[ENH] BEP044 - Stim-BIDS #2022
[ENH] BEP044 - Stim-BIDS #2022
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Implement the standardization of stimulus files and their annotations within the BIDS specifications.
* **Add new file `src/modality-specific-files/stimuli.md`**
- Describe the specifications for the stimuli directory.
- Include guidelines for storing stimulus files and their annotations.
- Define what goes into `stimuli.tsv/json`, `annotations.tsv/json`, and `stim-<label>.json`.
- Use the same style as other modality-specific docs to design the tables, variables, and examples.
* **Modify `src/modality-specific-files/task-events.md`**
- Add a section detailing the standardization of stimulus files and their annotations within the BIDS specifications.
- Include examples of how to use the `stim_file` and `stim_id` columns in `events.tsv` files.
- Provide guidelines for storing stimulus files in the `/stimuli` directory.
- Expand the definition of the `stim_file` column to include `stim_id`.
* **Modify `src/schema/objects/columns.yaml`**
- Update the definition of the `stim_file` column to ensure consistency in stimulus file references.
- Add the `stim_id` column definition for `events.tsv` files.
* **Modify `src/schema/rules/checks/events.yaml`**
- Add a check for missing stimulus files declared in `events.tsv`.
- Add a check for missing `stim_id` references in `events.tsv`.
* **Modify `src/schema/rules/sidecars/events.yaml`**
- Specify the `StimulusPresentation` metadata field for `events.tsv` files.
- Include the `stim_id` column in the metadata field specifications.
* **Modify `src/schema/objects/entities.yaml`**
- Add entities described in the document with proper requirement levels and descriptions.
* **Modify `src/schema/objects/suffixes.yaml`**
- Add suffixes for `{audio, image, video, audiovideo}`.
- Include the file extensions and descriptions for each suffix.
* **Add new file `src/schema/rules/sidecars/stimulus.yaml`**
- Define sidecar tables for `stimuli.tsv/json`, `annotations.tsv/json`, and `stim-<label>.json`.
- Use the same style as other modality-specific docs to design the tables.
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For more details, open the [Copilot Workspace session](https://copilot-workspace.githubnext.com/neuromechanist/bids-specification?shareId=XXXX-XXXX-XXXX-XXXX).
Add stimuli specifications to BIDS
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| The `stimuli.json` file provides detailed descriptions of the columns in the `stimuli.tsv` file. There can be extra entries in the `stimuli.json` in addition to the columns in the `stimuli.tsv` to provide more details about the stimulus. | ||
| In cases where the stimulus is not shared, the `stimuli.tsv` file can be used to provide metadata about the stimuli, including the license, copyright, URL, and description. This is simialr to the use of `stim-<label>_<suffix>.json` files for individual stimuli files. In the case of conflict between the metadata in the `stimuli.tsv` and `stim-<label>_<suffix>.json` files, the metadata in the `stim-<label>_<suffix>.json` file takes precedence. |
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Again, here _. It should be consistent. The _ appears in several places as does without the underbar. I'm not going to mark them further --- just need to be consistent.
for more information, see https://pre-commit.ci
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will do a bit of clean up to get less red in CI and maybe see if we can get the HTML version of the BEP to render |
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| The `stim_id` in the events file links to corresponding files: | ||
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| ```Text |
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needs MACROS___make_filetree_example until someone smart implements parsing... ref: #2014 (comment)
Co-authored-by: Yaroslav Halchenko <debian@onerussian.com>
Co-authored-by: Yaroslav Halchenko <debian@onerussian.com>
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Obserinvg #750 and the |
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I think this extension will be a very valuable addition to BIDS. I have read through the HTML rendered version and have the following typo corrections:
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Thanks very much @VisLab. The |
This PR addresses #153 by introducing specifications for handling and standardizing stimulus files and their annotations within the BIDS specifications. The changes focus on improving the organization, referencing, and metadata of stimulus files to enhance consistency, reusability, and efficiency.
Important
HTML render of the stimuli page : https://bids-specification--2022.org.readthedocs.build/en/2022/modality-specific-files/stimuli.html
Note
The issue: #153
Google Doc
Example PR: bids-standard/bids-examples#433
Known issues:
/src/schema/rules/files/rawrequiredatatype. Stimuli might be a special data type that can only be present at the root of the dataset. So, the datatype field is missing for now.cc: @bids-standard/bep044 and @monique2208