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Appendix VIII: Coordinate systems

Introduction

To interpret a coordinate (x, y, z), it is required that you know (1) relative to which origin the coordinate is expressed, (2) the interpretation of the three axes, and (3) 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. The directions are considered to be from the subject's perspective. For example, in the RAS coordinate system, a point to the subject's left will have a negative x value.

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 for example, doi: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 (for example, 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 for a coordinate system (origin and orientation) are specified in <CoordSysType>CoordinateSystem. The third piece of information for a coordinate system (units) are specified in <CoordSysType>CoordinateUnits. Here, <CoordSysType> can be one of of the following, depending on the data that is supposed to be documented:

  • MEG
  • EEG
  • iEEG
  • Fiducials
  • AnatomicalLandmark
  • HeadCoil
  • DigitizedHeadPoints

Allowed values for the <CoordSysType>CoordinateSystem field come from a list of restricted keywords, as listed in the sections below.

Note that Fiducials, AnatomicalLandmark, HeadCoil, and DigitizedHeadPoints CoordSysTypes share the restricted keywords with the data modality they are shared with. For example, if an AnatomicalLandmark field is shared as part of an EEG dataset, the EEG-specific coordinate systems apply. However, if it is shared as part of an MEG dataset, the MEG-specific coordinate systems apply.

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 all required details in the <CoordSysType>CoordinateSystemDescription field

If you believe a specific coordinate system should be added to the list of restricted keywords for MEG, EEG, or iEEG, please open a new issue on the bids-standard/bids-specification GitHub repository.

Note that the short descriptions below may not capture all details. For detailed descriptions of the coordinate systems below, please see the FieldTrip webpage.

Commonly used anatomical landmarks in MEG, EEG, and iEEG research

In the documentation below we refer to anatomical landmarks such as the Left Pre Auricular point (LPA) and the Right Pre Auricular point (RPA), or the left and right Helix-Tragus Junction (LHJ, RHJ).

These anatomical landmarks are commonly used in MEG, EEG, and iEEG research to define coordinate systems that capture digitized sensor positions.

More information can be obtained from the FieldTrip webpage.

MEG Specific Coordinate Systems

Restricted keywords for the <CoordSysType>CoordinateSystem 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
  • Any keyword from the list of Standard template identifiers

In the case that MEG was recorded simultaneously with EEG, the restricted keywords for EEG specific coordinate systems can also be applied to MEG:

  • CapTrak
  • EEGLAB
  • EEGLAB-HJ

EEG Specific Coordinate Systems

Restricted keywords for the <CoordSysType>CoordinateSystem field in the coordsystem.json file for EEG datasets:

  • CapTrak: RAS orientation and the origin approximately between LPA and RPA

  • EEGLAB: ALS orientation and the origin exactly between LPA and RPA. For more information, see the EEGLAB wiki page.

  • EEGLAB-HJ: ALS orientation and the origin exactly between LHJ and RHJ. For more information, see the EEGLAB wiki page.

  • Any keyword from the list of Standard template identifiers

In the case that EEG was recorded simultaneously with MEG, the restricted keywords for MEG specific coordinate systems can also be applied to EEG:

  • CTF
  • ElektaNeuromag
  • 4DBti
  • KitYokogawa
  • ChietiItab

iEEG Specific Coordinate Systems

Restricted keywords for the <CoordSysType>CoordinateSystem 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.

  • ScanRAS: The origin of the coordinate system is the center of the gradient coil for the corresponding T1w image of the subject, and the x-axis increases left to right, the y-axis increases posterior to to anterior and the z-axis increases inferior to superior. For more information see the Nipy Documentation. It is strongly encouraged to align the subject's T1w to ACPC so that the ACPC coordinate system can be used. If the subject's T1w in the BIDS dataset is not aligned to ACPC, ScanRAS should be used.

  • Any keyword from the list of Standard template identifiers

Image-based Coordinate Systems

The transformation of the real world geometry to an artificial frame of reference is described in <CoordSysType>CoordinateSystem. 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 <CoordSysType>CoordinateUnits field, the units are assumed to be mm.

Standard template identifiers

Coordinate System Description
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. https://brain-development.org/
fsaverage 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]).
fsaverageSym 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 fsaverageSym atlas also defines a symmetric surface reference system (formerly described as fsaveragesym).
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 https://www.bic.mni.mcgill.ca/ServicesAtlases/Colin27Highres
MNI152Lin Also known as ICBM (version with linear coregistration) https://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. https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009
MNI152NLin6Sym Also known as symmetric ICBM 6th generation (non-linear coregistration). Used by SPM99 - SPM8. https://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 doi:10.1016/j.neuroimage.2012.01.024.
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. https://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://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. However, their use is DEPRECATED.

Coordinate System Description RECOMMENDED alternative identifier
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 fsaverage[Sym]
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 UNCInfant

Nonstandard coordinate system identifiers

The following template identifiers are RECOMMENDED for individual- and study-specific reference spaces. In order for these spaces to be interpretable, SpatialReference metadata MUST be provided, as described in Common file level metadata fields.

In the case of multiple study templates, additional names may need to be defined.

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 referred to as fsnative.
study Custom space defined using a group/study-specific template. This coordinate system requires specifying an additional file to be fully defined.

Non-template coordinate system identifiers

The scanner coordinate system is implicit and assumed by default if the derivative filename does not define any space-<label>. Please note that space-scanner SHOULD NOT be used, it is mentioned in this specification to make its existence explicit.

Coordinate System Description
scanner The intrinsic coordinate system of the original image (the first entry of RawSources) after reconstruction and conversion to NIfTI or equivalent for the case of surfaces and dual volume/surface files.