Skip to content

Commit

Permalink
Add info about dataset_description.json.
Browse files Browse the repository at this point in the history
Add links to BIDS web.
Update derivatives section.
  • Loading branch information
valosekj committed Dec 13, 2022
1 parent d4a62e1 commit b89d175
Showing 1 changed file with 22 additions and 4 deletions.
26 changes: 22 additions & 4 deletions data/dataset-curation.md
Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ For details, see [BIDS specification](https://bids-specification.readthedocs.io/

### `README.md`

The `README.md` is a [markdown](https://markdown-guide.readthedocs.io/en/latest/index.html) file describing the dataset in more detail.
The [`README.md`](https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#readme) is a [markdown](https://markdown-guide.readthedocs.io/en/latest/index.html) file describing the dataset in more detail.

Below is a template - modify it!!!

Expand Down Expand Up @@ -110,16 +110,32 @@ The `participants.json` is a JSON file describing the column names in the `parti

</details>

### `dataset_description.json`

The [`dataset_description.json`](https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#dataset_descriptionjson) is a JSON file describing the dataset.

❗The `dataset_description.json` file within the top-level dataset should include `"DatasetType": "raw"`.

<details><summary>dataset_description.json template:</summary>

```json
{
"BIDSVersion": "BIDS X.Y.Z",
"Name": "<dataset_name>",
"DatasetType": "raw"
}
```

</details>

### `code/`

The data curation script(s) should be placed inside the BIDS datasets, under the `code/` folder. For more convenience, you can create a PR with a curation script that you are working on, so that others can give feedback; once the script is validated, you can simply close the PR and delete the branch without merging.


## derivatives structure

The `derivatives` will be organized according to the following:

https://github.com/ivadomed/ivadomed/wiki/repositories#derivatives
The [`derivatives`](https://bids-specification.readthedocs.io/en/stable/05-derivatives/01-introduction.html) are files generated from the top-level dataset such as segmentations or labels.

Convention for derivatives JSON metadata:

Expand All @@ -132,6 +148,8 @@ Convention for derivatives JSON metadata:

NOTE: "Date" is optional. We usually include it when running the manual correction via python scripts.

❗The `derivatives` must include its own `dataset_description.json` file (with `"DatasetType": "derivative"`).

## Changelog policy

We will use git log over [CHANGES](https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html#changes) BIDS file.
Expand Down

0 comments on commit b89d175

Please sign in to comment.