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yeatmanlab / AFQ-Browser

Browser-based visualization tools for AFQ results
BSD 3-Clause "New" or "Revised" License
33 stars 15 forks source link

work with pyAFQ tractometry outputs of QSIprep? #291

Open dkp opened 9 months ago

dkp commented 9 months ago

This looks like such a fantastic tool! Sadly, I'm not sure how to get it working with the qsiprep reconstruction pipeline pyAFQ_tractometry.

Can you please advise?

arokem commented 9 months ago

Hi Dianne -- sorry -- I saw that you also posted an issue on the other relevant repos and on Neurostars, but I have been beyond overwhelmed (maybe after OHBM deadline I will be less overwhelmed? We'll see...). I believe that you should be able to get what you want from pyAFQ, as the GroupAFQ object implemented there includes an export function specifically for AFQ-Browser outputs (https://github.com/yeatmanlab/pyAFQ/blob/master/AFQ/api/group.py#L841 and also export_all(), https://github.com/yeatmanlab/pyAFQ/blob/master/AFQ/api/group.py#L479) that produces the streamlines.json file based on one of the subjects in your dataset.

dkp commented 8 months ago

@arokem,
Thank you for the pointers. I've been learning a lot about my assumptions and the tools. Am I correct in believing that once a streamlines.json is generated for the default pyAFQ_tractometry pipeline, that streamlines.json will be the same for any other runs of pyAFQ_tractometry pipeline (as long as the selected tracts do not change)?