[Mne_analysis] Mne_analysis Digest, Vol 148, Issue 35

Mon Jun 1 18:58:33 EDT 2020

        External Email - Use Caution        

  I load the fif file in brainstorm and I have the 2 file as you see in the
attached image raw and channel, if I export them to matlab it seems to be
its extension name .edf and .pos respectively
the idea is to make them again as .fif file
I am interesting to load the fif file so that the info in the coil_def.dat
can be integrated after I made the changes in the channel file
BST team advice me to use the writing functions of the MNE-Matlab toolbox.
and  to ask the MNE-Python community, they might have easier solutions

On Sat, 30 May 2020 at 12:29, Abdallah Qusaibe <abdallah.qusaibe at gmail.com>
wrote:

> 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:
>>
>>    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>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>>         External Email - Use Caution
>>
>> 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
>> Message-ID:
>>         <CAAj1RLuvHLgwsUxzOnSNncy3JhQrNCzYApFXsDo=NZ=
>> 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:
>>         <
>> CAGu2niX6PxW9zcMU1xzkKVtEDTXX9AQMeyd5DTB85CTY_xt+_A at mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>>         External Email - Use Caution
>>
>> >
>> > -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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>
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