObj' object |
| dim-NeuroSpace-method | dim |
| dim_of-methods | Get the length of a given dimension of an object |
| drop_dim-methods | Drop a Dimension from an Object |
| drop-methods | 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 | FileBackedNeuroVec |
| FileBackedNeuroVec-class | FileBackedNeuroVec |
| FileFormat-class | FileFormatDescriptor |
| file_matches-methods | Generic function to test whether a file name conforms to the... |
| FileMetaInfo-class | FileMetaInfo |
| FileSource-class | FileSource |
| gaussian_blur | Blur a volumetric image with an isotropic discrete Gaussian... |
| 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 | Filter a volumetric image with an edge-preserving "guided"... |
| H5NeuroVec-class | H5NeuroVec |
| H5NeuroVol-class | H5NeuroVol |
| 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 | indices |
| inverse_trans-methods | Extract inverse image coordinate transformation |
| Kernel | Create a Kernel object from a function of distance from... |
| Kernel-class | Kernel |
| LatentNeuroVec-class | LatentNeuroVec |
| length-methods | Get length of 'NeuroVec'. This is the number of volumes in... |
| LogicalNeuroVol-class | LogicalNeuroVol |
| lookup | Index Lookup operation |
| lookup-methods | lookup |
| map-methods | Apply a function to an object. |
| MappedNeuroVec-class | MappedNeuroVec |
| MappedNeuroVecSource-class | MappedNeuroVecSource |
| map_values-methods | Map Values from One Set to Another Using a User-supplied... |
| MetaInfo-class | MetaInfo |
| NamedAxis-class | NamedAxis |
| ndim-methods | Extract the number of dimensions of an object |
| NeuroBucket-class | NeuroBucket |
| NeuroHyperVec-class | NeuroHyperVec |
| neuroim2 | neuroim2 |
| NeuroObj-class | NeuroObj Base class for all data objects with a cartesion... |
| NeuroSlice | Construct a NeuroSlice object |
| NeuroSlice-class | NeuroSlice |
| neuro_space | Constructor function for 'NeuroSpace' class |
| NeuroSpace-class | NeuroSpace Class |
| NeuroVec | H5NeuroVec |
| NeuroVec-class | NeuroVec |
| NeuroVec-methods | [[ |
| NeuroVecSeq | Create a NeuroVecSeq Instance |
| NeuroVecSeq-class | NeuroVecSeq |
| NeuroVecSeq-methods | [[ |
| NeuroVecSource | NeuroVecSource |
| NeuroVol | Construct a NeuroVol object |
| NeuroVol-class | NeuroVol |
| NeuroVolSource-class | Constructor for NeuroVolSource |
| num_clusters | Number of Clusters |
| num_clusters-methods | Number of Clusters |
| 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-methods | Extract permutation matrix associated with an image |
| plot-methods | plot an NeuroVol as a series of 2D slices |
| 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_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 a clustered searchlight iterator |
| searchlight_coords | Create an exhaustive searchlight iterator that only returns... |
| series-methods | Extract one or more series from object and return as ROI... |
| show-AxisSet1D-method | show an 'AxisSet1D' |
| show-AxisSet2D-method | show an 'AxisSet2D' |
| show-AxisSet3D-method | show an 'AxisSet3D' |
| show-AxisSet4D-method | show an 'AxisSet4D' |
| show-ClusteredNeuroVol-method | show a 'ClusteredNeuroVol' |
| show-FileMetaInfo-method | show a 'FileMetaInfo' |
| show-NamedAxis-method | show an 'NamedAxis' |
| show-NeuroSlice-method | show a 'NeuroSlice' |
| show-NeuroSpace-method | show a 'NeuroSpace' |
| show-NeuroVec-method | show a 'NeuroVec' |
| show-NeuroVecSource-method | show a 'NeuroVecSource' |
| 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 |
| SparseNeuroVec-methods | [[ |
| SparseNeuroVecSource-class | SparseNeuroVecSource |
| SparseNeuroVol-array | Convert SparseNeuroVol to array |
| SparseNeuroVol-class | SparseNeuroVol |
| SparseNeuroVol-numeric | Convert SparseNeuroVol to numeric |
| spherical_roi | Create a Spherical Region 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 |
| sub-SparseNeuroVol-numeric-numeric-ANY-method | extractor |
| sub_vector-methods | Generic function to extract a sub-vector from a 'NeuroVec'... |
| Summary-SparseNeuroVec-method | Summary of SparseNeuroVec |
| Summary-SparseNeuroVol-method | Summary of SparseNeuroVol |
| 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-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 |
