Voxels Space Orientation and Coordinate Conventions#


It is important to note that SCT Images, which are derived from NIFTI images, have their contents indexed in “Fortran order”, meaning that in an image of shape \((N_a, N_b, N_c)\), where we consider the a axis to be the first, two consecutive (in the sense of storage location) elements are in the a dimension, the first. This is by opposition to the C ordering which is more widely used in most software, and where the fastest varying element is indexed last.

Reference Spaces#

As in many other tools, SCT follows a standard nomenclature for reference spaces in which the world or local coordinates are expressed.

The string is formed from character label among (relative to a human subject):

  • L / R: left-right

  • P / A: posterior-anterior

  • I / S: inferior-superior

The character position corresponds to the axis index.

SCT uses the “from” convention, which for clarity we postfix by a dash.

The reference space for physical coordinates is LPI- (which is coming from nibabel and NIFTI).

An “image orientation” corresponds to the orientation of the surface/volume with regard to the reference orientation. It is encoded in the (NIFTI) file header.

For example, a RAS image orientation corresponds to a 3D image with:

  • X axis oriented L towards R;

  • Y axis oriented P towards A;

  • Z axis oriented I towards S.


  • nibabel, BIDS are using the “towards” convention, ie. SCT’s LPI(-) is their RAS(+).

Coordinate Conventions#

Local/Voxel Coordinates#

When voxel coordinates are integers, coordinates are indices. Indices are expressed starting from 0 and up to N-1 where N is the number of voxels in the considered dimension.

When voxel coordinates are real numbers, we are using an integer voxel center convention (consistent with nibabel and NIFTI).

This means that a coordinate such as (i,j,k) == np.round((i,j,k)) expresses the center of a voxel.

NB: Voxel coordinates are called \((i,j,k)\) in the NIFTI documentation.

Global/Physical Coordinates#

Physical coordinates are always expressed as real numbers. They are defined from the relation expressed by the transform and unit system expressed in a image header.

Physical coordinates are expressed relative to the LPI- frame, considering the voxel dimensions, affine transform between voxel coordinates and world coordinates, and the physical dimension unit, all of which is encoded in the NIFTI file header.

NB: Voxel coordinates are called \((x,y,z)\) in the NIFTI documentation.