What alignment information is stored in the NIfTI-1 header?
(Christian Haselgrove) Volume orientation is given by a transformation that maps voxel indices (i,j,k) to spatial coordinates (x,y,z), typically anatomical coordinates assigned by the scanner. This transformation (“Method 2” in the nifti1.h documentation) is generated using the voxel dimensions, a quaternion encoding a rotation matrix, and a 3D shift, all stored in the NIfTI-1 header; details can be found in the nifti1.h comments. The NIfTI-1 header also provides for a general affine transformation, separate from that described by Method 2. This transformation (“Method 3”) also maps voxel indices (i,j,k) to (x,y,z), which in this case are typically coordinates in a standard space such as the Talairach space. The elements of this transformation matrix are stored in the NIfTI-1 header. For example, the Method 2 transformation can be constructed from the attributes from a set of DICOM files; the Method 3 transform can be computed offline and inserted into the header later. The exact “mean
