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feat(spec): Render coordsystem JSON tables
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effigies committed Aug 19, 2024
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8 changes: 4 additions & 4 deletions src/modality-specific-files/electroencephalography.md
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Expand Up @@ -390,7 +390,7 @@ The definitions of the fields specified in these tables may be found in
A guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->
{{ MACROS___make_sidecar_table("eeg.EEGCoordsystemGeneral") }}
{{ MACROS___make_json_table("json.eeg.EEGCoordsystemGeneral") }}

Fields relating to the EEG electrode positions:

Expand All @@ -402,7 +402,7 @@ The definitions of the fields specified in these tables may be found in
A guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->
{{ MACROS___make_sidecar_table("eeg.EEGCoordsystemPositions") }}
{{ MACROS___make_json_table("json.eeg.EEGCoordsystemPositions") }}

Fields relating to the position of fiducials measured during an EEG session/run:

Expand All @@ -414,7 +414,7 @@ The definitions of the fields specified in these tables may be found in
A guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->
{{ MACROS___make_sidecar_table("eeg.EEGCoordsystemFiducials") }}
{{ MACROS___make_json_table("json.eeg.EEGCoordsystemFiducials") }}

Fields relating to the position of anatomical landmark measured during an EEG session/run:

Expand All @@ -426,7 +426,7 @@ The definitions of the fields specified in these tables may be found in
A guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->
{{ MACROS___make_sidecar_table(["eeg.EEGCoordsystemLandmark", "eeg.EEGCoordsystemLandmarkDescriptionRec"]) }}
{{ MACROS___make_json_table(["json.eeg.EEGCoordsystemLandmark", "json.eeg.EEGCoordsystemLandmarkDescriptionRec"]) }}

If the position of anatomical landmarks is measured using the same system or
device used to measure electrode positions, and if thereby the anatomical
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Expand Up @@ -389,7 +389,7 @@ The definitions of the fields specified in these tables may be found in
A guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->
{{ MACROS___make_sidecar_table("ieeg.iEEGCoordsystemGeneral") }}
{{ MACROS___make_json_table("json.ieeg.iEEGCoordsystemGeneral") }}

Fields relating to the iEEG electrode positions:

Expand All @@ -401,7 +401,7 @@ The definitions of the fields specified in these tables may be found in
A guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->
{{ MACROS___make_sidecar_table("ieeg.iEEGCoordsystemPositions") }}
{{ MACROS___make_json_table("json.ieeg.iEEGCoordsystemPositions") }}

### Recommended 3D coordinate systems

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12 changes: 6 additions & 6 deletions src/modality-specific-files/magnetoencephalography.md
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Expand Up @@ -343,7 +343,7 @@ The definitions of the fields specified in these tables may be found in
A guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->
{{ MACROS___make_sidecar_table("meg.MEGCoordsystemWithEEG") }}
{{ MACROS___make_json_table("json.meg.MEGCoordsystemWithEEG") }}

Head localization coils:

Expand All @@ -355,7 +355,7 @@ The definitions of the fields specified in these tables may be found in
A guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->
{{ MACROS___make_sidecar_table("meg.MEGCoordsystemHeadLocalizationCoils") }}
{{ MACROS___make_json_table("json.meg.MEGCoordsystemHeadLocalizationCoils") }}

Digitized head points:

Expand All @@ -367,7 +367,7 @@ The definitions of the fields specified in these tables may be found in
A guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->
{{ MACROS___make_sidecar_table("meg.MEGCoordsystemDigitizedHeadPoints") }}
{{ MACROS___make_json_table("json.meg.MEGCoordsystemDigitizedHeadPoints") }}

Anatomical MRI:

Expand All @@ -379,7 +379,7 @@ The definitions of the fields specified in these tables may be found in
A guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->
{{ MACROS___make_sidecar_table("meg.MEGCoordsystemAnatomicalMRI") }}
{{ MACROS___make_json_table("json.meg.MEGCoordsystemAnatomicalMRI") }}

Anatomical landmarks:

Expand All @@ -391,7 +391,7 @@ The definitions of the fields specified in these tables may be found in
A guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->
{{ MACROS___make_sidecar_table("meg.MEGCoordsystemAnatomicalLandmarks") }}
{{ MACROS___make_json_table("json.meg.MEGCoordsystemAnatomicalLandmarks") }}

It is also RECOMMENDED that the MRI voxel coordinates of the actual anatomical
landmarks for co-registration of MEG with structural MRI are stored in the
Expand Down Expand Up @@ -419,7 +419,7 @@ The definitions of the fields specified in these tables may be found in
A guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->
{{ MACROS___make_sidecar_table("meg.MEGCoordsystemFiducialsInformation") }}
{{ MACROS___make_json_table("json.meg.MEGCoordsystemFiducialsInformation") }}

For more information on the definition of anatomical landmarks, please visit:
[How are the Left and Right Pre-Auricular (LPA and RPA) points defined? - FieldTrip Toolbox](https://www.fieldtriptoolbox.org/faq/how_are_the_lpa_and_rpa_points_defined/)
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8 changes: 4 additions & 4 deletions src/modality-specific-files/near-infrared-spectroscopy.md
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Expand Up @@ -386,7 +386,7 @@ A guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->

{{ MACROS___make_sidecar_table("nirs.CoordsystemGeneral") }}
{{ MACROS___make_json_table("json.nirs.CoordsystemGeneral") }}

Fields relating to the NIRS optode positions:

Expand All @@ -399,7 +399,7 @@ A guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->

{{ MACROS___make_sidecar_table(["nirs.CoordinateSystem", "nirs.CoordinateSystemDescriptionRec"]) }}
{{ MACROS___make_json_table(["json.nirs.CoordinateSystem", "json.nirs.CoordinateSystemDescriptionRec"]) }}

Fields relating to the position of fiducials measured during an NIRS session/run:

Expand All @@ -412,7 +412,7 @@ A guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->

{{ MACROS___make_sidecar_table(["nirs.Fiducials", "nirs.FiducialsCoordinateSystemDescriptionRec"]) }}
{{ MACROS___make_json_table(["json.nirs.Fiducials", "json.nirs.FiducialsCoordinateSystemDescriptionRec"]) }}

Fields relating to the position of anatomical landmarks measured during an NIRS session/run:

Expand All @@ -425,7 +425,7 @@ A guide for using macros can be found at
https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
-->

{{ MACROS___make_sidecar_table(["nirs.AnatomicalLandmark", "nirs.AnatomicalLandmarkCoordinateSystemDescriptionRec"]) }}
{{ MACROS___make_json_table(["json.nirs.AnatomicalLandmark", "nirs.AnatomicalLandmarkCoordinateSystemDescriptionRec"]) }}

### Example `*_coordsystem.json`

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