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[FIX] clarify XXXCoord* in the coordinate systems appendix #520

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Aug 27, 2020
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[FIX] clarify XXXCoord* in the coordinate systems appendix #520

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651683c
clarify XXXCoord*
sappelhoff Jul 1, 2020
bb71c41
fix capitalization of Captrak -> CapTrak
sappelhoff Jul 1, 2020
98b49bb
Apply suggestions from code review
sappelhoff Aug 10, 2020
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51 changes: 31 additions & 20 deletions src/99-appendices/08-coordinate-systems.md
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Expand Up @@ -2,10 +2,10 @@

## 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.
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:

Expand All @@ -17,11 +17,14 @@ 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 e.g.,
[https://doi.org/10.1016/j.neuroimage.2012.01.024](https://www.sciencedirect.com/science/article/pii/S1053811912000419?via%3Dihub)).
[https://doi.org/10.1016/j.neuroimage.2012.01.024](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
Expand All @@ -42,20 +45,28 @@ different conventions used in specific software packages developed by different
## 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`.
information for a coordinate system (origin and orientation) are specified in
`<datatype>CoordinateSystem`.
The third piece of information for a coordinate system (units) are specified in
`<datatype>CoordinateSystemUnits`.
Here, `<datatype>` can be one of `MEG`, `EEG`, or `iEEG`, depending on the
modality that is being used.

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:
Allowed values for the `<datatype>CoordinateSystem` 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
- `Other`: Use this for other coordinate systems and specify further details
in the `<datatype>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](https://github.com/bids-standard/bids-specification/issues/new/choose).**

## MEG Specific Coordinate Systems

Restricted keywords for the `XXXCoordinateSystem` field in the
Restricted keywords for the `<datatype>CoordinateSystem` field in the
`coordinatesystem.json` file for MEG datasets:

- `CTF`: ALS orientation and the origin between the ears
Expand All @@ -70,18 +81,18 @@ detailed extensive descriptions of these EEG coordinate systems on the

## EEG Specific Coordinate Systems

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

- `Captrak`: RAS orientation and the origin between the ears
- `CapTrak`: RAS orientation and the origin between the ears
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Looks like a backwards incompatible change. Is it just a typo being fixed? Do we need to worry about someone taking it too seriously in the past?

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yes, a typo fix. I haven't seen any datasets that use CapTrak yet --> and in fact, the list of restricted keywords for CoordSystems is not yet validated, see: https://github.com/bids-standard/bids-validator/issues/945

due to that missing coverage in the validator we currently have several datasets on openneuro that specify their coordsystem as e.g., "ARS", which is invalid of course. (see e.g., https://openneuro.org/datasets/ds002680/versions/1.0.0)

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agreed, being specified as "ARS" we still don't know how to relate electrode positions to the anatomy of the head, whereas "Other" and some textual description could have given more information.


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](http://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined).

## iEEG Specific Coordinate Systems

Restricted keywords for the `XXXCoordinateSystem` field in the
Restricted keywords for the `<datatype>CoordinateSystem` field in the
`coordsystem.json` file for iEEG datasets:

- `Pixels`: If electrodes are localized in 2D space (only x and y are
Expand All @@ -103,11 +114,11 @@ Restricted keywords for the `XXXCoordinateSystem` field in the
## Image-based Coordinate Systems

The transformation of the real world geometry to an artificial frame of
reference is described in `XXXCoordinateSystem`.
reference is described in `<datatype>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 `XXXCoordinateSystemUnits` field,
the units are assumed to be mm.
Unless specified explicitly in the sidecar file in the
`<datatype>CoordinateSystemUnits` field, the units are assumed to be mm.

### Standard template identifiers

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