freesurferformats (version 1.1.0)

cifti.structure.data: Extract the data of one brain structure from a CIFTI-2 file.

Description

Get the data values of a single brain structure (e.g. one hemisphere) from a CIFTI-2 file, reconstructed for the full surface. The result has one row per vertex of the surface (in the order of the surface, which is the order the vertices have in the surface mesh files) and one column per index of the other matrix dimension of the file. Vertices of the surface that have no value in the file are reported as NA: grayordinates files have a reduced mesh (the medial wall vertices are missing), and returning the values for the complete surface is what makes such files usable together with the standard surface meshes of a subject.

Volume structures (a brain model of type 'CIFTI_MODEL_TYPE_VOXELS', which subcortical structures use) cannot be expanded like this, because the voxels a structure consists of are not a rectangular block of a volume and are not ordered in any meaningful way. For those, the data values are returned together with the voxel indices and the affine transformation that maps them to coordinates, see the Value section.

Usage

cifti.structure.data(x, structure = NULL, dim = NULL)

Value

If 'structure' is a single structure: a named list with the entries 'structure' (character string, the canonical name of the structure, e.g. 'CIFTI_STRUCTURE_CORTEX_LEFT'), 'structure_short' (the name without the prefix, e.g. 'CORTEX_LEFT'), 'model_type' (character string, one of 'SURFACE', 'VOXELS' or 'SURFACE_AND_VOXELS'), 'surface' and 'volume'. If 'structure' is NULL: a named list of such lists, one per structure, named by the short structure name.

For a selection that contains a surface model, the 'surface' entry holds a numeric (or integer) array with one row per vertex of the full surface and the remaining dimensions of the data, with NA for vertices that the file does not contain. Its dimensions beyond the first are named like in read.cifti. If the selection contains no surface model, 'surface' is NULL.

For a selection that contains a volume model, the 'volume' entry holds a named list with the entries 'values' (an array like 'surface', but with one row per voxel of the structure instead of per surface vertex), 'voxel_indices_ijk' (an n x 3 integer matrix of 0-based voxel indices, in the same order as the rows of 'values'), 'dimensions' (integer vector of length 3, the dimensions of the volume the voxel indices refer to) and 'transformation_matrix' and 'meter_exponent' (the 4x4 row-major matrix from the file that maps the voxel indices to coordinates in units of 10^meter_exponent, and the exponent). If the selection contains no volume model, 'volume' is NULL.

Arguments

x

an fs.cifti.data object, see read.cifti. An fs.cifti metadata object or the path of a CIFTI-2 file are accepted as well, in which case the data are read from the file.

structure

character string or NULL, the brain structure to extract the data for. The usual spellings are accepted ('lh', 'CORTEX_LEFT', 'CIFTI_STRUCTURE_CORTEX_LEFT'), see cifti.structure.canonical. If it is NULL, the data of all structures are returned.

dim

integer or NULL, the CIFTI matrix dimension that holds the brain structure (the brainordinate dimension). For most files there is only one such dimension and this can be left at NULL. Files in which both dimensions are brain models (.dconn and .pdconn) require an explicit value, since they contain the same structures in both dimensions.

See Also

Other cifti functions: cifti.axis.brain.models(), cifti.axis.from.template(), cifti.axis.labels(), cifti.axis.parcels(), cifti.axis.parcels.from.annot(), cifti.axis.scalars(), cifti.axis.series(), cifti.brain.model.surface(), cifti.brain.model.volume(), cifti.dim.labels(), cifti.file.type.for.axes(), cifti.grayordinates(), cifti.header.from.axes(), cifti.label.table(), cifti.parcel(), cifti.parcels(), cifti.series.info(), cifti.structures(), cifti.volume(), print.fs.cifti(), print.fs.cifti.data(), print.fs.connectome(), read.cifti(), read.cifti.header(), read.cifti.rows(), read.fs.connectome.cifti(), write.cifti(), write.fs.connectome.cifti(), write.fs.morph.cifti(), write.fs.parcellated.cifti(), write.fs.parcellation.cifti(), write.fs.series.cifti()

Examples

cifti_file <- system.file("extdata", "cifti", "tiny.dscalar.nii", package = "freesurferformats")
cii <- read.cifti(cifti_file)
lh_data <- cifti.structure.data(cii, "lh")
dim(lh_data$surface)
# vertices beyond the end of the mesh in the file are NA:
sum(is.na(lh_data$surface[, 1]))

# Volume structures are returned with their voxel indices:
vol_file <- system.file("extdata", "cifti", "tiny_volume.dscalar.nii",
                        package = "freesurferformats")
vol_cii <- read.cifti(vol_file)
cerebellum <- cifti.structure.data(vol_cii, "CEREBELLUM")
cerebellum$volume$voxel_indices_ijk