Improve documentation on masking options

[handwerkerd]

Summary

There have been several situations were the automasking that is built into tedana spectacularly fails. We should trace this down, but our sense is that many uses are providing their own masks anyway and that avoids this problem. We should add to the documentation make clear that this is a known issue that is resolved with user-provided masks.

Additional Detail

• Based on conversation in October 2022 Dev call
• Conversation focused on https://neurostars.org/t/visualisation-of-component-beta-maps-using-tedana/23658/3 (possible link to relevant section of code (

  tedana/tedana/utils.py

  Line 78 in c7924b5

  # NOTE: percentile is arbitrary

  ) but there have been other complaints about the built-in automask

Next Steps

• Supplement documentation
• If there are potential code changes to improve how masking is handed in tedana, open a new issue for that