[Mne_analysis] Convert brainstorm channel .xyz file or sfp file into mne raw fif

[Alexandre Gramfort]

        External Email - Use Caution        

what are you trying to do?

it seems that you use the sample dataset info for your EEG data which
should not be necessary.

Alex
On Fri, Dec 7, 2018 at 3:13 AM Liu, Feng <FLIU0 at mgh.harvard.edu> wrote:
>
> Sorry that I think it is more helpful to post the error message.
>
>
> montage = mne.channels.read_montage( '/home/scratch/brainstorm_db/Protocol01/data/106a_recon/BioSemi_128_A01.sfp')
> raw.set_montage(montage=montage)
>
> ValueError: None of the sensors defined in the montage were found in the info structure. Check the channel names.
>
>
> This is the structure of raw.info:
>
> <Info | 19 non-empty fields
>     bads : list | MEG 2443, EEG 053
>     ch_names : list | MEG 0113, MEG 0112, MEG 0111, MEG 0122, MEG 0123, ...
>     chs : list | 376 items (GRAD: 204, MAG: 102, STIM: 9, EEG: 60, EOG: 1)
>     comps : list | 0 items
>
>
> 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?
>
>
> Best,
>
> Feng Liu
>
> ________________________________
> From: mne_analysis-bounces at nmr.mgh.harvard.edu <mne_analysis-bounces at nmr.mgh.harvard.edu> on behalf of Liu, Feng <feng.liu at mavs.uta.edu>
> Sent: Thursday, December 6, 2018 8:55:39 PM
> To: Alexandre Gramfort; Discussion and support forum for the users of MNE Software
> Subject: Re: [Mne_analysis] Convert brainstorm channel .xyz file or sfp file into mne raw fif
>
>
>         External Email - Use Caution
>
> Hi Alex,
>
> 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.
>
> Best regards,
> 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: Thursday, December 6, 2018 1:31 PM
> To: Discussion and support forum for the users of MNE Software
> Subject: Re: [Mne_analysis] Convert brainstorm channel .xyz file or sfp file into mne raw fif
>
>         External Email - Use Caution
>
> see:
>
> 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
>
> and then
>
> raw.set_montage
>
> should do the job.
>
> HTH
> Alex
> On Thu, Dec 6, 2018 at 6:04 PM Liu, Feng <feng.liu at mavs.uta.edu> wrote:
> >
> >         External Email - Use Caution
> >
> > Dear MNE community,
> >
> >
> > 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?
> >
> >
> > Thank you very much for your time
> >
> >
> > Best,
> >
> >
> > Feng Liu
> >
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