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ENH: EEG pipeline implementation #82

Merged
merged 190 commits into from
Feb 21, 2022
Merged

ENH: EEG pipeline implementation #82

merged 190 commits into from
Feb 21, 2022

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joanrue
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@joanrue joanrue commented Mar 9, 2021

  • Added insvol interface in cmtklib/interfaces.

@sebastientourbier sebastientourbier linked an issue Apr 6, 2021 that may be closed by this pull request
Implementation of EEG pipeline #6
Closed
15 tasks
@joanrue
add createrois interface: creates .rois files for cartool inverse sol…
b6e3572 
…ution
@joanrue
add eeglab2fif interface: converts eeglab .set eegfile to mne compati…
aa9d037 
…ble .fif
@joanrue
add eegloader interface: loads all necessary data for eeg source reco…
b39f1d0 
…nstruction
@joanrue
add invsol interface: performs cartool based inverse solution
6016459
@joanrue
removed cmtklib_dev
d812628
@joanrue
add eeg_preparer stage: prepares data for loading according to parsed…
5d6809d 
… args
@joanrue
add eeg_loader stage: loads eeg data for source recons
7cd08c0
@joanrue
add eeg_inverse_solution stage: performs source recons
e30cb12
@joanrue
add eeg pipeline: performs eeg source recons based on the parsed args
4c98084
@joanrue
removed cmp_dev
5fee544
@joanrue
add notebook for debugging integration of eeg
2ba0fc2
@joanrue
FIX: changed temporary dev folders
738db36
@joanrue
FIX: changed temporary dev folders
56b05bc
@joanrue
ENH: add eeg part
c6a5141
@joanrue
ENH: add atlas info in eeg pipeline
93033df
@joanrue
ENH: add eeg part
682571e
@joanrue
ENH: add eeg part
25a8277
@joanrue
FIX: changed EEG to eeg
b1274e9
@joanrue
ENH: add eeg part
01ec82f
@joanrue
ENH: add eeg part
61e4a88
@joanrue
FIX: wrong identation level
3a90e2c
@joanrue
FIX: add eeg for 'participant' mode
f7662f0
@joanrue
FIX: wrong identation
af5bc3a
@joanrue
ENH: added eeg
ded3311
@joanrue
FIX: changed subject_id to subject
1a6fd94
joanrue and others added 16 commits February 18, 2022 15:54
@joanrue
[doc] filled 'TBC' examples in doc
ed907b0
@Katharinski
DOC: Added missing examples to docstrings of interfaces in mne.py.
b374709
@Katharinski
Merge remote-tracking branch 'joanrue/enh/6_eeg_pipeline_v3.0.0' into…
118f77c 
… enh/6_eeg_pipeline_v3.0.0
@sebastientourbier
ENH: Optimize conda environment of eeg tutorial [skip ci]
c88617f
@sebastientourbier
FIX: Fix issue in eeg config file [skip ci]
a6d5ac1
@sebastientourbier
UPD: Update to use VEPCON in notebook and review a little bit the ins…
4e113a8 
…tructions [skip ci]
@sebastientourbier
Merge branch 'enh/6_eeg_pipeline_v3.0.0' of https://github.com/joanru…
e1edc07 
…e/connectomemapper3 into pr/82
@sebastientourbier
ENH: Add module cmtklib.eeg with function to save connectome files
eff1319
@sebastientourbier
UPD: Update eeg tutorial environment with pyside2
8332d14
@sebastientourbier
DEL: Remove anatomical pipeline confi for eeg tutorial as we use the …
3fbc415 
…one of vepcon
@sebastientourbier
STY: Reformat mne eeg pipeline config file for tutorial
b53e7ac
@sebastientourbier
FIX: Correct saving of eeg connectome files in graphml format
216aeaf
@sebastientourbier
DOC: Update notebook of EEG pipeline with VEPCON and connectome files…
68c9005 
… are saved
@sebastientourbier
FIX: Correct metadata for thumbnail of eeg pipeline notebook [skip ci]
7a8511f
@sebastientourbier
FIX: Correct metadata for thumbnail of eeg pipeline notebook (2nd att…
6101d69 
…empt) [skip ci]
@sebastientourbier
FIX: Add missing comma in cell metadata [skip ci]
67bc8ac
sebastientourbier
sebastientourbier approved these changes Feb 21, 2022
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cmp/stages/eeg/inverse_solution.py Outdated Show resolved Hide resolved
cmp/stages/eeg/loader.py Outdated Show resolved Hide resolved
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docs/notebooks/EEG_tutorial_utils.py Outdated Show resolved Hide resolved
docs/notebooks/EEG_tutorial_utils.py Outdated Show resolved Hide resolved
@sebastientourbier
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This PR is ready to be merged 🚀

I am gonna skip the normal CI pipeline as the EEG pipeline does not impact on it. EEG pipeline and expected outputs have been already checked through the execution of docs/notebooks/EEG_pipeline_tutorial.ipynb with the latest version of this PR (commit 6c3cb92).

Thanks so much @joanrue and @Katharinski for such a hard work and this was definitely a huge effort 👏👏👏!!

@sebastientourbier sebastientourbier merged commit 21af76d into connectomicslab:release/v3.0.3 Feb 21, 2022
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@sebastientourbier sebastientourbier sebastientourbier approved these changes

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@joanrue joanrue

@Katharinski Katharinski

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Implementation of EEG pipeline
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@joanrue @sebastientourbier @Katharinski