[FIX] 1) Clarify appropriate labels for space entity, 2) Clarify chan…

…nels+electrodes do not have to match (#734)

* clarify that label of _space-<label> must be from appendix VIII

related to https://github.com/bids-standard/bids-validator/issues/743

* clarify that channels and electrodes do not have to match

closes #667

* catch typo again

* link channels+electrodes examples

* clarify _where_ restricted keywords for space entity come from

* fix typo L -> l (capitalization)

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* extend yml lint limit to 120 chard

* use existing .yamllint.yml file

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

.github/workflows/yml_lint.yml

@@ -14,4 +14,7 @@ jobs:
     - name: Install dependencies
       run: pip install yamllint
     - name: Lint yml files in src/schema
-      run: yamllint -f standard src/schema/
+      # for config, see:
+      # https://yamllint.readthedocs.io/en/stable/configuration.html#custom-configuration-without-a-config-file
+      run: |
+        yamllint -f standard src/schema/ -c .yamllint.yml

.yamllint.yml

@@ -2,4 +2,4 @@ extends: default
 
 rules:
   line-length:
-    max: 99
+    max: 120

src/04-modality-specific-files/03-electroencephalography.md

@@ -194,7 +194,14 @@ To avoid confusion, the channels SHOULD be listed in the order they
 appear in the EEG data file.
 Any number of additional columns may be added to provide additional information
 about the channels.
+
 Note that electrode positions SHOULD NOT be added to this file, but to [`*_electrodes.tsv`](./03-electroencephalography.md#electrodes-description-_electrodestsv).
+Furthermore, the entries in `*_electrodes.tsv` and `*_channels.tsv` do not have to match exactly,
+as for example in the case of recording a single `EOG` channel from a bipolar referencing scheme
+of two electrodes, or a data channel originating from an auxilliary, non-electrode device.
+That is, in most cases `*_electrodes.tsv` will have more entries than `*_channels.tsv`.
+See the examples for `*_channels.tsv` below, and for `*_electrodes.tsv` in
+["Electrodes description"](./03-electroencephalography.md#electrodes-description-_electrodestsv).
 
 The columns of the Channels description table stored in `*_channels.tsv` are:
 
@@ -247,14 +254,16 @@ Example of free-form text for field `description`
 
 -   n/a, stimulus, response, skin conductance, battery status
 
-Example:
+### Example `channels.tsv`
+
+See also the corresponding [`electrodes.tsv` example](#example-electrodestsv).
 
 ```Text
-name     type   units   description                     status  status_description
-VEOG     VEOG   uV      n/a                             good    n/a
-FDI      EMG    uV      left first dorsal interosseous  good    n/a
-Cz       EEG    uV      n/a                             bad     high frequency noise
-UADC001  MISC   n/a     envelope of audio signal        good    n/a
+name     type  units  description                     reference     status  status_description
+VEOG     VEOG  uV     left eye                        VEOG-, VEOG+  good    n/a
+FDI      EMG   uV     left first dorsal interosseous  FDI-, FDI+    good    n/a
+Cz       EEG   uV     n/a                             REF           bad     high frequency noise
+UADC001  MISC  n/a    envelope of audio signal        n/a           good    n/a
 ```
 
 ## Electrodes description (`*_electrodes.tsv`)
@@ -285,15 +294,19 @@ SHOULD be present:
 | material        | RECOMMENDED           | Material of the electrode  (for example, Tin, Ag/AgCl, Gold).          |
 | impedance       | RECOMMENDED           | Impedance of the electrode, units MUST be in `kOhm`.                   |
 
-Example:
+### Example `electrodes.tsv`
+
+See also the corresponding [`electrodes.tsv` example](#example-channelstsv).
 
 ```Text
-name  x         y        z         type      material
-A1    -0.0707   0.0000   -0.0707   clip-on   Ag/AgCl
-F3    -0.0567   0.0677   0.0469    cup       Ag/AgCl
-Fz    0.0000    0.0714   0.0699    cup       Ag/AgCl
-REF   -0.0742   -0.0200  -0.0100   cup       Ag/AgCl
-GND   0.0742    -0.0200  -0.0100   cup       Ag/AgCl
+name   x        y	       z        type     material
+VEOG+  n/a      n/a      n/a      cup      Ag/AgCl
+VEOG-  n/a      n/a      n/a      cup      Ag/AgCl
+FDI+   n/a      n/a      n/a      cup      Ag/AgCl
+FDI-   n/a      n/a      n/a      cup      Ag/AgCl
+GND    -0.0707  0.0000   -0.0707  clip-on  Ag/AgCl
+Cz     0.0000   0.0714   0.0699   cup      Ag/AgCl
+REF    -0.0742  -0.0200  -0.0100  cup      Ag/AgCl
 ```
 
 The [`acq-<label>`](../99-appendices/09-entities.md#acq) key/value pair can be used to indicate acquisition of the same data. For

src/04-modality-specific-files/04-intracranial-electroencephalography.md

@@ -288,9 +288,12 @@ that coordinates are expected in cartesian coordinates according to the
 `*_coordsystem.json` file MUST be specified as well.
 
 The optional [`space-<label>`](../99-appendices/09-entities.md#space) entity (`*[_space-<label>]_electrodes.tsv`) can be used to
-indicate the way in which electrode positions are interpreted. The space label
-needs to be taken from the list in
-[Appendix VIII](../99-appendices/08-coordinate-systems.md)
+indicate the way in which electrode positions are interpreted.
+The space `<label>` MUST be taken from one of the modality specific lists in
+[Appendix VIII](../99-appendices/08-coordinate-systems.md).
+For example for iEEG data, the restricted keywords listed under
+[iEEG Specific Coordinate Systems](../99-appendices/08-coordinate-systems.md#ieeg-specific-coordinate-systems)
+are acceptable for `<label>`.
 
 For examples:
 

src/schema/entities.yaml

@@ -197,7 +197,11 @@ space:
     the way in which electrode positions are interpreted
     (for EEG/MEG/iEEG data) or
     the spatial reference to which a file has been aligned (for MRI data).
-    The space label needs to be taken from the list in Appendix VIII.
+    The space `<label>` MUST be taken from one of the modality specific lists in
+    [Appendix VIII](../99-appendices/08-coordinate-systems.md).
+    For example for iEEG data, the restricted keywords listed under
+    [iEEG Specific Coordinate Systems](../99-appendices/08-coordinate-systems.md#ieeg-specific-coordinate-systems)
+    are acceptable for `<label>`.
 
     For EEG/MEG/iEEG data, this entity can be applied to raw data, but
     for other data types, it is restricted to derivative data.