Man pages for neuroim
Data Structures and Handling for Neuroimaging Data
| addDim-methods | Generic function to add a dimension to an object |
| AFNIFileDescriptor-class | AFNIFileDescriptor |
| AFNIMetaInfo-class | AFNIMetaInfo |
| as.array-BrainData-method | convert 'BrainData' instance to array |
| as.list-methods | as.list |
| as.logical-methods | as.logical |
| as.mask-methods | Convert to a LogicalBrainVolume |
| as.matrix-BrainData-method | convert 'BrainData' instance to matrix |
| as.matrix-methods | as.matrix |
| as-methods | conversion from DenseBrainVolume to array |
| as.numeric-methods | Convert SparseBrainVolume to numeric |
| as.raster-methods | as.raster |
| as.sparse-methods | Convert to from dense to sparse representation |
| as.vector-BrainData-method | convert 'BrainData' instance to vector |
| axes-methods | Generic getter function to extract image axes |
| AxisSet1D-class | AxisSet1D |
| AxisSet2D-class | AxisSet2D |
| AxisSet3D-class | AxisSet3D |
| AxisSet4D-class | AxisSet4D |
| AxisSet5D-class | AxisSet5D |
| AxisSet-class | Base |
| axisToIndex-methods | Generic function to convert 1-dimensional real axis... |
| Base-class | Base |
| BaseMetaInfo-class | BaseMetaInfo |
| BaseSource-class | BaseSource |
| BinaryReader | BinaryReader |
| BinaryReader-class | BinaryReader |
| BinaryWriter-class | BinaryWriter |
| BootstrapSearchlight | Create a searchlight iterator that samples regions from... |
| bounds-methods | Generic function to extract the spatial bounds (origin + dim... |
| BrainBucket-class | BrainBucket |
| BrainBucketSource-class | BrainBucketSource |
| BrainData-class | BrainData |
| BrainFileDescriptor-class | BrainFileDescriptor |
| BrainFileSource-class | BrainFileSource Base class for representing a data source for... |
| BrainMetaInfo-class | BrainMetaInfo This class contains meta information from an... |
| BrainSlice | BrainSlice constructor |
| BrainSlice-class | BrainSlice |
| BrainSource-class | BrainSource |
| BrainSpace | Constructor function for 'BrainSpace' class |
| BrainSpace-class | BrainSpace |
| BrainSurface-class | BrainSurface |
| BrainSurfaceSource-class | BrainSurfaceSource |
| BrainSurfaceVector-class | BrainSurfaceVector |
| BrainSurfaceVectorSource-class | BrainSurfaceVectorSource |
| BrainVector-class | BrainVector |
| BrainVectorSource | BrainVectorSource |
| BrainVectorSource-class | BrainVectorSource |
| BrainVolume | BrainVolume |
| BrainVolume-class | Base class for image representing 3D volumetric data. |
| BrainVolumeSource-class | BrainVolume BrainVolumeSource A class is used to produce a... |
| close-methods | close |
| clusterCenters-methods | clusterCenters |
| ClusteredBrainVolume-class | ClusteredBrainVolume |
| ColumnReader | ColumnReader |
| ColumnReader-class | ColumnReader |
| concat-methods | Concatenate two objects |
| connComp3D | Extract connected components from a 3D mask |
| connComp-methods | Find connected components |
| coords-methods | Extract coordinates |
| coordToGrid-methods | Generic function to convert N-dimensional real world... |
| coordToIndex-methods | Generic function to convert N-dimensional real world... |
| dataFileMatches-methods | Generic function to test whether a file name conforms to the... |
| dataFile-methods | Generic function to get the name of the data file, given a... |
| dataReader-methods | Generic function to create data reader |
| DenseBrainVector-class | DenseBrainVector |
| DenseBrainVolume-class | DenseBrainVolume |
| dim-BrainData-method | dim of 'BrainData' object |
| dim-BrainSpace-method | dim |
| dim-FileMetaInfo-method | dim of 'FileMetaInfo' |
| dropDim-methods | Generic function to drop a dimension from an object |
| eachSeries-methods | Generic functions to apply a function to each series of a 4D... |
| eachSlice-methods | Generic functions to apply a function to each (2D) slice of... |
| eachVolume-methods | Generic function to apply a function to each volume of a... |
| fileMatches-methods | Generic function to test whether a file name conforms to the... |
| FileMetaInfo-class | FileMetaInfo |
| fill-methods | Generic function to map values from one set to another using... |
| FreesurferAsciiSurfaceFileDescriptor-class | FresurferAsciiSurfaceFileDescriptor |
| FreeSurferSurfaceGeometryMetaInfo-class | FreeSurferSurfaceGeometryMetaInfo This class contains meta... |
| gridToCoord-methods | Generic function to convert N-dimensional grid coordinate... |
| gridToIndex-methods | Generic function to convert N-dimensional grid coordinate to... |
| headerFileMatches-methods | Generic function to test whether a file name conforms to the... |
| headerFile-methods | Generic function to get the name of the header file, given a... |
| imageGrid | imageGrid |
| image-methods | image |
| IndexLookupVolume-class | IndexLookupVolume |
| indexToCoord-methods | Generic function to convert 1D indices to N-dimensional real... |
| indexToGrid-methods | Generic function to convert 1D indices to N-dimensional grid... |
| indices-methods | Extract indices |
| internal-methods | .isExtension |
| inverseTrans-methods | Generic getter to extract inverse image coordinate... |
| Kernel | Create a Kernel object |
| Kernel-class | Kernel |
| Layer | Layer |
| Layer-class | Layer |
| length-methods | Get length of 'BrainVector'. This is the numbe rof volumes in... |
| loadBucket | loadBucket |
| loadData-methods | Generic function to load data from a data source |
| loadFSSurface | load Freesurfer ascii surface |
| loadSurface | load an surface from a set of files |
| loadVector | loadVector |
| loadVolume | Load an image volume from a file |
| loadVolumeList | loadVolList |
| LogicalBrainVolume-class | LogicalBrainVolume |
| lookup-methods | Index Lookup operation |
| makeVector | makeVector |
| makeVolume | makeVolume |
| map-methods | Generic function to apply a function to an object |
| mapToColors | mapToColors |
| matchAnatomy2D | given two named axes return AxisSet2D singleton |
| matchAnatomy3D | given three named axes return AxisSet3D singleton |
| matrixToVolumeList | matrixToVolumeList converts a matrix to a list of... |
| mergePartitions-methods | mergePartitions |
| MNI_SPACE_1MM | MNI SPACE 1MM |
| NamedAxis-class | NamedAxis |
| names-methods | names |
| ndim-methods | Generic function to extract the number of dimensions of an... |
| neuroim | neuroim |
| NIfTIFileDescriptor-class | NIfTIFileDescriptor |
| NIfTIMetaInfo-class | Constructor for 'NIfTIMetaInfo' class |
| NIMLSurfaceDataMetaInfo | Constructor for 'NIMLSurfaceDataMetaInfo' class |
| NIMLSurfaceDataMetaInfo-class | NIMLSurfaceDataMetaInfo This class contains meta information... |
| NIMLSurfaceFileDescriptor-class | NIMLSurfaceFileDescriptor |
| NullMetaInfo-class | NullMetaInfo |
| numClusters-methods | numClusters |
| origin-methods | Generic getter to extract image origin |
| overlay-methods | overlay two objects |
| partition-methods | partition |
| permMat-methods | Extract permutation matrix |
| pick-methods | pick |
| print-AxisSet2D-method | print a 'AxisSet2D' instance |
| print-AxisSet3D-method | print a 'AxisSet3D' instance |
| print-methods | Generic function to print an object |
| print-NamedAxis-method | print a 'NamedAxis' |
| RandomSearchlight | Create an Random Searchlight iterator |
| readAFNIHeader | readAFNIHeader |
| readColumns-methods | Generic function to read a set of column vector from an input... |
| readElements-methods | Generic function to read a sequence of elements from an input... |
| readHeader | read header information of an image file |
| readMetaInfo-methods | Generic function to read image meta info given a file and a... |
| RegionCube | Create A Cuboid Region of Interest |
| RegionSphere | Create A Spherical Region of Interest |
| RegionSquare | Create a square region of interest where the z-dimension is... |
| render-methods | Render an image to create a drawable image. |
| renderSlice-methods | Render a slice at z coordinate |
| ROIVolume | Create an instance of class ROIVolume |
| ROIVolume-class | ROIVolume |
| scaleSeries-methods | Generic functions to scale (center and/or normalize by... |
| Searchlight | Create an exhaustive searchlight iterator |
| seriesIter | seriesIter |
| series-methods | Extract vector series from object |
| 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-BaseMetaInfo-method | show a 'BaseMetaInfo' |
| show-BrainSpace-method | show a 'BrainSpace' |
| show-BrainVector-method | show a 'BrainVector' |
| show-BrainVectorSource-method | show a 'BrainVectorSource' |
| show-BrainVolume-method | show a 'BrainVolume' |
| show-FileMetaInfo-method | show a 'FileMetaInfo' |
| show-NamedAxis-method | show an 'NamedAxis' |
| show-NullMetaInfo-method | show a 'NullMetaInfo' |
| show-ROIVolume-method | show an 'ROIVolime' |
| show-SparseBrainVector-method | show a 'SparseBrainVector' |
| show-SurfaceDataMetaInfo-method | show an 'SurfaceDataMetaInfo' |
| show-SurfaceGeometryMetaInfo-method | show an 'SurfaceGeometryMetaInfo' |
| sliceData | sliceData |
| slice-methods | Extract a 2D slice from an image volume |
| space-methods | Generic function to extract geometric properties of an image. |
| spacing-methods | Generic function to extract the voxel dimensions of an image |
| SparseBrainVector-class | SparseBrainVector |
| SparseBrainVectorSource-class | SparseBrainVectorSource |
| SparseBrainVolume-class | SparseBrainVolume |
| splitFill-methods | Generic function to fill disjoint sets of values with the... |
| splitReduce-methods | Generic function to summarize subsets of an object by first... |
| splitScale-methods | Generic function to center/scale row-subsets of a matrix or... |
| stripExtension-methods | Generic function to strip extension from file name, given a... |
| sub-BrainBucket-index-missing-ANY-method | extract labeled volume from 'BrainBucket' |
| sub-ROIVolume-numeric-missing-ANY-method | extract data from 'ROIVolume' |
| sub-SparseBrainVector-missing-missing-ANY-method | extractor |
| sub-SparseBrainVector-missing-numeric-ANY-method | extractor |
| sub-SparseBrainVector-numeric-missing-ANY-method | extractor |
| sub-SparseBrainVector-numeric-numeric-ANY-method | extractor |
| sub-SparseBrainVolume-matrix-missing-ANY-method | extractor |
| sub-SparseBrainVolume-missing-missing-ANY-method | extractor |
| sub-SparseBrainVolume-missing-numeric-ANY-method | extractor |
| sub-SparseBrainVolume-numeric-missing-missing-method | extractor |
| sub-SparseBrainVolume-numeric-numeric-ANY-method | extractor |
| sub-sub-BrainBucket-index-missing-method | extract labeled volume from 'BrainBucket' |
| subVector-methods | Generic function to extract a sub-vector from a 'BrainVector'... |
| SurfaceDataMetaInfo | Constructor for 'SurfaceDataMetaInfo' class |
| SurfaceDataMetaInfo-class | SurfaceDataMetaInfo This class contains meta information for... |
| SurfaceGeometryMetaInfo | Constructor for 'SurfaceGeometryMetaInfo' class |
| SurfaceGeometryMetaInfo-class | SurfaceGeometryMetaInfo This class contains meta information... |
| takeSeries-methods | Generic function to extract a set of series from a 4D image |
| takeVolume-methods | Generic function to extract a one or more individual volumes... |
| tesselate-methods | tesselate |
| trans-methods | Generic getter to extract image coordinate transformation |
| values-methods | Generic function to extract data values of object |
| voxels-methods | extract voxel coordinates |
| writeElements-methods | Generic function to write a sequence of elements from an... |
| writeVector-methods | Generic function to write a 4D image vector to disk |
| writeVolume-methods | Generic function to write a 3D image volume to disk |
