> For the complete documentation index, see [llms.txt](https://docs.neuroinfodb.org/squirrel/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.neuroinfodb.org/squirrel/specifications/squirrel-vs-bids.md).

# squirrel vs BIDS

Understanding the differences between package formats

BIDS and squirrel are both file formats designed to store neuroimaging data. They are similar, but different in implementation. If you are familiar with BIDS, squirrel will be easy to understand.

## squirrel vs BIDS objects

| squirrel                | BIDS                                                                                                                                                                                                                                                                                                                                                               | Notes                                                                                                         |
| ----------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ------------------------------------------------------------------------------------------------------------- |
| subject                 | `sub-` directory                                                                                                                                                                                                                                                                                                                                                   | The subject object. BIDS sub-\* directories contain the ID. squirrel objects are identified by the ID.        |
| study                   | <p><code>ses-</code> directory<br><code>\*\_sessions.tsv</code></p>                                                                                                                                                                                                                                                                                                | Session/imaging study object.                                                                                 |
| series                  | <p><code>*.nii.gz</code> files<br><code>*.nii</code> files<br><code>anat</code> directory<br><code>func</code> directory<br><code>fmap</code> directory<br><code>ieeg</code> directory<br><code>perf</code> directory<br><code>eeg</code> directory<br><code>\*events.json</code> file<br><code>\*events.tsv</code> file<br><code>\<modality>.json</code> file</p> | Mapping series within BIDS can be tricky. There is limited mapping between squirrel and BIDS for this object. |
| analysis                | <p><code>derivatives</code> directory<br><code>figures</code> directory<br><code>motion</code> directory<br><code>\*\_scans.tsv</code> file</p>                                                                                                                                                                                                                    | The analysis results object/directory.                                                                        |
| pipeline                | `code` directory                                                                                                                                                                                                                                                                                                                                                   | Code, pipelines, scripts to perform analysis on raw data.                                                     |
| experiment              | <p><code>task-*.json</code><br><code>task-*.tsv</code></p>                                                                                                                                                                                                                                                                                                         | Details on the experiment.                                                                                    |
| root -> description     | `dataset_description.json`                                                                                                                                                                                                                                                                                                                                         | Details about the dataset.                                                                                    |
| root -> changes         | `CHANGES`                                                                                                                                                                                                                                                                                                                                                          | Any information about changes from to this dataset from a previous version.                                   |
| root -> readme          | <p><code>README</code><br><code>README.md</code></p>                                                                                                                                                                                                                                                                                                               | More details about the dataset.                                                                               |
| subject -> demographics | `participants.tsv` `participants.json`                                                                                                                                                                                                                                                                                                                             | Details about subject demographics.                                                                           |


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