[Mne_analysis] Mne_analysis Digest, Vol 148, Issue 35
Abdallah Qusaibe
abdallah.qusaibe at gmail.com
Sat May 30 05:29:25 EDT 2020
External Email - Use Caution
Thank you Eric for your reply,
can you please detail more,
as you in the attachment when I load the fif file in brainstorm then I have
2 file : link to raw file & neuromag channels
those what I want to reconvert to fif file
first of all at which type of file I should export it from brainstorm? and
then what code should In used in mne to convert it to fif file?
thank you for your answer
On Wed, 27 May 2020 at 21:22, <mne_analysis-request at nmr.mgh.harvard.edu>
wrote:
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> Today's Topics:
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> 1. Re: Pyvista foreground bug (Guillaume Favelier)
> 2. write fif files (Abdallah Qusaibe)
> 3. Re: write fif files (Eric Larson)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 27 May 2020 18:27:11 +0200 (CEST)
> From: Guillaume Favelier <guillaume.favelier at inria.fr>
> Subject: Re: [Mne_analysis] Pyvista foreground bug
> To: mne_analysis at nmr.mgh.harvard.edu
> Message-ID:
> <1336394876.9457745.1590596831250.JavaMail.zimbra at inria.fr>
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> Hi! Thanks for the nice feedback!
>
> The revamp of stc plots is still ongoing and some features are still
> missing.
> I investigated and it appears that the 'background' and 'foreground'
> parameters
> are not supported yet by the pyvista 3d backend.
>
> A way to track the progress of this work is on:
>
> https://github.com/mne-tools/mne-python/issues/7162
>
> I will update this list and I believe this should be fixed shortly.
>
> Guillaume
>
> > Dear developers
> >
> > Thanks for a terrific graphical update (pyvista stc plots)
> >
> > One small bug - when changing the background to 'white' and foreground
> > to 'black', text is not formatted accordingly (works as intended in
> > mayavi) (see images below)
> >
> > All the best
> >
> > Lau
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> Message: 2
> Date: Wed, 27 May 2020 19:56:12 +0300
> From: Abdallah Qusaibe <abdallah.qusaibe at gmail.com>
> Subject: [Mne_analysis] write fif files
> To: mne_analysis at nmr.mgh.harvard.edu
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> hhCBrqg at mail.gmail.com>
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> Dear mne programmers,
>
>
> I load from a tutorial in brainstorm the fif file:
> mind004_050924_median01_raw.fif
> as you seen in the attached image after loading we have the channel and raw
> file
>
>
> The information from the file coil_def.dat is integrated in the channel
> file when loading data from CTF .res4 or Elekta .fif files. But in my case
> I I edited the coil_def.dat file and aslo I edited the channel file after
> loading the fif file mind004_050924_median01_raw.fif,
>
> My questions:
>
> -Brainstorm does not provide any FIF writer. How can I write those file in
> MNE Python?
> -How can I deal with problem in mne ? editing the meg channel files and
> coil_def.dat channel, and making the information from the file
> coil_def.dat is integrated in the channel file then compute the forward
> problem?
>
> Best regards
> A
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> ------------------------------
>
> Message: 3
> Date: Wed, 27 May 2020 14:21:16 -0400
> From: Eric Larson <larson.eric.d at gmail.com>
> Subject: Re: [Mne_analysis] write fif files
> To: Discussion and support forum for the users of MNE Software
> <mne_analysis at nmr.mgh.harvard.edu>
> Message-ID:
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> CAGu2niX6PxW9zcMU1xzkKVtEDTXX9AQMeyd5DTB85CTY_xt+_A at mail.gmail.com>
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> >
> > -Brainstorm does not provide any FIF writer. How can I write those file
> > in MNE Python?
> >
>
> Read, edit, save:
>
> raw = mne.io.read_raw_fif(...) # filename, etc.
> raw.info['chs'][idx][...] = ... # edit however you need
> raw.save(...) # write to some new filename
>
>
> > -How can I deal with problem in mne ? editing the meg channel files and
> > coil_def.dat channel, and making the information from the file
> > coil_def.dat is integrated in the channel file then compute the forward
> > problem?
> >
>
> Make your own coil_def.dat and use
> https://mne.tools/stable/generated/mne.use_coil_def.html, see for example
>
> https://mne.tools/stable/auto_examples/datasets/plot_opm_data.html#sphx-glr-auto-examples-datasets-plot-opm-data-py
>
> Eric
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