Man pages for bbuchsbaum/neuroim2
Data Structures and Handling for Neuroimaging Data

add_dim-methodsGeneric function to add a dimension to an object
AFNIDescriptor-classAFNIFormat
AFNIMetaInfo-classAFNIMetaInfo
as.dense-methodsConvert to dense representation
as.list-methodsas.list
as.logical-methodsas.logical
as.mask-methodsConvert to a LogicalNeuroVol
as.matrix-methodsconvert a 'NeuroVec' to a matrix
as-methodsconversion from SparseNeuroVol to numeric
as.numeric-methodsConvert SparseNeuroVol to numeric
as.sparse-methodsConvert to from dense to sparse representation
axes-methodsGeneric getter function to extract image axes
AxisSet1D-classAxisSet1D
AxisSet2D-classAxisSet2D
AxisSet3D-classAxisSet3D
AxisSet4D-classAxisSet4D
AxisSet5D-classAxisSet5D
AxisSet-classAxisSet
BasisNeuroVecBasisNeuroVec
BinaryReaderBinaryReader
BinaryReader-classBinaryReader
BinaryWriter-classBinaryWriter
bounds-methodsGeneric function to extract the spatial bounds (origin + dim...
centroid-methodsreturn the centroid of an object
close-methodsclose
ClusteredNeuroVol-classClusteredNeuroVol
ColumnReaderColumnReader
ColumnReader-classColumnReader
concat-methodsConcatenate two objects in the time dimension
conn_comp_3DExtract connected components from a 3D mask
conn_comp-methodsFind connected components
coords-methodsExtract coordinates
coord_to_grid-methodsGeneric function to convert N-dimensional real world...
coord_to_index-methodsGeneric function to convert N-dimensional real world...
cuboid_roiCreate A Cuboid Region of Interest
data_file_matches-methodsGeneric function to test whether a file name conforms to the...
data_file-methodsGeneric function to get the name of the data file, given a...
data_reader-methodsGeneric function to create data reader
deferred_listdeferred_list
deferred_list2deferred_list2
DenseNeuroVec-classDenseNeuroVec
DenseNeuroVol-classDenseNeuroVol
dim-FileMetaInfo-methoddim of 'FileMetaInfo'
dim-methodsdim of 'NeuroObj' object
dim-NeuroSpace-methoddim
dim_of-methodsdim_of
drop_dim-methodsGeneric function to drop a dimension from an object
drop-methodsdrop
extractor3dArray-like access for 3-dimensional data structures
extractor4dArray-like access for 4-dimensional data structures
FileBackedNeuroVecConstuct a 'FileBackedNeuroVec' instance
FileBackedNeuroVec-classFileBackedNeuroVec
FileFormat-classFileFormatDescriptor
file_matches-methodsGeneric function to test whether a file name conforms to the...
FileMetaInfo-classFileMetaInfo
FileSource-classFileSource
grid_to_coord-methodsGeneric function to convert N-dimensional grid coordinate...
grid_to_grid-methodsGeneric function to convert voxel coordinates in the...
grid_to_index-methodsGeneric function to convert N-dimensional grid coordinate to...
H5NeuroVol-classH5NeuroVol
header_file_matches-methodsGeneric function to test whether a file name conforms to the...
header_file-methodsGeneric function to get the name of the header file, given a...
IndexLookupVol-classIndexLookupVol
index_to_coord-methodsGeneric function to convert 1D indices to N-dimensional real...
index_to_grid-methodsGeneric function to convert 1D indices to N-dimensional grid...
indices-methodsExtract indices
internal-methods.isExtension
inverse_trans-methodsGeneric getter to extract inverse image coordinate...
KernelCreate a Kernel object from a function of distance from...
Kernel-classKernel
length-methodsGet length of 'NeuroVec'. This is the number of volumes in...
linear_access-methodsGeneric function to extract values from an array-like object...
load_data-methodsGeneric function to load data from a data source
LogicalNeuroVol-classLogicalNeuroVol
lookup-methodsIndex Lookup operation
map-methodsGeneric function to apply a function to an object
MappedNeuroVec-classMappedNeuroVec
MappedNeuroVecSource-classMappedNeuroVecSource
map_values-methodsGeneric function to map values from one set of values to...
matchAnatomy2Dgiven two named axes return AxisSet2D singleton
matchAnatomy3Dgiven three named axes return AxisSet3D singleton
MetaInfo-classMetaInfo
NamedAxis-classNamedAxis
ndim-methodsGeneric function to extract the number of dimensions of an...
NeuroBucket-classNeuroBucket
NeuroHyperVecCreate an 'NeuroHyperVec' instance from a variable length...
NeuroHyperVec-classNeuroHyperVec
neuroim2neuroim2
NeuroObj-classNeuroObj Base class for all data objects with a cartesion...
NeuroSliceNeuroSlice constructor
NeuroSlice-classNeuroSlice
neuro_spaceConstructor function for 'NeuroSpace' class
NeuroSpace-classNeuroSpace
NeuroVec-classNeuroVec
NeuroVec-methods[[
NeuroVecSeqCreate an 'NeuroVecSeq' instance for a variable length list...
NeuroVecSeq-classNeuroVecSeq
NeuroVecSourceNeuroVecSource
NeuroVecSource-classNeuroVecSource
NeuroVolNeuroVol
NeuroVol-classNeuroVol
NeuroVolSource-classNeuroVolSource
NIFTIFileDescriptor-classNIFTIFormat
NIFTIMetaInfo-classConstructor for 'NIFTIMetaInfo' class
num_clusters-methodsnum_clusters
origin-methodsGeneric getter to extract image origin
partition-methodsGeneric function to partition an image into a set of disjoint...
patch_set-methodsExtract set of patches
perm_mat-methodsExtract permutation matrix
plot-methodsplot an image
print-AxisSet2D-methodprint a 'AxisSet2D' instance
print-AxisSet3D-methodprint a 'AxisSet3D' instance
print-methodsGeneric function to print an object
print-NamedAxis-methodprint a 'NamedAxis'
random_searchlightrandom_searchlight
read_afni_headerread_afni_header
read_columns-methodsGeneric function to read a set of column vector from an input...
read_elements-methodsGeneric function to read a sequence of elements from an input...
read_headerread header information of an image file
read_meta_info-methodsGeneric function to read image meta info given a file and a...
read_vecread_vec
read_volLoad an image volume from a file
read_vol_listread_vol_list
render-methodsRender an image to create a drawable image.
render_slice-methodsRender a slice at z coordinate
reorient-methodsGeneric function to remap the grid-to-world coordinates...
ROI-classROI
ROIVecCreate an instance of class 'ROIVec'
ROIVec-classROIVec
ROIVecWindow-classROIVecWindow
ROIVolCreate an instance of class 'ROIVol'
ROIVol-classROIVol
ROIVolWindow-classROIVolWindow
scale_series-methodsGeneric functions to scale (center and/or normalize by...
searchlightbootstrap_searchlight
series-methodsExtract one or more series from object and return as ROI...
show-AxisSet1D-methodshow an 'AxisSet1D'
show-AxisSet2D-methodshow an 'AxisSet2D'
show-AxisSet3D-methodshow an 'AxisSet3D'
show-AxisSet4D-methodshow an 'AxisSet4D'
show-ClusteredNeuroVol-methodshow a 'ClusteredNeuroVol'
show-FileMetaInfo-methodshow a 'FileMetaInfo'
show-NamedAxis-methodshow an 'NamedAxis'
show-NeuroSpace-methodshow a 'NeuroSpace'
show-NeuroVec-methodshow a 'NeuroVec'
show-NeuroVecSource-methodshow a 'NeuroVecSource'
show-NeuroVol-methodshow a 'NeuroVol'
show-ROIVec-methodshow an 'ROIVec'
show-ROIVol-methodshow an 'ROIVol'
show-SparseNeuroVec-methodshow a 'SparseNeuroVec'
show-SparseNeuroVol-methodshow a 'SparseNeuroVol'
slice-methodsslice
slices-methodsGeneric function to extract an ordered series of 2D slices
space-methodsGeneric function to extract geometric properties of an image.
spacing-methodsGeneric function to extract the voxel dimensions of an image
SparseNeuroVec-classSparseNeuroVec
SparseNeuroVec-methods[[
SparseNeuroVecSource-classSparseNeuroVecSource
SparseNeuroVol-classSparseNeuroVol
spherical_roiCreate a Spherical Region of Interest
split_blocks-methodsGeneric function to cut a vector-valued object into a list of...
split_clusters-methodsGeneric function to cut an object into a list of spatial or...
split_fill-methodsGeneric function to fill disjoint sets of values with the...
split_reduce-methodsGeneric function to summarize subsets of an object by first...
split_scale-methodsGeneric function to center/scale row-subsets of a matrix or...
square_roiCreate a square region of interest where the z-dimension is...
strip_extension-methodsGeneric function to strip extension from file name, given a...
sub-SparseNeuroVec-numeric-numeric-ANY-methodextractor
sub-SparseNeuroVol-numeric-numeric-ANY-methodextractor
sub_vector-methodsGeneric function to extract a sub-vector from a 'NeuroVec'...
trans-methodsGeneric getter to extract image coordinate transformation
values-methodsGeneric function to extract data values of object
vectors-methodsGeneric function to extract an ordered series of 1D vectors
vols-methodsGeneric function to extract an ordered series of 3D volumes
vol_subset-methodssubset an 'ROIVol'
voxels-methodsextract voxel coordinates
which_dim-methodswhich_dim
write_elements-methodsGeneric function to write a sequence of elements from an...
write_vec-methodsGeneric function to write a 4D image vector to disk
write_vol-methodsGeneric function to write a 3D image volume to disk
bbuchsbaum/neuroim2 documentation built on Oct. 15, 2019, 2:55 p.m.