(#72) Add fMRIprep-to-tedana recommendations Processing_Multi_Echo_Data#88
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bf777 wants to merge 5 commits into
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(#72) Add fMRIprep-to-tedana recommendations Processing_Multi_Echo_Data#88bf777 wants to merge 5 commits into
bf777 wants to merge 5 commits into
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…_Data.ipynb and associated .md and html files.
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Pull request overview
This PR updates the “Processing Multi-Echo Data” documentation to add guidance for using tedana with outputs from automated preprocessing pipelines (notably fMRIPrep) and for running tedana on HPC systems.
Changes:
- Adds a new “Pipeline-specific recommendations” section covering fMRIPrep usage considerations for ME-EPI + tedana.
- Adds an HPC/SLURM example for running tedana workflows at scale.
- Updates the built documentation artifacts (HTML +
_sources) to reflect the new content.
Reviewed changes
Copilot reviewed 4 out of 4 changed files in this pull request and generated 6 comments.
| File | Description |
|---|---|
| docs/content/Processing_Multi_Echo_Data.html | Published HTML updated with new pipeline/HPC guidance and TOC entries. |
| docs/_sources/content/Processing_Multi_Echo_Data.md | Generated page source updated to include the new recommendations and script snippet. |
| docs/_sources/content/Processing_Multi_Echo_Data.ipynb | Generated notebook source updated with the new markdown content. |
| content/Processing_Multi_Echo_Data.md | Canonical Jupyter Book source updated with fMRIPrep + HPC recommendations and example SLURM script. |
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Collaborator
Author
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@tsalo I've made some light changes, please let me know if all looks good and this works/didn't break other stuff - thanks! |
eurunuela
requested changes
Jun 14, 2026
| ### fMRIPrep | ||
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| When using `fMRIPrep` to preprocess ME-EPI data, we recommend the following: | ||
| - Use the `--me-output-echoes` flag to ensure that each echo is preprocessed separately, then run optimal combination |
Contributor
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Suggested change
| - Use the `--me-output-echoes` flag to ensure that each echo is preprocessed separately, then run optimal combination | |
| - Use the `--me-output-echos` flag to ensure that each echo is preprocessed separately, then run optimal combination |
Contributor
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Per the fMRIprep docs, it should be echos. Can you please confirm this?
Contributor
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Can you also update this on the ipynb?
| ### fMRIPrep | ||
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| When using `fMRIPrep` to preprocess ME-EPI data, we recommend the following: | ||
| - Use the `--me-output-echoes` flag to ensure that each echo is preprocessed separately, then run optimal combination |
Contributor
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Suggested change
| - Use the `--me-output-echoes` flag to ensure that each echo is preprocessed separately, then run optimal combination | |
| - Use the `--me-output-echos` flag to ensure that each echo is preprocessed separately, then run optimal combination |
Contributor
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Thanks @bf777! Just want to make sure the CLI argument is spelled correctly before we merge. |
Collaborator
Author
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Thanks for the feedback @eurunuela ! I've now made the requested changes. |
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Problem
The
Processing_Multi_Echo_Datanotebook lacked context on importing fMRI data from fMRIprep into tedana.Fix
These changes to
Processing_Multi_Echo_Data.ipynbadd and link to information and sample scripts to run tedana in parallel on a computing cluster and successfully import data from fMRIprep.