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

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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<http://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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see:

https://martinos.org/mne/dev/generated/mne.channels.read_montage.html

and then

raw.set_montage

should do the job.

HTH
Alex

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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

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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

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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

6

Hi Alex,

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.

Best,
Feng

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I would suggest your read our documentation about Measurement Info,
coregistration and how to use freesurfer

since you're at MGH you can certainly go see Sheraz Khan for help

Alex

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Sure, definitely. I will read through the documentation, if I can't figure out, I will ask Sheraz, he knows everything.

Thanks again,

Best
Feng