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bids-apps / oppni

runs fast optimization of preprocessing pipelines for BOLD fMRI
Apache License 2.0
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OPPNI is hardcoded only to run on datasets with tasks named "linebisection" #16

Closed chrisgorgo closed 4 years ago

chrisgorgo commented 7 years ago

https://github.com/BIDS-Apps/oppni/blob/master/oppni.py#L187

raamana commented 7 years ago

That's a shame it still exists like that. This was supposed to be a quick start to test few datasets, while pybids and grabbids are ready. I will update it. I remember the task name will be supplied to the OPPNI wrapper with the argument --task_name, yes?

chrisgorgo commented 7 years ago

I was not involved in writing the OPPNI wrapper - I do not know the answer to that question.

raamana commented 7 years ago

I guess my question was not clear. I was referring to how the BIDS app receive various info about the task to be run. Like --participant_label, do the BIDS app receive a --task_name argument when they are launched? If it's not supplied, we should of course try deduce it from the BIDS dataset itself.

chrisgorgo commented 7 years ago

I see. This has not been standardized, but --task_name seems reasonable.

raamana commented 7 years ago

That's probably another reason why we might have tried to do something to get the testing moving.

Which python package do you recommend to query bids dataset info? It seems pybids is the one, there are links and [uncorrected] references to grabbids and others, that are confusing to me in the documentation.

chrisgorgo commented 7 years ago

pybids is the only Python package for querying BIDS datasets I am aware of. Please open an issue describing which aspect of the documentation you find confusing or even better open a pull request with suggested improvement.

raamana commented 7 years ago

Thanks for the clarification, that's what I had in mind. Just wanted to get started from the right package.