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VisLab authored Jun 24, 2024
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Expand Up @@ -5,16 +5,16 @@ validating, summarizing, and analyzing your BIDS datasets.

**Table 1:** Useful Jupyter notebooks for processing BIDS datasets.

| Notebooks | Purpose |
|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------|
| [`extract_json_template`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/extract_json_template.ipynb) | Creates a JSON sidecar based on all the event files in a dataset. |
| [`find_event_combinations`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/find_event_combinations.ipynb) | Creates a spreadsheet of unique combinations of event values. |
| [`merge_spreadsheet_into_sidecar`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/merge_spreadsheed_into_sidecar.ipynb) | Merges a spreadsheet version of a sidecar into a JSON sidecar. |
| [`sidecar_to_spreadsheet`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/sidecar_to_spreadsheet.ipynb) | Converts the HED portion of a JSON sidecar into a 4-column spreadsheet. |
| [`summarize_events`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/summarize_events.ipynb) | Summarizes the contents of the event files, including value counts. |
| [`validate_bids_dataset`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/validate_bids_dataset.ipynb) | Validates the HED annotations in a BIDS dataset. |
| Notebooks | Purpose |
|------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------|
| [`extract_json_template`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/extract_json_template.ipynb) | Creates a JSON sidecar based on all the event files in a dataset. |
| [`find_event_combinations`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/find_event_combinations.ipynb) | Creates a spreadsheet of unique combinations of event values. |
| [`merge_spreadsheet_into_sidecar`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/merge_spreadsheet_into_sidecar.ipynb) | Merges a spreadsheet version of a sidecar into a JSON sidecar. |
| [`sidecar_to_spreadsheet`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/sidecar_to_spreadsheet.ipynb) | Converts the HED portion of a JSON sidecar into a 4-column spreadsheet. |
| [`summarize_events`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/summarize_events.ipynb) | Summarizes the contents of the event files, including value counts. |
| [`validate_bids_dataset`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/validate_bids_dataset.ipynb) | Validates the HED annotations in a BIDS dataset. |
| [`validate_bids_dataset_with_libraries`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/validate_bids_dataset_with_libraries.ipynb) | Demonstrates use of HED libraries in validation. |
| [`validate_bids_datasets`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/validate_bids_datasets.ipynb) | Validates the HED annotations in a list of BIDS datasets. |
| [`validate_bids_datasets`](https://github.com/hed-standard/hed-examples/blob/main/src/jupyter_notebooks/bids/validate_bids_datasets.ipynb) | Validates the HED annotations in a list of BIDS datasets. |

These notebooks require HEDTools, which can be installed using `pip` or directly.

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