Added ICLabel to the mne-bids pipeline #3

jschepers · 2024-06-26T14:52:53Z

Before merging …

Changelog has been updated (docs/source/changes.md)

Changes

Added the code from this PR by @hoechenberger
- Comment: In the newer version of mne-bids-pipeline the ICA is divided into two scripts, therefore I had to divide the code into these scripts.
@behinger added two config variables ica_use_ecg_detection and ica_use_eog_detection to control whether MNE eog/ecg detection should be used on the ICs
We implemented that the user can specify in the config file (using the variable icalabel_include) which labels/ICs to include. Default is ["brain","other"].
- Comment: We should add tests for this e.g. No value given -> Default should be used, Empty list or wrong labels -> Error
Added plots of the excluded ICs to the report together with their labels and the probability of the labels.
- Comment: The plotting needs improvement e.g. combine all single plots in one plot

Co-authored-by: Richard Höchenberger <[email protected]>

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Richard Höchenberger <[email protected]>

…is readable in light and dark theme (mne-tools#793) Co-authored-by: Eric Larson <[email protected]>

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…rameters; drop support for `loose=None` (mne-tools#915) Co-authored-by: Eric Larson <[email protected]>

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Eric Larson <[email protected]>

Co-authored-by: Richard Höchenberger <[email protected]>

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…#874)

…g from the dataset (mne-tools#928)

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…and subject or experimenter name) (mne-tools#931) Co-authored-by: Eric Larson <[email protected]>

…tools#933)

Co-authored-by: Eric Larson <[email protected]>

…structed ICA and SSP epochs (mne-tools#936)

mne-tools#938)

…s#937) Co-authored-by: Eric Larson <[email protected]>

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Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Eric Larson <[email protected]>

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

…input whether to do eog or ecg detection on ICs

hoechenberger and others added 30 commits July 4, 2023 10:11

Prepare for 1.4.0 release (mne-tools#753)

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MAINT: Cleanup dependencies and doc build (mne-tools#755)

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ENH: Add annotation of head velocity (mne-tools#757)

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BUG: Fix bug with cache invalidation (mne-tools#756)

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ENH: Add T1 and FLASH BEM to website (mne-tools#758)

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BUG: Fix bug with empty room processing (mne-tools#761)

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ENH: More compact logging (mne-tools#764)

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ENH: Add eSSS (mne-tools#762)

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ENH: Cache grand-average steps (mne-tools#765)

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MAINT: Test MD5 hashing too (mne-tools#768)

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ENH: Better logging of distances (mne-tools#769)

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MAINT: pre-commit.ci (mne-tools#774)

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Added deriv_root argument to CLI (mne-tools#773)

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MAINT: Use pooch for downloading web data (mne-tools#775)

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API: Change default to _cache (mne-tools#778)

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ENH: Validate inputs with pydantic (mne-tools#779)

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TST: Rerun CIs (mne-tools#781)

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BUG: Fix bug where individual invs were not rendered (mne-tools#782)

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MAINT: Fix bug with item (mne-tools#791)

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Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Richard Höchenberger <[email protected]>

Ensure link in "You're not viewing the latest stable version" banner …

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…is readable in light and dark theme (mne-tools#793) Co-authored-by: Eric Larson <[email protected]>

[pre-commit.ci] pre-commit autoupdate (mne-tools#795)

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hoechenberger and others added 30 commits April 2, 2024 12:14

Improve documentation and config validation of loose and depth pa…

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…rameters; drop support for `loose=None` (mne-tools#915) Co-authored-by: Eric Larson <[email protected]>

change default for info to use for inverse mne-tools#905 (mne-tools#919)

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Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Eric Larson <[email protected]>

ENH: Streamline ICA reporting (mne-tools#899)

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[pre-commit.ci] pre-commit autoupdate (mne-tools#923)

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Support variable time windows for epochs metadata creation (mne-tools…

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…#874)

Raise a more helpful error message when requested subjects are missin…

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…g from the dataset (mne-tools#928)

[pre-commit.ci] pre-commit autoupdate (mne-tools#929)

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Fix report section on original raw data (didn't contain bad channels …

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…and subject or experimenter name) (mne-tools#931) Co-authored-by: Eric Larson <[email protected]>

In the report TOC, don't put the run numbers in quotation marks (mne-…

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…tools#933)

Rename ica_ctps_ecg_threshold to ica_ecg_threshold (mne-tools#935)

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Co-authored-by: Eric Larson <[email protected]>

Improve logging output when rejecting epochs; and log number of recon…

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…structed ICA and SSP epochs (mne-tools#936)

Save ECG and EOG evokeds created during ICA artifact detection to disk (

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mne-tools#938)

Improve logging during ICA artifact discovery and rejection (mne-tool…

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…s#937) Co-authored-by: Eric Larson <[email protected]>

DOC: Fix typo (mne-tools#940)

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MAINT: Cleaner hook into mkdocstrings-python (mne-tools#943)

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remove ref-names from .git_archival.txt (mne-tools#948)

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MAINT: Cleaner traceback on error (mne-tools#951)

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[pre-commit.ci] pre-commit autoupdate (mne-tools#954)

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[MAINT] Switch to trusted publishing (mne-tools#957)

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Rework how we apply EEG montages (mne-tools#960)

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added iclabel code from PR, user input which IC labels to keep, user …

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…input whether to do eog or ecg detection on ICs

use brain and other as default for icalabel_include

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added rudimentary plot of excluded components + labels + probabilities

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Added ICLabel to the mne-bids pipeline #3

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jschepers commented Jun 26, 2024 •

edited by behinger

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jschepers commented Jun 26, 2024 • edited by behinger Loading Uh oh! There was an error while loading. Please reload this page.

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jschepers commented Jun 26, 2024 •

edited by behinger

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