Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Mismatch of coord systems between electrodes and channels/events #1082

Open
laemtl opened this issue Oct 14, 2022 · 5 comments
Open

Mismatch of coord systems between electrodes and channels/events #1082

laemtl opened this issue Oct 14, 2022 · 5 comments

Comments

@laemtl
Copy link
Contributor

laemtl commented Oct 14, 2022

Description of the problem

Channel//Epoch data are exported in the ALS coord space to follow the EEGLAB specs.
On the other hand, electrode data are exported in the head/captrak coord space.

Is there any reason to not export the electrode data in the same space?

Steps to reproduce

Exporting an EEGLAB dataset using
write_raw_bids(..., allow_preload=False, overwrite=False, verbose=False)

Link to data

No response

Expected results

Electrode data in the EEGLAB space

Actual results

Electrode data in the Captrak space

Additional information

Platform: Windows-10-10.0.19041-SP0
Python: 3.8.5 (tags/v3.8.5:580fbb0, Jul 20 2020, 15:57:54) [MSC v.1924 64 bit (AMD64)]
Executable: C:\Users\Lae\Documents\hbcd-eeg2bids\Scripts\python.exe
CPU: Intel64 Family 6 Model 142 Stepping 9, GenuineIntel: 4 cores
Memory: Unavailable (requires "psutil" package)
mne: 1.2.0
numpy: 1.20.3 {OpenBLAS 0.3.13.dev with 4 threads}
scipy: 1.9.2
matplotlib: 3.6.1 {backend=TkAgg}

sklearn: 1.1.2
numba: 0.56.2
nibabel: Not found
nilearn: Not found
dipy: Not found
openmeeg: Not found
cupy: Not found
pandas: 1.5.0
pyvista: Not found
pyvistaqt: Not found
ipyvtklink: Not found
vtk: Not found
qtpy: Not found
ipympl: Not found
pyqtgraph: Not found
pooch: v1.6.0

mne_bids: 0.10
mne_nirs: Not found
mne_features: 0.2.1
mne_qt_browser: Not found
mne_connectivity: Not found
mne_icalabel: Not found

@welcome
Copy link

welcome bot commented Oct 14, 2022

Hello! 👋 Thanks for opening your first issue here! ❤️ We will try to get back to you soon. 🚴🏽‍♂️

@laemtl
Copy link
Contributor Author

laemtl commented Oct 14, 2022

@agramfort

@hoechenberger
Copy link
Member

I think that's one for @sappelhoff to tackle 🤠

@sappelhoff
Copy link
Member

I think that's a classic case of "it was complicated and we only implemented what users needed at that time". I am afraid this will need a deep dive into the code base ...

@agramfort
Copy link
Member

@laemtl technically I think we can do what we do but coordinate systems should be given in the sidecar files. Now I don't know if we do it properly.

@laemtl can you share a folder with some data and a script to replicate / investigate and if possible use one of the mne demo datasets. We have some data in CTF format eg https://mne.tools/dev/auto_tutorials/io/60_ctf_bst_auditory.html

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

4 participants