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ClandininLab / brainsss2

refactor of the brainsss repo for 2-photon imaging analysis
MIT License
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common input API for workflow element functions #31

Open poldrack opened 2 years ago

poldrack commented 2 years ago

each elemental function should take the same arguments specifying the different directories or other specs (as defined in the argument spec to be written down shortly)

poldrack commented 2 years ago

spec for common input API:

--basedir: common directory in which all of the data live (e.g. /data/brainsss) --procdir: directory in which built/processed fly directories live (defaults to /processed) --atlasdir: directory in which atlases are stored (defaults to /atlas) --flyname: label for an individual fly (e.g. fly-001) --dirtype: in {func, anat} --scan: scan number (e.g. if there are two multiple functional scans, could be 1 and 2) - starts at 1