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A B C D E F G H I K L M N O P R S T V W misc
| addDim | Generic function to add a dimension to an object |
| addDim-method | Generic function to add a dimension to an object |
| AFNIFileDescriptor-class | This class supports the AFNI file format |
| AFNIMetaInfo | AFNIMetaInfo |
| AFNIMetaInfo-class | This class contains meta information from an image data file |
| as | conversion from ROIVolume to DenseBrainVolume |
| as.array-method | convert 'BrainData' instance to array |
| as.list-method | as.list |
| as.logical-method | as.logical |
| as.mask | Convert to a LogicalBrainVolume |
| as.mask-method | Convert to a LogicalBrainVolume |
| as.matrix-method | convert 'BrainData' instance to matrix |
| as.matrix-method | convert a DenseBrainVector to a matrix |
| as.numeric-method | Convert SparseBrainVolume to numeric |
| as.raster-method | as.raster |
| as.sparse | Convert to sparse representation |
| as.sparse-method | Convert to sparse representation |
| as.vector-method | convert 'BrainData' instance to vector |
| axes | Generic getter function to extract image axes |
| axes-method | Generic getter function to extract image axes |
| AxisSet-class | Virtual base class representing an ordered set of named axes. |
| AxisSet1D-class | A one-dimensional axis set |
| AxisSet2D-class | A two-dimensional axis set |
| AxisSet3D-class | A three-dimensional axis set |
| AxisSet4D-class | A four-dimensional axis set |
| AxisSet5D-class | A five-dimensional axis set |
| axisToIndex | Generic function to convert 1-dimensional real axis coordinates along a single axis dimension to an 1D index along the same axis |
| axisToIndex-method | Generic function to convert 1-dimensional real axis coordinates along a single axis dimension to an 1D index along the same axis |
| BaseMetaInfo-class | This is a base class to represent meta information |
| BaseSource-class | This is a base class to represent a data source |
| BinaryReader | BinaryReader |
| BinaryReader-class | BinaryReader |
| BinaryWriter | BinaryWriter |
| BinaryWriter-class | BinaryWriter |
| bounds | Generic function to extract the spatial bounds (origin + dim * spacing) of an image param x the object |
| bounds-method | Generic function to extract the spatial bounds (origin + dim * spacing) of an image param x the object |
| BrainBucket-class | BrainBucket |
| BrainBucketSource | BrainBucketSource |
| BrainBucketSource-class | BrainBucketSource |
| BrainData-class | BrainData |
| BrainFileDescriptor-class | This class represents a neuroimaging file format |
| BrainFileSource-class | Base class for representing a data source for images. The purpose of this class is to provide a layer in between low level IO and image loading functionality. |
| BrainMetaInfo | This class contains meta information from an image |
| BrainMetaInfo-class | This class contains meta information from an image |
| BrainSlice | BrainSlice constructor |
| BrainSlice-class | BrainSlice |
| BrainSource-class | Base class for representing a data source for images. The purpose of this class is to provide a layer in between low level IO and image loading functionality. |
| BrainSpace | Constructor function for 'BrainSpace' class |
| BrainSpace-class | BrainSpace |
| BrainVector | Four-dimensional brain image |
| BrainVector-class | Four-dimensional brain image |
| BrainVectorSource | BrainVectorSource |
| BrainVectorSource-class | BrainVectorSource |
| BrainVolume | Three-dimensional brain image |
| BrainVolume-class | Three-dimensional brain image |
| BrainVolumeSource | A class is used to produce a 'BrainVolume' instance |
| BrainVolumeSource-class | A class is used to produce a 'BrainVolume' instance |
| close-method | close |
| clusterCenters | clusterCenters |
| clusterCenters-method | clusterCenters |
| ClusteredBrainVolume | ClusteredBrainVolume |
| ClusteredBrainVolume-class | ClusteredBrainVolume |
| concat | Concatenate two objects |
| concat-method | Concatenate two objects |
| connComp | Find connected components |
| connComp-method | Find connected components |
| connComp3D | Extract connected components from a 3D mask |
| coords | Extract coordinates |
| coords-method | Extract coordinates |
| coordToGrid | Generic function to convert N-dimensional real world coordinates to grid coordinates |
| coordToGrid-method | Generic function to convert N-dimensional real world coordinates to grid coordinates |
| coordToIndex | Generic function to convert N-dimensional real world coordinates to 1D indices |
| coordToIndex-method | Generic function to convert N-dimensional real world coordinates to 1D indices |
| dataFile | Generic function to get the name of the data file, given a file name and a 'BrainFileDescriptor' instance. |
| dataFile-method | Generic function to get the name of the data file, given a file name and a 'BrainFileDescriptor' instance. |
| dataFileMatches | Generic function to test whether a file name conforms to the given a 'BrainFileDescriptor' instance. Will test for match to data file only |
| dataFileMatches-method | Generic function to test whether a file name conforms to the given a 'BrainFileDescriptor' instance. Will test for match to data file only |
| dataReader | Generic function to create data reader |
| dataReader-method | Generic function to create data reader |
| DenseBrainVector | DenseBrainVector |
| DenseBrainVector-class | DenseBrainVector |
| DenseBrainVolume | DenseBrainVolume |
| DenseBrainVolume-class | DenseBrainVolume |
| dim-method | dim |
| dropDim | Generic function to drop a dimension from an object |
| dropDim-method | Generic function to drop a dimension from an object |
| eachSeries | Generic functions to apply a function to each series of a 4D image That is, if the 4th dimension is 'time' each series is a 1D time series. |
| eachSeries-method | Generic functions to apply a function to each series of a 4D image That is, if the 4th dimension is 'time' each series is a 1D time series. |
| eachSlice | Generic functions to apply a function to each (2D) slice of an image |
| eachSlice-method | Generic functions to apply a function to each (2D) slice of an image |
| eachVolume | Generic function to apply a function to each volume of a four-dimensional image |
| eachVolume-method | Generic function to apply a function to each volume of a four-dimensional image |
| fileMatches | Generic function to test whether a file name conforms to the given 'BrainFileDescriptor' instance. Will test for match to either header file or data file |
| fileMatches-method | Generic function to test whether a file name conforms to the given 'BrainFileDescriptor' instance. Will test for match to either header file or data file |
| FileMetaInfo-class | This class contains meta information from an image data file |
| fill | Generic function to map values from one set to another using a user-supplied lookup table |
| fill-method | Generic function to map values from one set to another using a user-supplied lookup table |
| gridToIndex | Generic function to convert N-dimensional grid coordinate to 1D indices |
| gridToIndex-method | Generic function to convert N-dimensional grid coordinate to 1D indices |
| headerFile | Generic function to get the name of the header file, given a file name and a 'BrainFileDescriptor' instance. |
| headerFile-method | Generic function to get the name of the header file, given a file name and a 'BrainFileDescriptor' instance. |
| headerFileMatches | Generic function to test whether a file name conforms to the given 'BrainFileDescriptor' instance. Will test for match to header file only |
| headerFileMatches-method | Generic function to test whether a file name conforms to the given 'BrainFileDescriptor' instance. Will test for match to header file only |
| image-method | image |
| IndexLookupVolume | IndexLookupVolume |
| IndexLookupVolume-class | IndexLookupVolume |
| indexToCoord | Generic function to convert 1D indices to N-dimensional real world coordinates |
| indexToCoord-method | Generic function to convert 1D indices to N-dimensional real world coordinates |
| indexToGrid | Generic function to convert 1D indices to N-dimensional grid coordinates |
| indexToGrid-method | Generic function to convert 1D indices to N-dimensional grid coordinates |
| indices | Extract indices |
| indices-method | Extract indices |
| inverseTrans | Generic getter to extract inverse image coordinate transformation |
| inverseTrans-method | Generic getter to extract inverse image coordinate transformation |
| Kernel | Create a Kernel object |
| Kernel-class | Kernel |
| Layer | create a Layer object |
| Layer-class | Layer |
| length-method | length |
| length-method | Get length of 'BrainVector'. This is the numbe rof volumes in the volume vector (e.g. the 4th image dimension) |
| loadBucket | loadBucket |
| loadData | Generic function to load data from a data source |
| loadData-method | Generic function to load data from a data source |
| loadVector | loadVector |
| loadVolume | load an image volume from a file |
| loadVolumeList | loadVolList |
| LogicalBrainVolume | LogicalBrainVolume |
| LogicalBrainVolume-class | LogicalBrainVolume |
| lookup | Index Lookup operation |
| lookup-method | Index Lookup operation |
| makeVector | makeVector |
| makeVolume | makeVolume |
| map | Generic function to apply a function to an object |
| map-method | Generic function to apply a function to an object |
| matchAnatomy2D | given two named axes return AxisSet2D singleton |
| matchAnatomy3D | given three named axes return AxisSet3D singleton |
| mergePartitions | mergePartitions |
| mergePartitions-method | mergePartitions |
| NamedAxis-class | This class represents an axis with a name attribute |
| names-method | extract names of 'BrainBucketSource' instance |
| ndim | Generic function to extract the number of dimensions of an object |
| ndim-method | Generic function to extract the number of dimensions of an object |
| NIfTIFileDescriptor-class | This class supports the NIfTI file format |
| NIfTIMetaInfo | Constructor for 'NIfTIMetaInfo' class |
| NIfTIMetaInfo-class | This class contains meta information from an image data file |
| NullMetaInfo-class | This is class is used to denote the absense of meta information |
| numClusters | numClusters |
| numClusters-method | numClusters |
| origin | Generic getter to extract image origin |
| origin-method | Generic getter to extract image origin |
| overlay | overlay two objects |
| overlay-method | overlay two objects |
| partition | partition |
| partition-method | partition |
| permMat | extract permutation matrix |
| permMat-method | extract permutation matrix |
| pick | pick |
| print-method | print a 'NamedAxis' instance |
| RandomSearchlight | Create an Random Searchlight iterator |
| readElements | Generic function to read a sequence of elements from an input source |
| readElements-method | Generic function to read a sequence of elements from an input source |
| readHeader | read header information of an image file |
| readMetaInfo | Generic function to read image meta info given a file and a 'BrainFileDescriptor' instance. |
| readMetaInfo-method | Generic function to read image meta info given a file and a 'BrainFileDescriptor' instance. |
| RegionCube | Create A Cuboid Region of Interest |
| RegionSphere | Create A Spherical Region of Interest |
| ROIVolume | Create an instance of class ROIVolume |
| ROIVolume-class | ROIVolume |
| Searchlight | Create an exhaustive searchlight iterator |
| series | Extract vector series from object |
| series-method | Extract vector series from object |
| seriesIter | Construct a series iterator |
| seriesIter-method | Construct a series iterator |
| show-method | show |
| slice | extract a 2D slice from an image volume |
| slice-method | extract a 2D slice from an image volume |
| space | Generic function to extract the 'space' member variable |
| space-method | Generic function to extract the 'space' member variable |
| spacing | Generic function to extract the voxel dimensions of an image |
| spacing-method | Generic function to extract the voxel dimensions of an image |
| SparseBrainVector | SparseBrainVector |
| SparseBrainVector-class | SparseBrainVector |
| SparseBrainVectorSource | SparseBrainVectorSource |
| SparseBrainVectorSource-class | SparseBrainVectorSource |
| SparseBrainVolume | SparseBrainVolume |
| SparseBrainVolume-class | SparseBrainVolume |
| splitFill | Generic function to fill disjoint sets of values with the output of a function |
| splitFill-method | Generic function to fill disjoint sets of values with the output of a function |
| splitReduce | Generic function to summarize subsets of an object |
| splitReduce-method | Generic function to summarize subsets of an object |
| splitScale | Generic function to center/scale subsets of an object |
| splitScale-method | Generic function to center/scale subsets of an object |
| stripExtension | Generic function to strip extension from file name, given a 'BrainFileDescriptor' instance. |
| stripExtension-method | Generic function to strip extension from file name, given a 'BrainFileDescriptor' instance. |
| takeSeries | Generic function to extract a set of series from a 4D image |
| takeVolume | Generic function to extract a volume from a four-dimensional image |
| takeVolume-method | Generic function to extract a volume from a four-dimensional image |
| tesselate | tesselate |
| tesselate-method | tesselate |
| trans | Generic getter to extract image coordinate transformation |
| trans-method | Generic getter to extract image coordinate transformation |
| voxels | extract voxel coordinates |
| voxels-method | extract voxel coordinates |
| writeElements | Generic function to write a sequence of elements from an input source |
| writeElements-method | Generic function to write a sequence of elements from an input source |
| writeVector | Generic function to write an image vector to disk |
| writeVector-method | Generic function to write an image vector to disk |
| writeVolume | Generic function to write an image volume to disk |
| writeVolume-method | Generic function to write an image volume to disk |
| [-method | extract data from 'ROIVolume' |
| [-method | extract data from SparseBrainVector |
| [-method | extract data from SparseBrainVector |
| [-method | extract data from SparseBrainVector |
| [-method | extract data from SparseBrainVector |
| [[-method | extract labeled volume from 'BrainBucket' |
| [[-method | extract indexed volume from 'BrainBucket' |