Raw and derivatives seperation

3

Hi @nirjac

You can use triple-backticks as follows:

```
<pre-formatted text>
```

This will preserve the spaces. I’m guessing you had something like:

Project Name/
  raw_bids/
    sub-0001/…
    sub-0002/…
    …
  derivatives/
    pipeline1/
      sub-0001/…
      sub-0002/…
    …
  sourcedata/

This is perfectly fine. In this case your BIDS directory would be Project Name/raw_bids/, which is a valid name, and derivatives datasets may be standalone. derivatives/ and sourcedata/ are only required directory names when you want to nest datasets, but even here there’s some flexibility. My preferred arrangement is actually the inverse of the prototype from the spec:

Project/
  derivatives/
    fmriprep/
      sourcedata/  # original dataset as a datalad submodule
        sub-01/
        ...
      code/
        fmriprep_<version>.simg
      sub-01/
      ...

This allows the specific version of the source data and the preprocessing pipeline to be stored with the derivatives dataset.