Coordinate Systems for MEG EEG iEEG

Coordinate Systems for MEG/EEG/iEEG

General rules

From now on MEG/EEG/iEEG is referred to as ephys.

In BIDS we can specify the following coordinate systems across ephys:

• Fiducials*
• AnatomicalLandmarks*
• HeadCoil*
• DigitizedHeadPoints*
• EEG*
• MEG*
• iEEG*

for all of these, usually three fields can be defined:

• *CoordinateSystem
• *CoordinateSystemDescription
• *CoordinateUnits

but some of these may allow for more fields:

• *Description (only for Fiducials*)
• *Coordinates (only for Fiducials*, AnatomicalLandmarks*, HeadCoil*)

and see Exceptions below.

The "allowed" values for the *CoordinateSystem fields are described in Appendix VIII of the BIDS specification. The idea is to provide a list of restricted keywords in the specification, which can then be used in the datasets. If dataset readers then want to find out more about the coordinate system, they can check the specification by searching for the relevant keyword.

If the *CoordinateSystem is not part of BIDS, the value Other can be used, in which case *CoordinateSystemDescription MUST be used to exhaustively describe the *CoordinateSystem. However, it is generally advised that users open an issue on the BIDS specification repository to discuss adding new keywords to the Appendix VIII.

*CoordinateUnits usually have to be in mm, cm, or m.

In FiducialsDescription, data curators describe how Fiducials were placed.

In *Coordinates, data curators specify an object of arrays such as {"name": [x_coord, y_coord, z_coord]}, where name is the name of the electrode, fiducial, anatomical landmark, or similar, and the *_coord are the actual coordinates as numbers.

Validation

The BIDS validator checks the relevant coordinate system fields in the following three JSON schema files:

• https://github.com/bids-standard/bids-validator/blob/master/bids-validator/validators/json/schemas/coordsystem_eeg.json
• https://github.com/bids-standard/bids-validator/blob/master/bids-validator/validators/json/schemas/coordsystem_meg.json
• https://github.com/bids-standard/bids-validator/blob/master/bids-validator/validators/json/schemas/coordsystem_ieeg.json

Exceptions

• Not all coordinate systems are available for each modality.
  • iEEG
    • only iEEG*
      • but two extra for iEEG* fields (not present for other modalitites): iEEGCoordinateProcessingDescription, iEEGCoordinateProcessingReference
  • EEG
    • EEG*
    • Fiducials*
    • AnatomicalLandmarks*
  • MEG
    • EEG* only in case EEG is recorded along with the MEG system, not with a separate EEG system
    • Fiducials* ... but only FiducialsDescription, not the other fields
    • AnatomicalLandmarks*
    • HeadCoil*
    • DigitizedHeadPoints*
      • here, a DigitizedHeadPointsCoordinates does not exist, but the field DigitizedHeadPoints provides a link to a file where the coordinates are saved, in manufacturer specific formats, as described in the MEG section of the specification.

Open questions

• Should T1w be a valid value for *CoordinateSystem? If yes, should this always be in voxels? or mm, etc.? Relevant for the IntendedFor field. See also:
  • https://github.com/bids-standard/bids-specification/issues/661
  • https://github.com/bids-standard/bids-specification/pull/520#issuecomment-672757321
  • currently, T1w is NOT valid, and should be Other instead, with an accompanying *CoordinateSystemDescription
• Should we allow all coordinate systems for all modalities, instead of supporting idiosyncrasies that are hard to argue for in some cases?
  • we are currently allowing MEG for EEG and vice versa, if the modalities have been recorded simultaneously
• Should all supported *CoordinateSystem keywords be documented in the specification, or is "elsewhere" fine?
  • https://github.com/bids-standard/bids-specification/issues/658
• in MRI, anatomical landmarks can be specified with "voxels" as units ... should we generally allow that (see also IntendedFor field and discussion), or should that be an MRI-only thing?
• As mentioned above, the MEG DigitizedHeadPoints field points to a *_headshape.<ext> file, however these files are currently not very well specified in BIDS. How can we improve that state?
  • https://github.com/bids-standard/bids-specification/issues/20