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Appendix VIII: preferred names of Coordinate systems

To interpret a coordinate (x, y, z), it is required that you know relative to which origin the coordinates are expressed, you have to know the interpretation of the three axes, and you have to know the units in which the numbers are expressed. This information is sometimes called the coordinate system.

These letters help describe the coordinate system definition:

A/P means anterior/posterior L/R means left/right S/I means superior/inferior

For example: RAS means that the first dimension (X) points towards the right hand side of the head, the second dimension (Y) points towards the Anterior aspect of the head, and the third dimension (Z) points towards the top of the head.

Besides coordinate systems, defined by their origin and direction of the axes, BIDS defines "spaces" as an artificial frame of reference, created to describe different anatomies in a unifying manner (see e.g. https://doi.org/10.1016/j.neuroimage.2012.01.024). The "space" and all coordinates expressed in this space are by design a transformation of the real world geometry, and nearly always different from the individual subject space that it stems from. An example is the Talairach-Tournoux space, which is constructed by piecewise linear scaling of an individual's brain to that of the Talairach-Tournoux 1988 atlas. In the Talairach-Tournoux space, the origin of the coordinate system is at the AC and units are expressed in mm.

The coordinate systems below all relate to neuroscience and therefore to the head or brain coordinates. Please be aware that all data acquisition starts with "device coordinates" (scanner), which does not have to be identical to the initial "file format coordinates" (DICOM), which are again different from the "head" coordinates (e.g. NIFTI). Not only do device coordinate vary between hardware manufacturers, but also the head coordinates differ, mostly due to different conventions used in specific software packages developed by different (commercial or academic) groups.

MEG specific Coordinate Systems

The first two pieces of information (origin, orientation) are specified in XXXCoordinateSystem, the units are specified in XXXCoordinateSystemUnits.

Restricted keywords for the XXXCoordinateSystem field in the coordinatesystem.json file for MEG datasets:

  • CTF: ALS orientation and the origin between the ears

  • ElektaNeuromag: RAS orientation and the origin between the ears

  • 4DBti: ALS orientation and the origin between the ears

  • KitYokogawa: ALS orientation and the origin between the ears

  • ChietiItab: RAS orientation and the origin between the ears

  • Other: Use this for other coordinate systems and specify further details in the XXXCoordinateSystemDescription field

Note that the short descriptions above do not capture all details, there are detailed descriptions of these coordinate systems on the FieldTrip toolbox web page: http://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined

EEG specific Coordinate Systems

The first two pieces of information (origin, orientation) are specified in XXXCoordinateSystem, the units are specified in XXXCoordinateSystemUnits.

Restricted keywords for the XXXCoordinateSystem field in the coordsystem.json file for EEG datasets:

  • BESA: Although natively this is a spherical coordinate system, the electrode positions should be expressed in Cartesian coordinates, with a RAS orientation. The X axis is the T8-T7 line, positive at T8. The Y axis is the Oz-Fpz line, positive at Fpz. The origin of the sphere fitted to the electrodes is approximately 4 cm above the point between the ears.

  • Captrak: RAS orientation and the origin between the ears

Note that the short descriptions above do not capture all details, There are detailed extensive descriptions of these EEG coordinate systems on the FieldTrip toolbox web page and on the BESA wiki: http://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined http://wiki.besa.de/index.php?title=Electrodes_and_Surface_Locations#Coordinate_systems

Template based Coordinate Systems

The transformation of the real world geometry to an artificial frame of reference is described in XXXCoordinateSystem. Unless otherwise specified below, the origin is at the AC and the orientation of the axes is RAS. Unless specified explicitly in the sidecar file in the XXCoordinateSystemUnits field, the units are assumed to be mm.

Coordinate System Description
MNI152Lin Also known as ICBM (version with linear coregistration) http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin
MNI152NLin6[Sym|Asym] Also known as ICBM 6th generation (non-linear coregistration). Used by SPM99 - SPM8 and FSL (MNI152NLin6Sym). http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6
MNI152NLin2009[a-c][Sym|Asym] Also known as ICBM (non-linear coregistration with 40 iterations, released in 2009). It comes in either three different flavours each in symmetric or asymmetric version. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009
MNIColin27 Average of 27 T1 scans of a single subject http://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres
MNI305 Also known as avg305.
NIHPD Pediatric templates generated from the NIHPD sample. Available for different age groups (4.5–18.5 y.o., 4.5–8.5 y.o., 7–11 y.o., 7.5–13.5 y.o., 10–14 y.o., 13–18.5 y.o. This template also comes in either -symmetric or -asymmetric flavor. http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1
Talairach Piecewise linear scaling of the brain is implemented as described in TT88. http://www.talairach.org/
OASIS30AntsOASISAnts https://figshare.com/articles/ANTs_ANTsR_Brain_Templates/915436
OASIS30Atropos http://www.mindboggle.info/data.html
ICBM452AirSpace Reference space defined by the "average of 452 T1-weighted MRIs of normal young adult brains" with "linear transforms of the subjects into the atlas space using a 12-parameter affine transformation" http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml
ICBM452Warp5Space Reference space defined by the "average of 452 T1-weighted MRIs of normal young adult brains" "based on a 5th order polynomial transformation into the atlas space" http://www.loni.usc.edu/ICBM/Downloads/Downloads_452T1.shtml
IXI549Space Reference space defined by the average of the "549 (...) subjects from the IXI dataset" linearly transformed to ICBM MNI 452.Used by SPM12. http://www.brain-development.org/
fsaverage[3|4|5|6|sym] Images were sampled to the FreeSurfer surface reconstructed from the subject’s T1w image, and registered to an fsaverage template
UNCInfant[0|1|2]V[21|22|23] Infant Brain Atlases from Neonates to 1- and 2-year-olds. https://www.nitrc.org/projects/pediatricatlas