Add QC + Full MNE Report tutorial #13532
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varshaa-1616
requested review from
agramfort,
dengemann,
drammock and
larsoner
as code owners
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| # OptiPNG version 0.7.8 | |||
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I will look more fully next week. But in the meantime, these files should not be added
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Oh, okay, got it. I'll remove those files and wait for your review. Thank you!
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Looks like some incorrect files are still there
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Rather than changing |
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Sorry for the delayed response — I had exams and wasn’t able to check
emails or work on it earlier. I’ll create a separate tutorial instead of
modifying 70_report.py by the end of the week. I'll also remove the
unnecessary files. Thank you for the guidance!
…On Fri, 12 Dec 2025 at 00:58, Eric Larson ***@***.***> wrote:
*larsoner* left a comment (mne-tools/mne-python#13532)
<#13532 (comment)>
Rather than changing 70_report.py the idea -- since it's complementary
info -- would be to create a new tutorial/example instead
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@larsoner Please let me know if you’d like any structural or content changes. |
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| Quality control (QC) is the process of systematically inspecting M/EEG data | ||
| before any serious preprocessing, modeling, or source analysis is attempted. |
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Actually mne.Report can be used to QC at all steps of a pipeline, not just at the raw data stage. I'd actually recommend looking at all stages to make sure things "look okay"
| Authors: The MNE-Python contributors | ||
| License: BSD-3-Clause |
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These go in a code comment not in the __doc__
| events_path = sample_dir / "sample_audvis_filt-0-40_raw-eve.fif" | ||
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| raw = mne.io.read_raw(raw_path, preload=True) | ||
| raw.pick(["meg", "eeg", "eog", "stim"]) |
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Do we need to do this? If so -- or if it helps in some way -- a code comment saying why would help users understand
| if __name__ == "__main__": | ||
| report.save("qc_report.html", overwrite=True) |
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We usually don't protect these with __name__ == "__main__" actually, see the other Report tutorial -- we write a lot actually. We probably should have a open_browser=False in here either way
| ICA fitting is computationally expensive and therefore <b>not executed | ||
| during documentation builds</b>. To inspect ICA components locally, |
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We actually do compute ICA in several examples and tutorials. There are tricks to make it faster for when users (and doc builds) run it. Can you update to use ICA similar to what we do elsewhere?
Also, let's not refer to "doc build" anywhere in this tutorial -- the fact that we build these examples is an implementation / maintenance detail that end users don't need to care about. You can instead talk about making things faster or more memory efficient when running these examples (which will be true both for end users -- which they will care about -- and for our doc build -- which they probably won't and shouldn't need to care about).
2 participants
Reference issue
Fixes #13493
What does this implement/fix?
This PR implements a combined QC + Full MNE report workflow.
It merges the essential QC steps used in the mne-bids-pipeline with the standard MNE report features, allowing users to generate a comprehensive HTML report without requiring anatomical dependencies (BEM, coregistration, or forward/inverse solutions).
The report includes:
Additional information