<p><span style="padding: 3px 10px; border-radius: 5px; color: #ffffff; font-weight: bold; display: inline-block; background-color: #ff0000;"> External Email - Use Caution </span></p><p></p><div dir="ltr">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:<div><br></div><div><a href="https://mne.tools/stable/overview/matlab.html">https://mne.tools/stable/overview/matlab.html</a><br></div><div><br></div><div>Eric</div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Jun 1, 2020 at 8:01 PM Abdallah Qusaibe <<a href="mailto:abdallah.qusaibe@gmail.com">abdallah.qusaibe@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><p><span style="padding:3px 10px;border-radius:5px;color:rgb(255,255,255);font-weight:bold;display:inline-block;background-color:rgb(255,0,0)"> External Email - Use Caution </span></p><p></p><div dir="ltr">
<div><span style="color:rgb(34,34,34);font-family:Helvetica,Arial,sans-serif;font-size:15px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;display:inline;float:none"></span></div><div><span style="color:rgb(34,34,34);font-family:Helvetica,Arial,sans-serif;font-size:15px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;display:inline;float:none">
<span style="color:rgb(34,34,34);font-family:Helvetica,Arial,sans-serif;font-size:15px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;display:inline;float:none">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</span><br style="color:rgb(34,34,34);font-family:Helvetica,Arial,sans-serif;font-size:15px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial"><span style="color:rgb(34,34,34);font-family:Helvetica,Arial,sans-serif;font-size:15px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;display:inline;float:none">the idea is to make them again as .fif file</span><br style="color:rgb(34,34,34);font-family:Helvetica,Arial,sans-serif;font-size:15px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial"><span style="color:rgb(34,34,34);font-family:Helvetica,Arial,sans-serif;font-size:15px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;display:inline;float:none">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</span></span></div><div><span style="color:rgb(34,34,34);font-family:Helvetica,Arial,sans-serif;font-size:15px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;display:inline;float:none"><span style="color:rgb(34,34,34);font-family:Helvetica,Arial,sans-serif;font-size:15px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;display:inline;float:none">BST team advice me
to use the writing functions of the MNE-Matlab toolbox.
and <span style="color:rgb(34,34,34);font-family:Helvetica,Arial,sans-serif;font-size:15px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;display:inline;float:none">to ask the MNE-Python community, they might have easier solutions</span><br></span></span></div><div><span style="color:rgb(34,34,34);font-family:Helvetica,Arial,sans-serif;font-size:15px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;display:inline;float:none"><span style="color:rgb(34,34,34);font-family:Helvetica,Arial,sans-serif;font-size:15px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration-style:initial;text-decoration-color:initial;display:inline;float:none"></span>
</span></div>
</div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sat, 30 May 2020 at 12:29, Abdallah Qusaibe <<a href="mailto:abdallah.qusaibe@gmail.com" target="_blank">abdallah.qusaibe@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>Thank you Eric for your reply,</div><div>can you please detail more,</div><div>as you in the attachment when I load the fif file in brainstorm then I have 2 file : link to raw file & neuromag channels</div><div>those what I want to reconvert to fif file</div><div>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?</div><div><br></div><div>thank you for your answer<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, 27 May 2020 at 21:22, <<a href="mailto:mne_analysis-request@nmr.mgh.harvard.edu" target="_blank">mne_analysis-request@nmr.mgh.harvard.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Send Mne_analysis mailing list submissions to<br>
<a href="mailto:mne_analysis@nmr.mgh.harvard.edu" target="_blank">mne_analysis@nmr.mgh.harvard.edu</a><br>
<br>
To subscribe or unsubscribe via the World Wide Web, visit<br>
<a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" rel="noreferrer" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a><br>
or, via email, send a message with subject or body 'help' to<br>
<a href="mailto:mne_analysis-request@nmr.mgh.harvard.edu" target="_blank">mne_analysis-request@nmr.mgh.harvard.edu</a><br>
<br>
You can reach the person managing the list at<br>
<a href="mailto:mne_analysis-owner@nmr.mgh.harvard.edu" target="_blank">mne_analysis-owner@nmr.mgh.harvard.edu</a><br>
<br>
When replying, please edit your Subject line so it is more specific<br>
than "Re: Contents of Mne_analysis digest..."<br>
<br>
<br>
Today's Topics:<br>
<br>
1. Re: Pyvista foreground bug (Guillaume Favelier)<br>
2. write fif files (Abdallah Qusaibe)<br>
3. Re: write fif files (Eric Larson)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Wed, 27 May 2020 18:27:11 +0200 (CEST)<br>
From: Guillaume Favelier <<a href="mailto:guillaume.favelier@inria.fr" target="_blank">guillaume.favelier@inria.fr</a>><br>
Subject: Re: [Mne_analysis] Pyvista foreground bug<br>
To: <a href="mailto:mne_analysis@nmr.mgh.harvard.edu" target="_blank">mne_analysis@nmr.mgh.harvard.edu</a><br>
Message-ID:<br>
<<a href="mailto:1336394876.9457745.1590596831250.JavaMail.zimbra@inria.fr" target="_blank">1336394876.9457745.1590596831250.JavaMail.zimbra@inria.fr</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
External Email - Use Caution <br>
<br>
Hi! Thanks for the nice feedback! <br>
<br>
The revamp of stc plots is still ongoing and some features are still missing. <br>
I investigated and it appears that the 'background' and 'foreground' parameters <br>
are not supported yet by the pyvista 3d backend. <br>
<br>
A way to track the progress of this work is on: <br>
<br>
<a href="https://github.com/mne-tools/mne-python/issues/7162" rel="noreferrer" target="_blank">https://github.com/mne-tools/mne-python/issues/7162</a> <br>
<br>
I will update this list and I believe this should be fixed shortly. <br>
<br>
Guillaume <br>
<br>
> Dear developers <br>
> <br>
> Thanks for a terrific graphical update (pyvista stc plots) <br>
> <br>
> One small bug - when changing the background to 'white' and foreground <br>
> to 'black', text is not formatted accordingly (works as intended in <br>
> mayavi) (see images below) <br>
> <br>
> All the best <br>
> <br>
> Lau <br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <a href="http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20200527/2d66be3c/attachment-0001.html" rel="noreferrer" target="_blank">http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20200527/2d66be3c/attachment-0001.html</a> <br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Wed, 27 May 2020 19:56:12 +0300<br>
From: Abdallah Qusaibe <<a href="mailto:abdallah.qusaibe@gmail.com" target="_blank">abdallah.qusaibe@gmail.com</a>><br>
Subject: [Mne_analysis] write fif files<br>
To: <a href="mailto:mne_analysis@nmr.mgh.harvard.edu" target="_blank">mne_analysis@nmr.mgh.harvard.edu</a><br>
Message-ID:<br>
<CAAj1RLuvHLgwsUxzOnSNncy3JhQrNCzYApFXsDo=NZ=<a href="mailto:hhCBrqg@mail.gmail.com" target="_blank">hhCBrqg@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
External Email - Use Caution <br>
<br>
Dear mne programmers,<br>
<br>
<br>
I load from a tutorial in brainstorm the fif file:<br>
mind004_050924_median01_raw.fif<br>
as you seen in the attached image after loading we have the channel and raw<br>
file<br>
<br>
<br>
The information from the file coil_def.dat is integrated in the channel<br>
file when loading data from CTF .res4 or Elekta .fif files. But in my case<br>
I I edited the coil_def.dat file and aslo I edited the channel file after<br>
loading the fif file mind004_050924_median01_raw.fif,<br>
<br>
My questions:<br>
<br>
-Brainstorm does not provide any FIF writer. How can I write those file in<br>
MNE Python?<br>
-How can I deal with problem in mne ? editing the meg channel files and<br>
coil_def.dat channel, and making the information from the file<br>
coil_def.dat is integrated in the channel file then compute the forward<br>
problem?<br>
<br>
Best regards<br>
A<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <a href="http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20200527/6a771a3b/attachment-0001.html" rel="noreferrer" target="_blank">http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20200527/6a771a3b/attachment-0001.html</a> <br>
-------------- next part --------------<br>
A non-text attachment was scrubbed...<br>
Name: loading.png<br>
Type: image/png<br>
Size: 5019 bytes<br>
Desc: not available<br>
Url : <a href="http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20200527/6a771a3b/attachment-0001.png" rel="noreferrer" target="_blank">http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20200527/6a771a3b/attachment-0001.png</a> <br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Wed, 27 May 2020 14:21:16 -0400<br>
From: Eric Larson <<a href="mailto:larson.eric.d@gmail.com" target="_blank">larson.eric.d@gmail.com</a>><br>
Subject: Re: [Mne_analysis] write fif files<br>
To: Discussion and support forum for the users of MNE Software<br>
<<a href="mailto:mne_analysis@nmr.mgh.harvard.edu" target="_blank">mne_analysis@nmr.mgh.harvard.edu</a>><br>
Message-ID:<br>
<<a href="mailto:CAGu2niX6PxW9zcMU1xzkKVtEDTXX9AQMeyd5DTB85CTY_xt%2B_A@mail.gmail.com" target="_blank">CAGu2niX6PxW9zcMU1xzkKVtEDTXX9AQMeyd5DTB85CTY_xt+_A@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
External Email - Use Caution <br>
<br>
><br>
> -Brainstorm does not provide any FIF writer. How can I write those file<br>
> in MNE Python?<br>
><br>
<br>
Read, edit, save:<br>
<br>
raw = mne.io.read_raw_fif(...) # filename, etc.<br>
<a href="http://raw.info" rel="noreferrer" target="_blank">raw.info</a>['chs'][idx][...] = ... # edit however you need<br>
raw.save(...) # write to some new filename<br>
<br>
<br>
> -How can I deal with problem in mne ? editing the meg channel files and<br>
> coil_def.dat channel, and making the information from the file<br>
> coil_def.dat is integrated in the channel file then compute the forward<br>
> problem?<br>
><br>
<br>
Make your own coil_def.dat and use<br>
<a href="https://mne.tools/stable/generated/mne.use_coil_def.html" rel="noreferrer" target="_blank">https://mne.tools/stable/generated/mne.use_coil_def.html</a>, see for example<br>
<a href="https://mne.tools/stable/auto_examples/datasets/plot_opm_data.html#sphx-glr-auto-examples-datasets-plot-opm-data-py" rel="noreferrer" target="_blank">https://mne.tools/stable/auto_examples/datasets/plot_opm_data.html#sphx-glr-auto-examples-datasets-plot-opm-data-py</a><br>
<br>
Eric<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <a href="http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20200527/168cf530/attachment.html" rel="noreferrer" target="_blank">http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20200527/168cf530/attachment.html</a> <br>
<br>
------------------------------<br>
<br>
_______________________________________________<br>
Mne_analysis mailing list<br>
<a href="mailto:Mne_analysis@nmr.mgh.harvard.edu" target="_blank">Mne_analysis@nmr.mgh.harvard.edu</a><br>
<a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" rel="noreferrer" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a><br>
<br>
End of Mne_analysis Digest, Vol 148, Issue 35<br>
*********************************************<br>
</blockquote></div>
</blockquote></div>
_______________________________________________<br>
Mne_analysis mailing list<br>
<a href="mailto:Mne_analysis@nmr.mgh.harvard.edu" target="_blank">Mne_analysis@nmr.mgh.harvard.edu</a><br>
<a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" rel="noreferrer" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a></blockquote></div>