> 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

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.                                                                           |


---

# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.

## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter:

```
GET https://docs.neuroinfodb.org/squirrel/specifications/squirrel-vs-bids.md?ask=<question>&goal=<endgoal>
```

`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal.

The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.