Questions about visualization the coregistration

[system]

Hello,

I am trying to compute head model and forward solution according to this tutorial?http://martinos.org/mne/stable/auto_tutorials/plot_forward.html

But I got an error called ?surface with id 4 not found? when I visualize the coregistration using mne.viz.plot_trans.

Could anyone give any suggestions?

Thank you !

- Daisy
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[system]

hi Daisy,

what you have in the bem folder of your subject?

cf. subjects/sample/bem

for mne sample data.

what command did you run successfully before?

Alex

[system]

Here are documents in bem folder:
sample-head.fif
inner_skull.surf
outer_skin.surf
outer_skull.surf
watershed

I compute BEM surfaces with mne watershed_bem
And then use mkheadsurf and mne_surf2bem to obtain -head.fif
Then -trans.fif was created by mne_analyze

Then I check .surf with mne.viz.plot_bem, it was rcorrect.
Then I want to check .trans ?

import os
os.environ['ETS_TOOLKIT'] = 'qt4'
os.environ['QT_API'] = 'pyqt'
from pyface.qt import QtGui, QtCore

%gui qt
trans='/Users/daisy/Documents/Experiment/feeback_face_meg/S1/zouinyou-trans.fif'
fname_epochs ='/Users/daisy/Documents/Experiment/feeback_face_meg/S1/face_bp2_30-epo.fif'
info = mne.io.read_info(fname_epochs)
mne.viz.plot_trans(info, trans, subject=subject, dig=True,
                  meg_sensors=True, subjects_dir=subjects_dir)

-Daisy

[system]

can you try:

mne.viz.plot_trans(info, trans, subject=subject, dig=True, source='head'
                  meg_sensors=True, subjects_dir=subjects_dir)

also please confirm that you use the latest version of mne-python ie v0.13

Alex

[system]

Thank you so much!

The version of mne-python I use is v0.13??I update it several hours ago
After setting source=?head?,it works

But it still can not plot digitization points. My data was collected from CTF. I am not sure what is wrong here??

-Daisy

[system]

The version of mne-python I use is v0.13??I update it several hours ago
After setting source=?head?,it works

good.

maybe it should have worked out of the box.

But it still can not plot digitization points. My data was collected from CTF. I am not sure what is wrong here??

what do you have in

raw.info['dig']

?

do you see the digitization data in this ?

Alex

[system]

looks like this?

-Daisy

The version of mne-python I use is v0.13??I update it several hours ago
After setting source=?head?,it works

good.

maybe it should have worked out of the box.

But it still can not plot digitization points. My data was collected from CTF. I am not sure what is wrong here??

what do you have in

raw.info['dig']

?

do you see the digitization data in this ?

Alex

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[system]

hi,

so you have only 3 HPI coils. Your other digitized points are not there.

Alex

looks like this?

-Daisy

The version of mne-python I use is v0.13??I update it several hours ago
After setting source=?head?,it works

good.

maybe it should have worked out of the box.

But it still can not plot digitization points. My data was collected from
CTF. I am not sure what is wrong here??

what do you have in

raw.info['dig']

?

do you see the digitization data in this ?

Alex

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Mne_analysis at nmr.mgh.harvard.edu
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The information in this e-mail is intended only for the person to whom it
is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in
error
but does not contain patient information, please contact the sender and
properly
dispose of the e-mail.

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The information in this e-mail is intended only for the person to whom it
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e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
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