coordinate system

The main function of coordinates is to associate neuro-imaging data with an anatomical space. Always register data to a standardized coordinate system that is broadly used and (generally) associated with a stereotaxic atlas. Additionally, coordinates specify the size of voxels, which must be known for registration and display. Changing resolution scales will stretch or compress images.

The coordinate convention used by jip is very simple. Only the resolution , origin, and direction of progression are used to convert voxels to spatial positions, so coordinates are always parallel or anti-parallel with voxel indices.


The first voxel in the data array has (i j k) =  (0 0 0), the distance between adjacent voxels is given by the resolution (delta’s above) , and spatial positions step in a direction that is ± 1. There is no particular anatomical convention assigned to the spatial coordinates (or even to the voxel coordinates, given the different conventions between rodents and primates).

In mosaic display mode, slices in the i-j plane are shown by default, with the k index starting at 0 in the top left panel and increasing in panels to the right and down. Within each panel, the (x y) =   (0 0 )  voxel is shown at the bottom left. The orientation of y voxels can be flipped upside-down in order to accommodate difference imposed by software development platforms (OpenGL versus X11) or convention (DICOM versus NIFTI). In order to flip orientation, use the “-y” option at startup, or keyboard “y” interactively. Flipping the orientation does not change the association between voxels and coordinates.

jip/NIFTI compatibility

While the NIFTI format can always accommodate the jip convention, the reverse is not always true. Although the jip display software will properly reflect the coordinates of NIFTI file in terms of mapping coordinates onto voxels, it is important to realize that reading a NIFTI file and writing another file (either NIFTI or some other format) through jip can change the convention of the new file under some circumstance. Namely, jip does not provide for (x y z) coordinate systems that are rotated with respect to the corresponding (i j k) voxels by other than 180 degree rotations. If data are registered through jip software, this won't be an issue, as the output will be NIFTI compatible. If there is any doubt about voxels and coordinates, 1) the jip display tool shows both voxels and coordinates, and 2) the jip can write files using a simple ASCII header, so the origin, direction, and resolution can be found there.

In summary:

  1. The display program will correctly indicate coordinates for any NIFTI file.
  2. Data sets that are run through "jip" to create new files will always have coordinates that either are parallel or anti-parallel to the respective voxel indices.
  3. For reason #2 above, don't use alignment templates that have rotations between the voxel indices(i,j,k) and the coordinates (x,y,z).
Joseph B. Mandeville, Athinoula A. Martinos Center for Biomedical Imaging at MGH/MIT/Harvard