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Hi Alex,<br>
<br>
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I am trying to compare the forward models and signal changes among control vs patients, I only have the T1 scans. I have to make assumed locations for all the channels. I have done recon all, I need something like raw.info and trans file to get it done. If
you have any suggestions, I would appreciate it a lot.<br>
<br>
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Best,<br>
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Feng<br>
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Alexandre Gramfort <alexandre.gramfort@inria.fr><br>
<b>Sent:</b> Friday, December 7, 2018 6:59:10 AM<br>
<b>To:</b> Liu, Feng<br>
<b>Cc:</b> Discussion and support forum for the users of MNE Software<br>
<b>Subject:</b> Re: [Mne_analysis] Convert brainstorm channel .xyz file or sfp file into mne raw fif</font>
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<div class="PlainText"> External Email - Use Caution <br>
<br>
what are you trying to do?<br>
<br>
it seems that you use the sample dataset info for your EEG data which<br>
should not be necessary.<br>
<br>
Alex<br>
On Fri, Dec 7, 2018 at 3:13 AM Liu, Feng <FLIU0@mgh.harvard.edu> wrote:<br>
><br>
> Sorry that I think it is more helpful to post the error message.<br>
><br>
><br>
> montage = mne.channels.read_montage( '/home/scratch/brainstorm_db/Protocol01/data/106a_recon/BioSemi_128_A01.sfp')<br>
> raw.set_montage(montage=montage)<br>
><br>
> ValueError: None of the sensors defined in the montage were found in the info structure. Check the channel names.<br>
><br>
><br>
> This is the structure of raw.info:<br>
><br>
> <Info | 19 non-empty fields<br>
> bads : list | MEG 2443, EEG 053<br>
> ch_names : list | MEG 0113, MEG 0112, MEG 0111, MEG 0122, MEG 0123, ...<br>
> chs : list | 376 items (GRAD: 204, MAG: 102, STIM: 9, EEG: 60, EOG: 1)<br>
> comps : list | 0 items<br>
><br>
><br>
> I think when I use setup_montage, it will check the original channel names, it will assign the value only if the name under montage match the name under raw.info['ch_names']. So do I need to delete all the raw.info['ch_names'] and re-assign channels names?<br>
><br>
><br>
> Best,<br>
><br>
> Feng Liu<br>
><br>
> ________________________________<br>
> From: mne_analysis-bounces@nmr.mgh.harvard.edu <mne_analysis-bounces@nmr.mgh.harvard.edu> on behalf of Liu, Feng <feng.liu@mavs.uta.edu><br>
> Sent: Thursday, December 6, 2018 8:55:39 PM<br>
> To: Alexandre Gramfort; Discussion and support forum for the users of MNE Software<br>
> Subject: Re: [Mne_analysis] Convert brainstorm channel .xyz file or sfp file into mne raw fif<br>
><br>
><br>
> External Email - Use Caution<br>
><br>
> Hi Alex,<br>
><br>
> Thank you for your reply. I can read sfp files using raw.set_montage, do you know should I manually replace the raw.info with the montage information, in the end, I want to build the forward model using mne.make_forward_solution(), as you know this function
requires raw.info as a mandatory input. I thought there should be a link from montage to raw.info.<br>
><br>
> Best regards,<br>
> Feng<br>
> ________________________________<br>
> From: mne_analysis-bounces@nmr.mgh.harvard.edu <mne_analysis-bounces@nmr.mgh.harvard.edu> on behalf of Alexandre Gramfort <alexandre.gramfort@inria.fr><br>
> Sent: Thursday, December 6, 2018 1:31 PM<br>
> To: Discussion and support forum for the users of MNE Software<br>
> Subject: Re: [Mne_analysis] Convert brainstorm channel .xyz file or sfp file into mne raw fif<br>
><br>
> External Email - Use Caution<br>
><br>
> see:<br>
><br>
> <a href="https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmartinos.org%2Fmne%2Fdev%2Fgenerated%2Fmne.channels.read_montage.html&amp;data=02%7C01%7Cfeng.liu%40mavs.uta.edu%7Ccb95432d21b947f4d5ba08d65bb16de0%7C5cdc5b43d7be4caa8173729e3b0a62d9%7C0%7C0%7C636797214942900171&amp;sdata=j6ayJB%2BsHBO8nHke9L2vXXa5s3GH%2Ba%2B%2BWGOerPRZmdQ%3D&amp;reserved=0">
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmartinos.org%2Fmne%2Fdev%2Fgenerated%2Fmne.channels.read_montage.html&amp;data=02%7C01%7Cfeng.liu%40mavs.uta.edu%7Ccb95432d21b947f4d5ba08d65bb16de0%7C5cdc5b43d7be4caa8173729e3b0a62d9%7C0%7C0%7C636797214942900171&amp;sdata=j6ayJB%2BsHBO8nHke9L2vXXa5s3GH%2Ba%2B%2BWGOerPRZmdQ%3D&amp;reserved=0</a><br>
><br>
> and then<br>
><br>
> raw.set_montage<br>
><br>
> should do the job.<br>
><br>
> HTH<br>
> Alex<br>
> On Thu, Dec 6, 2018 at 6:04 PM Liu, Feng <feng.liu@mavs.uta.edu> wrote:<br>
> ><br>
> > External Email - Use Caution<br>
> ><br>
> > Dear MNE community,<br>
> ><br>
> ><br>
> > I want to use a set of electrode channel locations for my subjects. I have channel location files in format of .xyz and .sfp generated from brainstorm (already coregistered), does anyone know how to convert to fif file? I can setup montage by reading sfp
files, but I don't know how to replace the raw.info using the montage information. Also how to get the trans.fif file?<br>
> ><br>
> ><br>
> > Thank you very much for your time<br>
> ><br>
> ><br>
> > Best,<br>
> ><br>
> ><br>
> > Feng Liu<br>
> ><br>
> > _______________________________________________<br>
> > Mne_analysis mailing list<br>
> > Mne_analysis@nmr.mgh.harvard.edu<br>
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