Get the geometry of a volume.

Transformation matrices of the voxel-to-voxel kind can only be interpreted relative to the volumes they relate, so the conversion functions need the geometry of those volumes: their dimensions, voxel sizes and the matrix that maps voxel indices to RAS coordinates.

The voxel indices are zero-based and the origin of the RAS space is the one used by FreeSurfer for MGH headers and by NIfTI for the sform, i.e. this is the same convention as mghheader.vox2ras.

Usage

volume.geometry(volume)

Arguments

volume

an fs.volume instance (as returned by read.fs.volume or read.fs.mgh), a nifti instance (from the oro.nifti package), or a named list with the entries 'vox2ras_matrix', 'voldim' and 'voxelsize'.

Value

named list with the entries 'vox2ras' (4x4 numerical matrix), 'dim' (integer vector of length 3) and 'voxelsize' (numerical vector of length 3).