[Mne_analysis] mismatch of coregistration from Brainstorm to MNE-python

[Liu, Feng]

Thank you.


Q: is this alignment in brainstorm coming from a template EEG cap?

A: Yes, it is from a template EEG cap and then I coregistered with a brain in brainstorm which aligns extremely well, now I figured out brainstorm use a Subject Coordinate System (SCS) for each subject, mapping back is very tricky.


I think I have to do it manually again in mne-python gui.


Best,

Feng

________________________________
From: mne_analysis-bounces at nmr.mgh.harvard.edu <mne_analysis-bounces at nmr.mgh.harvard.edu> on behalf of Alexandre Gramfort <alexandre.gramfort at inria.fr>
Sent: Monday, December 17, 2018 7:23:55 AM
To: Discussion and support forum for the users of MNE Software
Subject: Re: [Mne_analysis] mismatch of coregistration from Brainstorm to MNE-python


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is this alignment in brainstorm coming from a template EEG cap? or uses 3D digitization of electrodes?

yes you will need a trans file

Alex



On Sun, Dec 16, 2018 at 11:35 PM Liu, Feng <FLIU0 at mgh.harvard.edu<mailto:FLIU0 at mgh.harvard.edu>> wrote:

Dear MNE-Python List,


I finished EEG electrodes registration using brainstorm as I am more familiar to brainstorm and exported the channel coordinates to a .sfp file.


Then I read .sfp file  into mne-python, I used plot_alignment to visualize the coregistration.

fig = plot_alignment(myinfo,  subject=mysubject, subjects_dir=elder_sub_dir)


I found the following mismached plots:


[cid:167bc1e60212b1f06e71]



I found I miss some trans file, is that the reason the second plot is not aligned well? Do I need to do it manually generate using mne.gui.coregistration(), as I have many subjects, do we have more efficient ways?



Best regards,

Feng


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