From 943c20e619567855ccee2896b65c1001f338010c Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Thu, 11 Apr 2024 18:41:58 +0200
Subject: [PATCH] [FIX] Move ``_stim.<ext>`` specification within the Task
 Events module (#1750)

* fix: move ``_stim.<ext>`` specification within the task events module

Depends-on: #1749.

* Apply suggestions from code review

Co-authored-by: Remi Gau <remi_gau@hotmail.com>

* Update src/modality-specific-files/task-events.md

* Update src/modality-specific-files/physiological-recordings.md

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* enh: improve admonitions

* Apply suggestions from code review

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

* fix: markdown link with linebreak

* fix: missing literal closing backtick

* Apply suggestions from code review

Co-authored-by: Remi Gau <remi_gau@hotmail.com>

* fix: typo

* fix: consistency and ``[recording-<label>]`` soft removal

* enh: add synthetic example

* fix: defining links inside admonition

* Apply suggestions from code review

* Update src/modality-specific-files/task-events.md

---------

Co-authored-by: Remi Gau <remi_gau@hotmail.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 mkdocs.yml                                    |  4 +-
 ...ordings.md => physiological-recordings.md} | 33 +++----
 src/modality-specific-files/task-events.md    | 87 ++++++++++++++++++-
 3 files changed, 99 insertions(+), 25 deletions(-)
 rename src/modality-specific-files/{physiological-and-other-continuous-recordings.md => physiological-recordings.md} (84%)

diff --git a/mkdocs.yml b/mkdocs.yml
index 051aa2aaa6..114e05c135 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -12,7 +12,7 @@ nav:
           - Electroencephalography: modality-specific-files/electroencephalography.md
           - Intracranial Electroencephalography: modality-specific-files/intracranial-electroencephalography.md
           - Task events: modality-specific-files/task-events.md
-          - Physiological and other continuous recordings: modality-specific-files/physiological-and-other-continuous-recordings.md
+          - Physiological recordings: modality-specific-files/physiological-recordings.md
           - Behavioral experiments (with no neural recordings): modality-specific-files/behavioral-experiments.md
           - Genetic Descriptor: modality-specific-files/genetic-descriptor.md
           - Positron Emission Tomography: modality-specific-files/positron-emission-tomography.md
@@ -122,7 +122,7 @@ plugins:
         "04-modality-specific-files/03-electroencephalography.md": "modality-specific-files/electroencephalography.md"
         "04-modality-specific-files/04-intracranial-electroencephalography.md": "modality-specific-files/intracranial-electroencephalography.md"
         "04-modality-specific-files/05-task-events.md": "modality-specific-files/task-events.md"
-        "04-modality-specific-files/06-physiological-and-other-continuous-recordings.md": "modality-specific-files/physiological-and-other-continuous-recordings.md"
+        "04-modality-specific-files/06-physiological-and-other-continuous-recordings.md": "modality-specific-files/physiological-recordings.md"
         "04-modality-specific-files/07-behavioral-experiments.md": "modality-specific-files/behavioral-experiments.md"
         "04-modality-specific-files/08-genetic-descriptor.md": "modality-specific-files/genetic-descriptor.md"
         "04-modality-specific-files/09-positron-emission-tomography.md": "modality-specific-files/positron-emission-tomography.md"
diff --git a/src/modality-specific-files/physiological-and-other-continuous-recordings.md b/src/modality-specific-files/physiological-recordings.md
similarity index 84%
rename from src/modality-specific-files/physiological-and-other-continuous-recordings.md
rename to src/modality-specific-files/physiological-recordings.md
index 8ecd00febe..897deb3d1b 100644
--- a/src/modality-specific-files/physiological-and-other-continuous-recordings.md
+++ b/src/modality-specific-files/physiological-recordings.md
@@ -1,11 +1,8 @@
-# Physiological and other continuous recordings
+# Physiological recordings
 
-## Physiological recordings
-
-Physiological recordings such as cardiac and respiratory signals and other
-continuous measures (such as parameters of a film or audio stimuli) MAY be
+Physiological recordings such as cardiac and respiratory signals MAY be
 specified using a [compressed tabular file](../common-principles.md#compressed-tabular-files)
-([TSVGZ file](../glossary.md#tsvgz-extensions)) and a corresponding
+([TSV.GZ file](../glossary.md#tsvgz-extensions)) and a corresponding
 JSON file for storing metadata fields (see below).
 
 !!! example "Example datasets"
@@ -24,8 +21,6 @@ sub-<label>/[ses-<label>/]
     <datatype>/
         <matches>[_recording-<label>]_physio.tsv.gz
         <matches>[_recording-<label>]_physio.json
-        <matches>[_recording-<label>]_stim.tsv.gz
-        <matches>[_recording-<label>]_stim.json
 ```
 
 For the template directory name, `<datatype>` can correspond to any data
@@ -37,12 +32,12 @@ before the suffix.
 For example for the file `sub-control01_task-nback_run-1_bold.nii.gz`,
 `<matches>` would correspond to `sub-control01_task-nback_run-1`.
 
-!!! note "TSVGZ headers are specified in metadata files."
+!!! warning "Caution"
 
-    TSVGZ files MUST NOT include a header line,
-    as established by the [common-principles](../common-principles.md#compressed-tabular-files).
-    As a result, when supplying a `*_<physio|stim>.tsv.gz` file, an accompanying
-    `*_<physio|stim>.json` MUST be supplied as well.
+    `<matches>_physio.tsv.gz` files MUST NOT include a header line, as established by the
+    [common-principles](../common-principles.md#compressed-tabular-files).
+    As a result, when supplying a `<matches>_physio.tsv.gz` file, an accompanying
+    `<matches>_physio.json` MUST be present to indicate the column names.
 
 The [`recording-<label>`](../appendices/entities.md#recording)
 entity MAY be used to distinguish between several recording files.
@@ -51,10 +46,9 @@ the eyetracking data in a certain sampling frequency, and
 `sub-01_task-bart_recording-breathing_physio.tsv.gz` to contain respiratory
 measurements in a different sampling frequency.
 
-Physiological recordings (including eyetracking) SHOULD use the `_physio`
-suffix, and signals related to the stimulus SHOULD use `_stim` suffix.
+Physiological recordings (including eyetracking) MUST use the `_physio` suffix.
 
-The following tables specify metadata fields for the `*_<physio|stim>.json` file.
+The following tables specify metadata fields for the `*_physio.json` file.
 
 <!-- This block generates a metadata table.
 These tables are defined in
@@ -174,13 +168,8 @@ stored in separate files
 (and the [`recording-<label>`](../appendices/entities.md#recording)
 entity MAY be used to distinguish these files).
 
-If the same continuous recording has been used for all subjects (for example in
-the case where they all watched the same movie), one file MAY be used and
-placed in the root directory.
-For example, `task-movie_stim.tsv.gz`
-
 For motion parameters acquired from MRI scanner side motion correction, the
-`_physio` suffix SHOULD be used.
+`_physio` suffix MUST be used.
 
 For multi-echo data, a given `physio.tsv` file is applicable to all echos of
 a particular run.
diff --git a/src/modality-specific-files/task-events.md b/src/modality-specific-files/task-events.md
index 9b0ffa69f3..c3822094a5 100644
--- a/src/modality-specific-files/task-events.md
+++ b/src/modality-specific-files/task-events.md
@@ -126,7 +126,7 @@ Note that in the example above:
 
 1.  The `channel` column contains a list of values that are separated
     by a delimiter (`|`), as is declared in the `Delimiter` metadata
-    field of the `events.json file.
+    field of the `events.json` file.
     Thus, the channels related to the event in the third row of the example
     are called `F,1`, `F,2`, and `Cz`.
 
@@ -311,3 +311,88 @@ in the accompanying JSON sidecar as follows (based on the example of the previou
     "VisionCorrection": "lenses"
 }
 ```
+
+### Continuously-sampled, stimulus-related signals
+
+!!! example "Example datasets"
+
+      The following [BIDS-Examples](https://bids-standard.github.io/bids-examples/#dataset-index)
+      showcase stimulus-related signals and may be used as a reference
+      when curating a new dataset:
+
+      -   ["synthetic" example dataset](https://github.com/bids-standard/bids-examples/tree/master/synthetic).
+
+Signals related to stimuli (such as parameters of a film or audio stimuli) that are
+evenly recorded at a constant sampling frequency MUST be specified using a
+[compressed tabular file](../common-principles.md#compressed-tabular-files)
+([TSV.GZ file](../glossary.md#tsvgz-extensions)) and a corresponding
+JSON file for storing metadata fields (see below).
+
+Template:
+
+```Text
+sub-<label>/[ses-<label>/]
+    <datatype>/
+        <matches>_stim.tsv.gz
+        <matches>_stim.json
+```
+
+For the template directory name, `<datatype>` can correspond to any data
+recording modality.
+
+In the template filenames, the `<matches>` part corresponds to task filename
+before the suffix.
+For example for the file `sub-control01_task-nback_run-1_bold.nii.gz`,
+`<matches>` would correspond to `sub-control01_task-nback_run-1`.
+
+!!! warning "Caution"
+
+    `<matches>_stim.tsv.gz` files MUST NOT include a header line,
+    as established by the [common-principles](../common-principles.md#compressed-tabular-files).
+    As a result, when supplying a `<matches>_stim.tsv.gz` file, an accompanying
+    `<matches>_stim.json` MUST be present to indicate the column names.
+
+If the same continuous recording has been used for all subjects (for example in
+the case where they all watched the same movie), one file placed in the
+root directory (for example, `<root>/task-movie_stim.<tsv.gz|json>`) MAY be used
+and will apply to all `<matches>_task-movie_<matches>_<suffix>.<ext>` files.
+In the following example, the two `task-nback_stim.<json|tsv.gz>` apply
+to all the `task-nback` runs across the two available subjects:
+
+<!-- This block generates a file tree.
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_filetree_example({
+  "sub-01": {
+    "func": {
+      "sub-01_task-nback_run-1_bold.nii.gz": "",
+      "sub-01_task-nback_run-2_bold.nii.gz": "",
+    },
+  },
+  "sub-02": {
+    "func": {
+      "sub-02_task-nback_run-1_bold.nii.gz": "",
+      "sub-02_task-nback_run-2_bold.nii.gz": "",
+    },
+  },
+  "task-nback_stim.json": "",
+  "task-nback_stim.tsv.gz": "",
+}) }}
+
+The following table specifies metadata fields for the
+`<matches>_stim.json` file.
+
+<!-- This block generates a metadata table.
+These tables are defined in
+  src/schema/rules/sidecars
+The definitions of the fields specified in these tables may be found in
+  src/schema/objects/metadata.yaml
+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(["continuous.Continuous"]) }}
+
+Additional metadata may be included as in
+[any TSV file](../common-principles.md#tabular-files) to specify, for
+example, the units of the recorded time series for each column.