Agenda 9/10/2021

[F-said]

Updates

• Submitted brainBox issue for database/framework idea of standardized preprocessing tool-EEG4p brainBox#7
  • Included this since it would emerge from PEPPER
• Merged in exception handling. @yanbin-niu sorry! Will cause merge issues for dev-feature-ica. Please tag me in PR when relevant so that I can manually resolve it.
• Tested and documented singularity stability for main document singularity stability  #307
• Created informal exception handling strategy Create robust error-handling for user_params in relation to load, write, and features #314
  • implemented branch implementing above mentioned exception handling
  • when subject is skipped, intermediate output_preproc is written as well.
• created branch implementing feature to omit already written files and exits on exceptions
• They're making another Matrix? Who asked for this?
• 4/9 data back to .tar

Blocks/Challenges

• Is data being BIDS compliant a hard pre-condition for our pipeline

Next Actions

• Decide on pre-release date?
  • One more PR to main should occur to update exception handling and ensure tests are stable!
• I propose making CONTRIBUTING.md more lightweight by placing the planning documents in the ndclab.wiki

[F-said]

Removed exceptions for the write module, because how annoying would it be for data not to write because of a non-existent path?

[DMRoberts]

Some other things we could briefly talk about:

• Adding montage early in processing
• Removing reference channel prior to ICA
• Testing for bridged electrodes?

[georgebuzzell]

Thank you, @F-said and @DMRoberts !!

Another thing to add to the discussion (highish priority?):
-submodule groupings for breaking up preprocess. py

[georgebuzzell]

Continued discussion of brain vs noise metrics. and, relatedly, datasets to use.

the cmi dataset will cover our needs in terms of child, adolescent, adult. but is crucially missing infant. infant will be the hardest to find.

[georgebuzzell]

possible dataset for infant/toddler eeg (same used for HAPPE): https://zenodo.org/record/998965#.YTtXFBNKifE

[F-said]

Issues

• make "rewrite" param more efficient
• load in montage early in preprocessing
  • montage file should be specified in load submodule
  • refactor other submodules that are reliant on montage
• remove step that removes ref channel in ICA @yanbin-niu
  • firstly merge in OG PR
• remove bridged electrodes in bad_chans (post-release)
• Create g-drive & Zotero shared folder or PEPPER papers
  • bioRxiv

Notes

• Pre-release released around start of paper
  • bioRxiv
  • and then make final after contributions
• Requirements for pre-release (Sept. 30th)
  • all test cases passed
  • all containers stable
  • contributing docs
  • re-org of sub-modules
  • formal road-map written
  • load in montage early in preprocessing
    • montage file should be specified in load submodule
    • refactor other submodules that are reliant on montage
• Informal lit. review (g-drive)
  • HAPPE
  • PREP
  • Scientific Software
  • MADE

[F-said]

Turned pre-release requirements into issue and closed #334