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DCAN-Labs / abcd-hcp-pipeline

bids application for processing functional MRI data, robust to scanner, acquisition and age variability.
https://hub.docker.com/r/dcanumn/abcd-hcp-pipeline
BSD 3-Clause "New" or "Revised" License
49 stars 19 forks source link

freesurfer output #33

Closed mriedel56 closed 3 years ago

mriedel56 commented 3 years ago

Is it possible to make the direct freesurfer output available for the ABCD data? Ive checked out the filemapper and it looks like those files are just skipped over (presumably bc they are intermediary for final output files). Is space an issue for that?

arueter1 commented 3 years ago

Thanks for the question! Someone from our team will check in on this as soon as we are able.

ericfeczko commented 3 years ago

Hi mriedel56! Unfortunately, the output from the intermediate Freesurfer stage (see here for further information: https://collection3165.readthedocs.io/en/stable/pipeline/#stage-2-freesurfer ) remains quite large (~ 612 MB per subject, ~6 TB total ~ approximately 10 percent of the size of current derivatives), and is not available right now.

However, the anat derivative folder contains the midthickness surfaces for both MNI and native spaces, surface-based morphometrics stored as CIFTIs, the volume in MNI space, and the correspond anatomical segmentation. Depending on what you are interested in doing, we may be able to help you answer your question using the derivatives that are already available ( https://collection3165.readthedocs.io/en/stable/derivatives/).

Please let us know how we can help further, thanks!

-Eric

mriedel56 commented 3 years ago

Thanks for the response, I figured that space had something to do with it. We were potentially interested in running fMRIPREP on the BIDS dataset (just what we use and are more familiar with in our lab). Having freesurfer previously run would have expedited the process, but I think fMRIPREP prefers a newer version of freesurfer. As it stands, the hcp derivatives work perfectly fine for our needs. Thanks again.