---
# System prepended metadata

title: 2023/12/5 (notes)
tags: [TechMon]

---

# 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 <elodie.savary@outlook.com>
- **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.
