Custom HCP pipeline output as open /derivatives/?

openneuro
#1

We want to share the images from our “preprocessing comparisons” dataset, but have been wondering the best way to do it.

Would it be appropriate to upload the dataset as BIDS, and then include both the HCP and fMRIPrep preprocessed images under /derivatives/? I’m not envisioning releasing all of the files produced by the pipelines, just the resulting 4d NIfTI, gifti/cifti, and motion regressors.

If it’s not appropriate to put these preprocessed images into openneuro, do you have suggestions for alternatives? OSF linked to box seems like an option, though unwieldy given the file sizes.

thanks!

#2

Hi @jaetzel, yes, it would be appropraite to include these under /derivatives. The current recommendation would be to do something like:

dataset/
    dataset_description.json
    derivatives/
        HCP-<version>/
            dataset_description.json
            sub-01/
                ...
            ...
        fmriprep-<version>/
            dataset_description.json
            sub-01/
                ...
            ...
    sub-01/
        ...
    ...

fMRIPrep should produce a valid dataset_description.json, and you can find a specification here as part of the BIDS Derivatives (draft) specification.

I suspect it will be fairly straightforward to crib the naming conventions from fMRIPrep and apply them to HCP, though you may need to reference the spec/check back to determine the space- names.

#3

Thanks, we’ll (eventually) submit the dataset.