Appendix VIII: 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 TalairachTournoux space, which is constructed by piecewise linear scaling of an individual's brain to that of the TalairachTournoux 1988 atlas. In the TalairachTournoux 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.
Coordinate Systems applicable to MEG, EEG, and iEEG
Generally, across the MEG, EEG, and iEEG modalities, the first two pieces of
information (origin, orientation) are specified in XXXCoordinateSystem
, and
the units are specified in XXXCoordinateSystemUnits
.
Allowed values for the XXXCoordinateSystem
field come from a list of
restricted keywords, as listed in the sections below. If no value from the
list of restricted keywords fits, there is always the option to specify the
value as follows:
Other
: Use this for other coordinate systems and specify further details in theXXXCoordinateSystemDescription
field
MEG Specific Coordinate Systems
Restricted keywords for the XXXCoordinateSystem
field in the
coordinatesystem.json
file for MEG datasets:
CTF
: ALS orientation and the origin between the earsElektaNeuromag
: RAS orientation and the origin between the ears4DBti
: ALS orientation and the origin between the earsKitYokogawa
: ALS orientation and the origin between the earsChietiItab
: 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
EEG Specific Coordinate Systems
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 T8T7 line, positive at T8. The Y axis is the OzFpz 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.
iEEG Specific Coordinate Systems
Restricted keywords for the XXXCoordinateSystem
field in the
coordsystem.json
file for iEEG datasets:

Pixels
: If electrodes are localized in 2D space (only x and y are specified and z is n/a), then the positions in this file must correspond to the locations expressed in pixels on the photo/drawing/rendering of the electrodes on the brain. In this case, coordinates must be (row,column) pairs, with (0,0) corresponding to the upper left pixel and (N,0) corresponding to the lower left pixel. 
ACPC
: The origin of the coordinate system is at the Anterior Commissure and the negative yaxis is passing through the Posterior Commissure. The positive zaxis is passing through a midhemispheric point in the superior direction. The anatomical landmarks are determined in the individual's anatomical scan and no scaling or deformations have been applied to the individual's anatomical scan. For more information, see the ACPC site on the FieldTrip toolbox wiki.
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.
Standard template identifiers
Coordinate System  Description 

ICBM452AirSpace  Reference space defined by the "average of 452 T1weighted MRIs of normal young adult brains" with "linear transforms of the subjects into the atlas space using a 12parameter affine transformation" https://www.loni.usc.edu/research/atlases 
ICBM452Warp5Space  Reference space defined by the "average of 452 T1weighted MRIs of normal young adult brains" "based on a 5th order polynomial transformation into the atlas space" https://www.loni.usc.edu/research/atlases 
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.braindevelopment.org/ 
fsaverage[Sym]  The fsaverage is a dual template providing both volumetric and surface coordinates references. The volumetric template corresponds to a FreeSurfer variant of MNI305 space. The fsaverage atlas also defines a surface reference system (formerly described as fsaverage[3456sym]). The fsaverageSym is the symmetric counterpart of fsaverage . 
fsLR  The fsLR is a dual template providing both volumetric and surface coordinates references. The volumetric template corresponds to MNI152NLin6Asym . Surface templates are given at several sampling densities: 164k (used by HCP pipelines for 3T and 7T anatomical analysis), 59k (used by HCP pipelines for 7T MRI bold and DWI analysis), 32k (used by HCP pipelines for 3T MRI bold and DWI analysis), or 4k (used by HCP pipelines for MEG analysis) fsaverage_LR surface reconstructed from the T1w image. 
MNIColin27  Average of 27 T1 scans of a single subject http://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres 
MNI152Lin  Also known as ICBM (version with linear coregistration) http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152Lin 
MNI152NLin2009[ac][SymAsym]  Also known as ICBM (nonlinear 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 
MNI152NLin6Sym  Also known as symmetric ICBM 6th generation (nonlinear coregistration). Used by SPM99  SPM8. http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin6 
MNI152NLin6Asym  A variation of MNI152NLin6Sym built by A. Janke that is released as the MNI template of FSL. Volumetric templates included with HCPPipelines correspond to this template too. See 10.1016/j.neuroimage.2012.01.024. 
MNI305  Also known as avg305. 
NIHPD[SymAsym]  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/NIHPDobj1 
OASIS30AntsOASISAnts  https://figshare.com/articles/ANTs_ANTsR_Brain_Templates/915436 
OASIS30Atropos  https://mindboggle.info/data.html 
Talairach  Piecewise linear scaling of the brain is implemented as described in TT88. http://www.talairach.org/ 
UNCInfant  Infant Brain Atlases from Neonates to 1 and 2yearolds. https://www.nitrc.org/projects/pediatricatlas 
The following template identifiers are retained for backwards compatibility of BIDS implementations. Their use is NOT RECOMMENDED for new BIDS datasets and tooling, but their presence MUST NOT produce a validation error.
Coordinate System  Recommended identifier 

fsaverage[3456sym]  fsaverage[Sym] 
UNCInfant[012]V[212223]  UNCInfant 