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[ENH, MRG] Clarify intracranial narrative for why individual coordinates are preferred #975

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merged 6 commits into from
Mar 7, 2022

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alexrockhill
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@alexrockhill alexrockhill commented Mar 3, 2022

Covering the use of the Talairach transform for intracranial data without pointing out that it's quite inaccurate and citing examples MNE-Python was fixed because it's misleading to present it as just as good without comment.

Merge checklist

Maintainer, please confirm the following before merging:

  • All comments resolved
  • This is not your own PR
  • All CIs are happy
  • PR title starts with [MRG]
  • whats_new.rst is updated
  • PR description includes phrase "closes <#issue-number>"

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codecov bot commented Mar 3, 2022

Codecov Report

Merging #975 (90caa3c) into main (d298752) will increase coverage by 0.05%.
The diff coverage is n/a.

Impacted file tree graph

@@            Coverage Diff             @@
##             main     #975      +/-   ##
==========================================
+ Coverage   94.58%   94.63%   +0.05%     
==========================================
  Files          25       25              
  Lines        3584     3600      +16     
==========================================
+ Hits         3390     3407      +17     
+ Misses        194      193       -1     
Impacted Files Coverage Δ
mne_bids/config.py 97.46% <0.00%> (ø)
mne_bids/read.py 96.16% <0.00%> (+0.04%) ⬆️
mne_bids/utils.py 96.53% <0.00%> (+0.10%) ⬆️
mne_bids/dig.py 91.37% <0.00%> (+0.74%) ⬆️

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doc/whats_new.rst Outdated Show resolved Hide resolved
examples/convert_ieeg_to_bids.py Outdated Show resolved Hide resolved
examples/convert_ieeg_to_bids.py Outdated Show resolved Hide resolved
@@ -282,6 +292,7 @@
raw = mne.io.read_raw_fif(op.join(
misc_path, 'seeg', 'sample_seeg_ieeg.fif'))
raw.info['line_freq'] = 60 # specify power line frequency as required by BIDS
raw.set_channel_types({ch: 'ecog' for ch in raw.ch_names}) # fake intracranial
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why do you need this?

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It seems like it makes sense for it to be intracranial data in the raw file. This really should be checked by mne-bids that the data type matches too

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In the BIDSPath matches the raw file

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Why isn't the channel type set correctly automatically when reading the file with MNE? Is there a problem with the data? Or a bug with MNE?

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Okay to merge?

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I should read that more carefully I thought it was the meg and eeg sample data, I'll fix in asap.

@agramfort agramfort merged commit 66a568f into mne-tools:main Mar 7, 2022
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thx @alexrockhill

@alexrockhill alexrockhill deleted the ieeg branch March 7, 2022 16:15
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3 participants