HCP pipelines "final" functional output files

[paola.o...@yale.edu]

Hi Chris,

Thank you for all your contributions to reproducible science! My lab has managed to use your BIDS HCP-pipelines App to run the HCP minimal preprocessing pipeline on our in-house data (collected using HCP parameters), which is amazing! As you know, this gives us A LOT of output files, and we're having some trouble making sense of them. Could you point us to where in the documentation we could find more info about what each output file is? We've looked into the Glasser paper as well as this documentation but can't seem to find specific info about what all the filenames (and the appended filename endings) actually represent.

Additionally, we are in a bit of a hurry to analyze the functional data for a preliminary report and want to run the Level 1 and Level 2 analyses on FSL as soon as possible. Could you point us to where the "final" preprocessed functional file is and what it is named after the fMRISurface step?

Thanks so much in advance for your help!

Best,

Paola

[eric...@gmail.com]

Paola,

This might be a better question for the HCP folks' email list (on the right of the page https://www.humanconnectome.org/contact-us).  As far as I know, Chris just wrote the wrapper to wrap their pipelines into a BIDS App thing.

~Eric

[odrio...@gmail.com]

Thank you so much, Eric!
You’re right, I have now posted this question there too and will link to it here when it’s answered so that BIDS Apps users can find this information more easily.

Best,
Paola