nifti.io (version 1.0.0)

info.nii: Retrieve NIfTI Header Information

Description

Retrieve information from the NIfTI header of the specified file. The entire header can be retrieved as a list, or a single or subset of items can be specified as a character vector to get specific information. There are several special cases implemented including getting number of voxels, number of volumes, image spacing, and orientation.

Usage

info.nii(nii.file, field="hdr")

Arguments

nii.file

Full directory listing to NIfTI file.

field

A character vector of field names to be returned.

Value

A vector or named list containing the requested output

Details

Fields can take a number of different values indicating the entire header, a specific item or subset of header values or set of useful values. Number of voxels in XYZ planes: 'dimensions', 'dims', 'size', 'sz', 'voxels', 'vxls', 'xyz' Voxel spacing: 'space', 'spacing' Number of Volumes: 'volumes', 'vols', 'trs' Orientation fields: 'orientation' Entire Header as list object: 'hdr' Subset of specific header items: 'sizeof_hdr', 'data_type', 'db_name', 'extents', 'session_error', 'regular', 'dim_info', 'dim', 'intent_p1', 'intent_p2', 'intent_p3', 'intent_code', 'datatype', 'bitpix', 'slice_start', 'pixdim', 'vox_offset', 'scl_slope', 'scl_inter', 'slice_end', 'slice_code', 'xyzt_units', 'cal_max', 'cal_min', 'slice_duration', 'toffset', 'glmax', 'glmin', 'descrip', 'aux_file', 'qform_code', 'sform_code', 'quatern_b', 'quatern_c', 'quatern_d', 'qoffset_x', 'qoffset_y', 'qoffset_z', 'srow_x', 'srow_y', 'srow_z', 'intent_name', 'magic'

Examples

# NOT RUN {
# get filename for example NII file included in nifti.io package
nii.eg <- system.file("extdata", "egBrain.nii", package="nifti.io")

# get the number of voxels in the 3-dimensional volume of the specified image
image.size <- info.nii(nii.file = nii.eg, field = "dimensions")

# get the size in mm of the volume
image.spacing <- info.nii(nii.file = nii.eg, field = "spacing")

# get the number of volumes
image.volumes <- info.nii(nii.file = nii.eg, field = "volumes")

# get list containing orientation parameters
image.orientation <- info.nii(nii.file = nii.eg, field = "orientation")

# get entire header from NII file
image.hdr <- info.nii(nii.file = nii.eg, field = "hdr")

# get a specific element in the header
image.hdr.datatype <- info.nii(nii.file = nii.eg, field = "datatype")
# }