[Mne_analysis] Mne_analysis Digest, Vol 148, Issue 35
Eric Larson
larson.eric.d at gmail.com
Wed Jun 3 12:56:52 EDT 2020
External Email - Use Caution
You could try using the MNE-MATLAB functions (I think they come bundled
with Brainstorm?), feel free to read here to see if you can put something
together that will work:
https://mne.tools/stable/overview/matlab.html
Eric
On Mon, Jun 1, 2020 at 8:01 PM Abdallah Qusaibe <abdallah.qusaibe at gmail.com>
wrote:
> 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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>>> External Email - Use Caution
>>>
>>> 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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