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Minor formatting, clarified derivative warning
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jcohenadad authored Dec 5, 2023
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Expand Up @@ -295,16 +295,19 @@ Analysis scripts should not be kept here. Keep them in separate repositories, us
First, it is important to understand what are [BIDS derivatives](https://bids-specification.readthedocs.io/en/stable/05-derivatives/01-introduction.html#bids-derivatives) folders:

"Derivatives are outputs of common processing pipelines, capturing data and meta-data sufficient for a researcher to understand and (critically) reuse those outputs in subsequent processing. Standardizing derivatives is motivated by use cases where formalized machine-readable access to processed data enables higher level processing."
> Derivatives are outputs of common processing pipelines, capturing data and meta-data sufficient for a researcher to understand and (critically) reuse those outputs in subsequent processing. Standardizing derivatives is motivated by use cases where formalized machine-readable access to processed data enables higher level processing.
Basically, derivative folders are derived datasets generated from a raw dataset. They must include **ONLY** processed data obtained from a specific raw dataset (i.e. segmentations, masks, labels...).

```{warning}
DIFFERENT data obtained using DIFFERENT processes/workflows should be stored using DIFFERENT derivatives folders.
Derivative data obtained using DIFFERENT processes/workflows should be stored using DIFFERENT derivatives folders. Eg:
- `derivatives/labels/`
- `derivatives/sct_5.6/`
- `derivatives/fmriprep_2.3/`
```

```{note}
According to BIDS, derived datasets could be stored inside a parent folder [`derivatives/`](https://bids-specification.readthedocs.io/en/stable/common-principles.html#storage-of-derived-datasets) "to make a clear distinction between raw data and results of data processing". This folder should also follow the same folder logic as the one used for the `raw` data.
According to BIDS, derived datasets could be stored inside a parent folder [`derivatives/`](https://bids-specification.readthedocs.io/en/stable/common-principles.html#storage-of-derived-datasets) _"to make a clear distinction between raw data and results of data processing"_. This folder should also follow the same folder logic as the one used for the `raw` data.
```

### Folders structure and filenames
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