Bids-specification: Define supported coordinate systems in the BIDS specification instead of FieldTrip wiki

[sappelhoff]

The FieldTrip wiki is a great resource full of information that's hard to get by otherwise.

We are currently linking to this wiki for the coordinate systems that are "accepted" in M(i)EEG.

See: https://bids-specification.readthedocs.io/en/latest/99-appendices/08-coordinate-systems.html

Screenshot for example:

That's linking to this page in the wiki where coordinate systems are defined.

I want to gather some opinions: Should we rather define the BIDS accepted coordinate systems within the BIDS specification?

Benefits:

• have everything in one place (the spec)
• the information are released with the spec, and thus stable instead of captured in a wiki

Drawbacks:

• information is maintained in two places
• takes some initial work to carry over the information from wiki to spec

cc @bids-standard/raw-electrophys

[hoechenberger]

I want to gather some opinions: Should we rather define the BIDS accepted coordinate systems within the BIDS specification?

Benefits:

• have everything in one place (the spec)
• the information are released with the spec, and thus _stable_ instead of captured in a wiki

+1 for this. I'm hoping that maybe that in the long run, the situation will invert: BIDS becomes the authority, and other places like the FT Wiki will link to the BIDS spec. :)

[VisLab]

+1 Agree that it should be in BIDS.

I suspect that there will need to be a great deal more work to be done in
this area on coordinate systems and frames of reference as BEP's such as
motion capture and eye tracking are incorporated. A good starting point is
to have the Head coordinate systems nailed down in the spec and the
terminology clarified.

On Sun, Nov 1, 2020 at 3:39 AM Richard Höchenberger <
[email protected]> wrote:

I want to gather some opinions: Should we rather define the BIDS accepted
coordinate systems within the BIDS specification?

Benefits:

• have everything in one place (the spec)
• the information are released with the spec, and thus stable
  instead of captured in a wiki

+1 for this. I'm hoping that maybe that in the long the situating will
invert: BIDS becomes the authority, and other places like the FT Wiki will
link to the BIDS spec. :)

—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
https://github.com/bids-standard/bids-specification/issues/658#issuecomment-720060856,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/AAJCJOQO5CR6SNXBX7WC7JLSNUUFHANCNFSM4TGNJRIQ
.

[adam2392]

I want to gather some opinions: Should we rather define the BIDS accepted coordinate systems within the BIDS specification?
Benefits:

• have everything in one place (the spec)
• the information are released with the spec, and thus _stable_ instead of captured in a wiki

+1 for this. I'm hoping that maybe that in the long run, the situation will invert: BIDS becomes the authority, and other places like the FT Wiki will link to the BIDS spec. :)

Would also greatly prefer it to all be in the spec and explicitly clarified.

[teonbrooks]

adding the chorus, +1 for having it in the spec and having it becoming the go-to place for referencing

[robertoostenveld]

Let me chime in, not so much from the perspective of being involved in FieldTrip, but in general.

One of the key principles and strengths of BIDS is that it refers to external ontologies and vocabularies, such as the Cognitive Atlas and CogPo, but also DICOM (for permitted values in tags) and SI (for units). Rather than re-inventing naming schemes, it builds on existing and adopted naming schemes.

The fieldtrip website page on this collected many existing definitions. But it does not define them: these are all definitions that come from outside of FieldTrip itself. For example, the CTF coordinate system is defined on page 5 in the CTF "MRI Viewer release v4.14" manual (which I know is in our MEG lab in paper, and which I have as a pdf).

So here I am not sure what you aim to achieve. The definition would stay where it is: in the documentation of the respective system. A more formal or complete description (as an ontology) would be nice, as would be a more central availability of that description. But is the BIDS standard the best place for making and maintaining that vocabulary?

[sappelhoff]

For those who are generally interested in coordinate systems in BIDS, I have created a wiki page that summarizes the status quo and also lists currently open questions and issues. --> https://github.com/bids-standard/bids-specification/wiki/Coordinate-Systems-for-MEG-EEG-iEEG

It's a WIKI, so please add and/or correct items!

[guiomar]

Thanks @sappelhoff !! How are comments made?

[sappelhoff]

there is an "edit" button on the right next to the heading: