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<body lang="FR" link="blue" vlink="purple"><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>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Dear MNE users, dear all,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">We are hiring a post doc in our lab in Grenoble (France), a beautiful city in the center of Alpes mountains !
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">The position is funded by the regional council Auvergne Rhone Alpes.
</span><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">The post is currently for 12 months with possibility for further extension (6 or 12 months).
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">You will work on He4 OPM for MEG imaging, in collaboration with the Center of Research in Neurosciences in Lyon. You will contribute
to MEG experiments and the data processing.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Attached to this mail the job description and contacts.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Two other positions are also available, more focused on instrumentation and engineering.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">We hope that this position will excite some of you ! <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Best regards<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">De :</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> mne_analysis-bounces@nmr.mgh.harvard.edu <mne_analysis-bounces@nmr.mgh.harvard.edu>
<b>De la part de</b> Alexandre Gramfort<br>
<b>Envoyé :</b> vendredi 27 septembre 2019 09:15<br>
<b>À :</b> Discussion and support forum for the users of MNE Software <mne_analysis@nmr.mgh.harvard.edu><br>
<b>Objet :</b> Re: [Mne_analysis] Digitization and Channel Positions<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p><b><span style="color:white;background:red"> External Email - Use Caution </span></b><o:p></o:p></p>
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<p class="MsoNormal">Dear Jason,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">if you now use version 0.19 you should be using:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><a href="https://mne.tools/stable/generated/mne.channels.read_dig_polhemus_isotrak.html#mne.channels.read_dig_polhemus_isotrak">https://mne.tools/stable/generated/mne.channels.read_dig_polhemus_isotrak.html#mne.channels.read_dig_polhemus_isotrak</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">something like:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">montage = mne.channels.read_dig_polhemus_isotrak(fname)<o:p></o:p></p>
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<p class="MsoNormal">raw.set_montage(montage)<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">should just work. If not please open an issue on github<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Alex<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal">On Fri, Sep 27, 2019 at 12:50 AM Geller, Jason <<a href="mailto:jason-geller@uiowa.edu">jason-geller@uiowa.edu</a>> wrote:<o:p></o:p></p>
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<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt">
<p class="MsoNormal"> External Email - Use Caution <br>
<br>
Hello, <br>
<br>
I am creating digitization montage files I obtained from a Polhemus system using the read_dig_montage and setting it with set_montage(rawfile, set_dig=True). When I go to run ICA, I get this warning:
<br>
<br>
WARNING:root:Did not find any electrode locations (in the info object), will attempt to use digitization points instead. However, if digitization points do not correspond to the EEG electrodes, this will lead to bad results. Please verify that the sensor locations
in the plot are accurate.<br>
<br>
My question is: how do I set the channel positions for a dig montage? Any help would be greatly appreciated.
<br>
<br>
Thanks, <br>
<br>
J <br>
<br>
<br>
> On Sep 26, 2019, at 5:35 PM, <a href="mailto:mne_analysis-request@nmr.mgh.harvard.edu" target="_blank">
mne_analysis-request@nmr.mgh.harvard.edu</a> wrote:<br>
> <br>
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> Today's Topics:<br>
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> 1. Re: mne.minimum_norm.compute_source_psd (Dan McCloy)<br>
> 2. Re: mne.minimum_norm.compute_source_psd (Vivek Sharma)<br>
> <br>
> <br>
> ----------------------------------------------------------------------<br>
> <br>
> Message: 1<br>
> Date: Thu, 26 Sep 2019 11:30:04 -0700<br>
> From: Dan McCloy <<a href="mailto:dan.mccloy@gmail.com" target="_blank">dan.mccloy@gmail.com</a>><br>
> Subject: Re: [Mne_analysis] mne.minimum_norm.compute_source_psd<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>
> <CAOE0pYk7QJxJvsOD5QR1pg0HNObfDjnLh=<a href="mailto:CnCwB_roJ07DZt3A@mail.gmail.com" target="_blank">CnCwB_roJ07DZt3A@mail.gmail.com</a>><br>
> Content-Type: text/plain; charset="utf-8"<br>
> <br>
> External Email - Use Caution <br>
> <br>
> Ah, Victor is right. Sorry Vivek for giving you the wrong advice; I looked<br>
> only at the repr of the object, which had a tmin, tmax, and tstep; I didn't<br>
> dig through the example that got you there.<br>
> <br>
> On Thu, Sep 26, 2019 at 3:30 AM Victor Ferat <<a href="mailto:victor.ferat@fcbg.ch" target="_blank">victor.ferat@fcbg.ch</a>> wrote:<br>
> <br>
>> External Email - Use Caution<br>
>> <br>
>> It should be the number of frequencies.<br>
>> For each source (8064) you have 1025 values of power density, one per<br>
>> frequency . (frequencies ranging from 0 Hz to 100Hz with 97.65625mHz step).<br>
>> This tutorial<br>
>> <<a href="https://www.nmr.mgh.harvard.edu/mne/stable/auto_examples/time_frequency/plot_source_power_spectrum.html#sphx-glr-auto-examples-time-frequency-plot-source-power-spectrum-py" target="_blank">https://www.nmr.mgh.harvard.edu/mne/stable/auto_examples/time_frequency/plot_source_power_spectrum.html#sphx-glr-auto-examples-time-frequency-plot-source-power-spectrum-py</a>><br>
>> should help you understand how it works ( especially the last plot)<br>
>> <br>
>> <br>
>> Best,<br>
>> Victor<br>
>> ------------------------------<br>
>> *From:* <a href="mailto:mne_analysis-bounces@nmr.mgh.harvard.edu" target="_blank">
mne_analysis-bounces@nmr.mgh.harvard.edu</a> <<br>
>> <a href="mailto:mne_analysis-bounces@nmr.mgh.harvard.edu" target="_blank">mne_analysis-bounces@nmr.mgh.harvard.edu</a>> on behalf of Vivek Sharma <<br>
>> <a href="mailto:vivek.sharma1510@gmail.com" target="_blank">vivek.sharma1510@gmail.com</a>><br>
>> *Sent:* Thursday, September 26, 2019 8:17 AM<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>
>> *Subject:* Re: [Mne_analysis] mne.minimum_norm.compute_source_psd<br>
>> <br>
>> <br>
>> External Email - Use Caution<br>
>> <br>
>> The total time I have considered is 574 seconds so how it is related to<br>
>> 1025 time points.<br>
>> <br>
>> On Wed, Sep 25, 2019 at 8:46 PM Daniel McCloy <<a href="mailto:dan.mccloy@gmail.com" target="_blank">dan.mccloy@gmail.com</a>><br>
>> wrote:<br>
>> <br>
>> External Email - Use Caution<br>
>> <br>
>> It is the number of time points.<br>
>> <br>
>> On September 25, 2019 2:27:52 AM PDT, Vivek Sharma <<br>
>> <a href="mailto:vivek.sharma1510@gmail.com" target="_blank">vivek.sharma1510@gmail.com</a>> wrote:<br>
>>> External Email - Use Caution<br>
>>> <br>
>>> In continuation of the above thread, I unable to understand what does<br>
>>> 1025<br>
>>> mean in data shape.<br>
>>> <SourceEstimate | 8064 vertices, subject : Collin, tmin : 0.0 (ms),<br>
>>> tmax<br>
>>> : 100000.0 (ms), tstep : 97.65625 (ms),<br>
>>> *data shape : (8064, 1025)>*<br>
>>> <br>
>>> <br>
>>> On Fri, Jun 14, 2019 at 4:33 PM Vivek Sharma<br>
>>> <<a href="mailto:vivek.sharma1510@gmail.com" target="_blank">vivek.sharma1510@gmail.com</a>><br>
>>> wrote:<br>
>>> <br>
>>>> Thank You.<br>
>>>> <br>
>>>> On Wed, Jun 12, 2019 at 11:53 AM Alexandre Gramfort <<br>
>>>> <a href="mailto:alexandre.gramfort@inria.fr" target="_blank">alexandre.gramfort@inria.fr</a>> wrote:<br>
>>>> <br>
>>>>> External Email - Use Caution<br>
>>>>> <br>
>>>>> hi,<br>
>>>>> <br>
>>>>> this function hacks a SourceEstimate object : stc_psd to store PSDs.<br>
>>> So<br>
>>>>> what you read<br>
>>>>> with time:<br>
>>>>> <br>
>>>>> <SourceEstimate | 8064 vertices, subject : Collin, tmin : 0.0<br>
>>> (ms),<br>
>>>>> tmax : 100000.0 (ms), tstep : 97.65625 (ms), data shape : (8064,<br>
>>> 1025)><br>
>>>>> <br>
>>>>> should be:<br>
>>>>> <br>
>>>>> <SourceEstimate | 8064 vertices, subject : Collin, fmin : 0.0<br>
>>> (Hz),<br>
>>>>> fmax : 100000.0 (mHz), fstep : 97.65625 (mHz), data shape : (8064,<br>
>>> 1025)><br>
>>>>> <br>
>>>>> HTH<br>
>>>>> Alex<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" target="_blank">
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a><br>
>>>> <br>
>>>> <br>
>>>> <br>
>>>> --<br>
>>>> Vivek Sharma<br>
>>>> <br>
>>> <br>
>>> <br>
>>> --<br>
>>> Vivek Sharma<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" target="_blank">
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a><br>
>> <br>
>> <br>
>> <br>
>> --<br>
>> Vivek Sharma<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" target="_blank">
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a><br>
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> <br>
> ------------------------------<br>
> <br>
> Message: 2<br>
> Date: Fri, 27 Sep 2019 04:05:30 +0530<br>
> From: Vivek Sharma <<a href="mailto:vivek.sharma1510@gmail.com" target="_blank">vivek.sharma1510@gmail.com</a>><br>
> Subject: Re: [Mne_analysis] mne.minimum_norm.compute_source_psd<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>
> <CAKzh67FKy0ShTSUCEO496cZF7K-7QJbzNT6fmKC_7=<a href="mailto:KVY6v31Q@mail.gmail.com" target="_blank">KVY6v31Q@mail.gmail.com</a>><br>
> Content-Type: text/plain; charset="utf-8"<br>
> <br>
> External Email - Use Caution <br>
> <br>
> Hi,<br>
> Thanks for the information.<br>
> <br>
> On Fri, Sep 27, 2019 at 12:00 AM Dan McCloy <<a href="mailto:dan.mccloy@gmail.com" target="_blank">dan.mccloy@gmail.com</a>> wrote:<br>
> <br>
>> External Email - Use Caution<br>
>> <br>
>> Ah, Victor is right. Sorry Vivek for giving you the wrong advice; I<br>
>> looked only at the repr of the object, which had a tmin, tmax, and tstep; I<br>
>> didn't dig through the example that got you there.<br>
>> <br>
>> On Thu, Sep 26, 2019 at 3:30 AM Victor Ferat <<a href="mailto:victor.ferat@fcbg.ch" target="_blank">victor.ferat@fcbg.ch</a>> wrote:<br>
>> <br>
>>> External Email - Use Caution<br>
>>> <br>
>>> It should be the number of frequencies.<br>
>>> For each source (8064) you have 1025 values of power density, one per<br>
>>> frequency . (frequencies ranging from 0 Hz to 100Hz with 97.65625mHz step).<br>
>>> This tutorial<br>
>>> <<a href="https://www.nmr.mgh.harvard.edu/mne/stable/auto_examples/time_frequency/plot_source_power_spectrum.html#sphx-glr-auto-examples-time-frequency-plot-source-power-spectrum-py" target="_blank">https://www.nmr.mgh.harvard.edu/mne/stable/auto_examples/time_frequency/plot_source_power_spectrum.html#sphx-glr-auto-examples-time-frequency-plot-source-power-spectrum-py</a>><br>
>>> should help you understand how it works ( especially the last plot)<br>
>>> <br>
>>> <br>
>>> Best,<br>
>>> Victor<br>
>>> ------------------------------<br>
>>> *From:* <a href="mailto:mne_analysis-bounces@nmr.mgh.harvard.edu" target="_blank">
mne_analysis-bounces@nmr.mgh.harvard.edu</a> <<br>
>>> <a href="mailto:mne_analysis-bounces@nmr.mgh.harvard.edu" target="_blank">mne_analysis-bounces@nmr.mgh.harvard.edu</a>> on behalf of Vivek Sharma <<br>
>>> <a href="mailto:vivek.sharma1510@gmail.com" target="_blank">vivek.sharma1510@gmail.com</a>><br>
>>> *Sent:* Thursday, September 26, 2019 8:17 AM<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>
>>> *Subject:* Re: [Mne_analysis] mne.minimum_norm.compute_source_psd<br>
>>> <br>
>>> <br>
>>> External Email - Use Caution<br>
>>> <br>
>>> The total time I have considered is 574 seconds so how it is related to<br>
>>> 1025 time points.<br>
>>> <br>
>>> On Wed, Sep 25, 2019 at 8:46 PM Daniel McCloy <<a href="mailto:dan.mccloy@gmail.com" target="_blank">dan.mccloy@gmail.com</a>><br>
>>> wrote:<br>
>>> <br>
>>> External Email - Use Caution<br>
>>> <br>
>>> It is the number of time points.<br>
>>> <br>
>>> On September 25, 2019 2:27:52 AM PDT, Vivek Sharma <<br>
>>> <a href="mailto:vivek.sharma1510@gmail.com" target="_blank">vivek.sharma1510@gmail.com</a>> wrote:<br>
>>>> External Email - Use Caution<br>
>>>> <br>
>>>> In continuation of the above thread, I unable to understand what does<br>
>>>> 1025<br>
>>>> mean in data shape.<br>
>>>> <SourceEstimate | 8064 vertices, subject : Collin, tmin : 0.0 (ms),<br>
>>>> tmax<br>
>>>> : 100000.0 (ms), tstep : 97.65625 (ms),<br>
>>>> *data shape : (8064, 1025)>*<br>
>>>> <br>
>>>> <br>
>>>> On Fri, Jun 14, 2019 at 4:33 PM Vivek Sharma<br>
>>>> <<a href="mailto:vivek.sharma1510@gmail.com" target="_blank">vivek.sharma1510@gmail.com</a>><br>
>>>> wrote:<br>
>>>> <br>
>>>>> Thank You.<br>
>>>>> <br>
>>>>> On Wed, Jun 12, 2019 at 11:53 AM Alexandre Gramfort <<br>
>>>>> <a href="mailto:alexandre.gramfort@inria.fr" target="_blank">alexandre.gramfort@inria.fr</a>> wrote:<br>
>>>>> <br>
>>>>>> External Email - Use Caution<br>
>>>>>> <br>
>>>>>> hi,<br>
>>>>>> <br>
>>>>>> this function hacks a SourceEstimate object : stc_psd to store PSDs.<br>
>>>> So<br>
>>>>>> what you read<br>
>>>>>> with time:<br>
>>>>>> <br>
>>>>>> <SourceEstimate | 8064 vertices, subject : Collin, tmin : 0.0<br>
>>>> (ms),<br>
>>>>>> tmax : 100000.0 (ms), tstep : 97.65625 (ms), data shape : (8064,<br>
>>>> 1025)><br>
>>>>>> <br>
>>>>>> should be:<br>
>>>>>> <br>
>>>>>> <SourceEstimate | 8064 vertices, subject : Collin, fmin : 0.0<br>
>>>> (Hz),<br>
>>>>>> fmax : 100000.0 (mHz), fstep : 97.65625 (mHz), data shape : (8064,<br>
>>>> 1025)><br>
>>>>>> <br>
>>>>>> HTH<br>
>>>>>> Alex<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" target="_blank">
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a><br>
>>>>> <br>
>>>>> <br>
>>>>> <br>
>>>>> --<br>
>>>>> Vivek Sharma<br>
>>>>> <br>
>>>> <br>
>>>> <br>
>>>> --<br>
>>>> Vivek Sharma<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" target="_blank">
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a><br>
>>> <br>
>>> <br>
>>> <br>
>>> --<br>
>>> Vivek Sharma<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" target="_blank">
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a><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" target="_blank">
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a><br>
> <br>
> <br>
> <br>
> -- <br>
> Vivek Sharma<br>
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