nifti.header.to.vox2ras: Compute the voxel-to-RAS matrix from the geometry fields of a...

In freesurferformats: Read and Write 'FreeSurfer' Neuroimaging File Formats

Compute the voxel-to-RAS matrix from the geometry fields of a NIFTI v1 header.

Description

The NIFTI v1 header can store up to two descriptions of the mapping from voxel indices to world coordinates: the sform (a full affine matrix in the srow_x, srow_y and srow_z fields) and the qform (a rotation, given as a quaternion, plus a translation, given in the quoffset fields). Each of them is only valid if the corresponding code field is not zero, and the sform takes precedence over the qform if both are present. This is the same rule that the NIFTI standard defines and that other implementations (nibabel, oro.nifti) follow.

Usage

nifti.header.to.vox2ras(niiheader)

Arguments

niiheader

named list, a NIFTI v1 header as returned by read.nifti1.header.

Value

a 4x4 numeric matrix (the voxel-to-RAS transformation), or NULL if the header contains neither an sform nor a qform. The matrix implements the NIFTI convention that the rotation of the qform applies to the left of the scaled voxel axes and that the third axis is flipped if the qfac field (pix_dim[1]) is negative.

Note

This is a header based re-implementation of the geometry computation of read.fs.volume.nii, which reads an oro.nifti instance. The two are compared against each other in the unit tests, and against nibabel in dev_tools/check_analyze_conversion.R.

freesurferformats documentation built on Sept. 25, 2026, 1:07 a.m.