[ENH] Derive masks to support native-space data

ME-ICA / aroma

ICA-AROMA, as a Python package. A work in progress.

Apache License 2.0

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[ENH] Derive masks to support native-space data #24

Open tsalo opened 3 years ago

tsalo commented 3 years ago

References #2 and stems from https://github.com/Brainhack-Donostia/ica-aroma-org/pull/49.

Changes proposed in this pull request:

Add function to derive masks from EPI data and CSF tissue probability map or mask.
Have the ICA function return the relevant ICA outputs instead of inferring the filenames in the main workflow function.
Use the new derived masks throughout the workflow.

eurunuela commented 3 years ago

Thank you @tsalo ! I tried running the integration tests and it fails.

I think it's related to nibabel. Could you check it out please?

tsalo commented 3 years ago

I didn't get any errors in the workflow itself, but it looks like the masks are different enough that the ICA produces different components, which is causing the test to fail.

oesteban commented 3 years ago

I tried running the integration tests and it fails.

You guys mean locally right? Because the integration tests on Circle don't seem to have ever worked, correct?

tsalo commented 3 years ago

Right. The integration tests are going to fail on CircleCI until we get rid of FSL completely- unless we set up a Dockerfile with FSL installed, which we haven't done because we ultimately want to drop the dependency anyway.

eurunuela commented 3 years ago

That's a weird error you got here. Is it somehow related to nilearn's load_niimg() function?