# Technical Monitoring (notes) - 2023 December 5

:::info
- **Date:** Dec 5, 2023 16:00(UTC)
- **Participants:**
- Elodie
- Chris
- Celine
- Mathias
- Eilidh
- Oscar
- Ross
- Teresa
- Ariel
- Alex
- Taylor Salo
- **Contact:** ES <[e-mail]>
- **Host:** ES
- **Reference:** -

:::

## Agenda

* Multi-echo fMRIPrep - fit+transform and potential improvement
* Templateflow - problems with datalad (23.1.0) - [python-client#112](https://github.com/templateflow/python-client/issues/112)
* [Test data organization](https://demo.hedgedoc.org/JI8jZIhoQlO7MTDX__y9ZA#)
* Bikeshed: Adopt ruff? ([smriprep#397](https://github.com/nipreps/smriprep/pull/397) for example)

## Suggestions / TBD

## Notes

* Multi-echo fMRIPrep
* CCG noticed that fMRIPrep was using tedana's adaptive mask (which is often overly conservative).
* In June, fMRIPrep started dilating the brain mask and passes that to tedana.
* For a while before that, fMRIPrep passed the regular brain mask to tedana, so it's been a while since fMRIPrep used the tedana-generated mask.
* Should be resolved at this point.
* TODO: Improve documentation about integrating fMRIPrep + tedana denoising.
* Thinking about developing an [fMRIPost-tedana](https://github.com/ME-ICA/fmripost-tedana) App.
* Tedana team could use help with two elements:
* Convert tedana to a monorepo structure to let fMRIPrep install base version of tedana (e.g., without bokeh and jinja). Basically have `tedana-core` and `tedana` packages within the tedana repo.
* https://github.com/ME-ICA/tedana/issues/934
* Improve memory usage in optimal combination step.
* https://github.com/ME-ICA/tedana/issues/856
* OHBM 2022 [abstract](https://hackmd.io/XkdrkcBWRp20pHfMbLtzFw)
* Templateflow datalad issue
* Test data organization
* Test data is spread across OSF, GIN, etc.
* Not clear where to put new test data (e.g., updated FreeSurfer derivatives).
* Need to document best practices.
* Adopt ruff?
* Supports lots of flake8 plugins
* Has linter and formatter
* Allows single quotes
* TODO: Copy config from smriprep to cookiecutter repo.