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[FIX] Clarify that BIDS standard template data is to be in scanner coordinates (MEG, iEEG, EEG) #1031

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7 changes: 6 additions & 1 deletion src/99-appendices/08-coordinate-systems.md
Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,7 @@ 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
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).
Expand Down Expand Up @@ -195,6 +195,11 @@ Unless specified explicitly in the sidecar file in the

### Standard template identifiers

When using any of the below templates, coordinates should be in "world" (RAS+) space,
and not voxel indices.
If `<CoordSysType>CoordinateUnits` is not defined or applicable, then the units SHALL
be assumed to be millimeters (mm).
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This is stated in ll. 193-194 above, I think.

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Fair enough. I missed that this was a subheading of Image-based Coordinate Systems.

Suggested change
If `<CoordSysType>CoordinateUnits` is not defined or applicable, then the units SHALL
be assumed to be millimeters (mm).


| **Coordinate System** | **Description** | **Used by** | **Reference** |
| ---------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------ | ---------------------------------------------------------------------------------------------------------------------------------- |
| 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](https://www.loni.usc.edu/research/atlases) |
Expand Down