Appendix VIII: Preferred Names of Coordinate Systems

Introduction

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.

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 the XXXCoordinateSystemDescription 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 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

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 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.

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 y-axis is passing through the Posterior Commissure. The positive z-axis is passing through a mid-hemispheric 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.

Common for Surface and Volume

Coordinate System Description
individual Participant specific anatomical space (for example derived from T1w and/or T2w images). This coordinate system requires specifying an additional, participant-specific file to be fully defined. In context of surfaces this space has been refered to as fsnative.
custom Custom space defined using a group/study-specific template. This coordinate system requires specifying an additional file to be fully defined.

Standard template identifiers

Coordinate System Description
FS305 FreeSurfer variant of the MNI305 space
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" https://www.loni.usc.edu/research/atlases
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" 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.brain-development.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[3|4|5|6|sym]). 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[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
MNI152NLin6Sym Also known as symmetric ICBM 6th generation (non-linear 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 HCP-Pipelines correspond to this template too. See 10.1016/j.neuroimage.2012.01.024.
MNI152NLin6AsymConte69 Template based on MNI152NLin6Asym using Conte69 data. Built by Human Connectome Project. https://github.com/Washington-University/HCPpipelines/tree/master/global/templates
MNI305 Also known as avg305.
NIHPD[Sym|Asym] 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
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 2-year-olds. 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[3|4|5|6|sym] fsaverage[|Sym]
UNCInfant[0|1|2]V[21|22|23] UNCInfant

Hybrid (Volume/Surface) aliases

Hybrid spaces combining surface and volume data used with CIFTI files.

Coordinate System Description
HCPMNIfsLR32k Combination of MNI152NLin6AsymConte69 subcortical volumetric space (with 2mm grid) and fsLR32k surface space resulting in 91282 data points per timepoint. Used in Human Connectom Project. https://github.com/Washington-University/HCPpipelines/tree/master/global/templates/91282_Greyordinates
HCPMNIfsLR59k Combination of MNI152NLin6AsymConte69 subcortical volumetric space (with 1.6mm grid) and fsLR59k surface space resulting in 170494 data points per timepoint. Used in Human Connectom Project. https://github.com/Washington-University/HCPpipelines/tree/master/global/templates/170494_Greyordinates