# Questions about visualization the coregistration **URL:** \ **Category:** Mailing List Archive (read-only)\ **Tags:** list-archive\ **Created:** [October 20, 2016, 4:02am UTC](https://mne.discourse.group/t/questions-about-visualization-the-coregistration/1101 "2016-10-20T04:02:03Z")\ **Posts on this page:** 8\ **Page:** 1
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [October 20, 2016, 4:02am UTC](https://mne.discourse.group/t/questions-about-visualization-the-coregistration/1101/1 "2016-10-20T04:02:03Z")
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](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 -------------- next part -------------- An HTML attachment was scrubbed... URL: [http://mail.nmr.mgh.harvard.edu/pipermail/mne\_analysis/attachments/20161020/a1ef5ad4/attachment.html](http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20161020/a1ef5ad4/attachment.html) ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [October 20, 2016, 6:27am UTC](https://mne.discourse.group/t/questions-about-visualization-the-coregistration/1101/2 "2016-10-20T06:27:53Z")
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 ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [October 20, 2016, 6:49am UTC](https://mne.discourse.group/t/questions-about-visualization-the-coregistration/1101/3 "2016-10-20T06:49:03Z")
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 ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [October 20, 2016, 7:05am UTC](https://mne.discourse.group/t/questions-about-visualization-the-coregistration/1101/4 "2016-10-20T07:05:28Z")
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 ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [October 20, 2016, 7:34am UTC](https://mne.discourse.group/t/questions-about-visualization-the-coregistration/1101/5 "2016-10-20T07:34:20Z")
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 ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [October 20, 2016, 8:17am UTC](https://mne.discourse.group/t/questions-about-visualization-the-coregistration/1101/6 "2016-10-20T08:17:27Z")
> 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 ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [October 20, 2016, 8:30am UTC](https://mne.discourse.group/t/questions-about-visualization-the-coregistration/1101/7 "2016-10-20T08:30:19Z")
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 > > \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ > Mne\_analysis mailing list > Mne\_analysis at nmr.mgh.harvard.edu > [https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne\_analysis](https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis) > > 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](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. -------------- next part -------------- An HTML attachment was scrubbed... URL: [http://mail.nmr.mgh.harvard.edu/pipermail/mne\_analysis/attachments/20161020/f49a21f3/attachment-0001.html](http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20161020/f49a21f3/attachment-0001.html) -------------- next part -------------- A non-text attachment was scrubbed... Name: PastedGraphic-1.png Type: image/png Size: 84456 bytes Desc: not available Url : [http://mail.nmr.mgh.harvard.edu/pipermail/mne\_analysis/attachments/20161020/f49a21f3/attachment-0001.png](http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20161020/f49a21f3/attachment-0001.png) ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [October 20, 2016, 12:08pm UTC](https://mne.discourse.group/t/questions-about-visualization-the-coregistration/1101/8 "2016-10-20T12:08:59Z")
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 > > \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ > Mne\_analysis mailing list > Mne\_analysis at nmr.mgh.harvard.edu > [https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne\_analysis](https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis) > > 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](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. > > \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ > Mne\_analysis mailing list > Mne\_analysis at nmr.mgh.harvard.edu > [https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne\_analysis](https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis) > > 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](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. -------------- next part -------------- An HTML attachment was scrubbed... URL: [http://mail.nmr.mgh.harvard.edu/pipermail/mne\_analysis/attachments/20161020/c60dfb56/attachment-0001.html](http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20161020/c60dfb56/attachment-0001.html) -------------- next part -------------- A non-text attachment was scrubbed... Name: PastedGraphic-1.png Type: image/png Size: 84456 bytes Desc: not available Url : [http://mail.nmr.mgh.harvard.edu/pipermail/mne\_analysis/attachments/20161020/c60dfb56/attachment-0001.png](http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20161020/c60dfb56/attachment-0001.png)