[Mne_analysis] Digitization and Channel Positions
Geller, Jason
jason-geller at uiowa.edu
Thu Sep 26 18:49:43 EDT 2019
External Email - Use Caution
Hello,
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:
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.
My question is: how do I set the channel positions for a dig montage? Any help would be greatly appreciated.
Thanks,
J
> On Sep 26, 2019, at 5:35 PM, mne_analysis-request at nmr.mgh.harvard.edu wrote:
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> 1. Re: mne.minimum_norm.compute_source_psd (Dan McCloy)
> 2. Re: mne.minimum_norm.compute_source_psd (Vivek Sharma)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 26 Sep 2019 11:30:04 -0700
> From: Dan McCloy <dan.mccloy at gmail.com>
> Subject: Re: [Mne_analysis] mne.minimum_norm.compute_source_psd
> To: Discussion and support forum for the users of MNE Software
> <mne_analysis at nmr.mgh.harvard.edu>
> Message-ID:
> <CAOE0pYk7QJxJvsOD5QR1pg0HNObfDjnLh=CnCwB_roJ07DZt3A at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
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> External Email - Use Caution
>
> Ah, Victor is right. Sorry Vivek for giving you the wrong advice; I looked
> only at the repr of the object, which had a tmin, tmax, and tstep; I didn't
> dig through the example that got you there.
>
> On Thu, Sep 26, 2019 at 3:30 AM Victor Ferat <victor.ferat at fcbg.ch> wrote:
>
>> External Email - Use Caution
>>
>> It should be the number of frequencies.
>> For each source (8064) you have 1025 values of power density, one per
>> frequency . (frequencies ranging from 0 Hz to 100Hz with 97.65625mHz step).
>> This tutorial
>> <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>
>> should help you understand how it works ( especially the last plot)
>>
>>
>> Best,
>> Victor
>> ------------------------------
>> *From:* mne_analysis-bounces at nmr.mgh.harvard.edu <
>> mne_analysis-bounces at nmr.mgh.harvard.edu> on behalf of Vivek Sharma <
>> vivek.sharma1510 at gmail.com>
>> *Sent:* Thursday, September 26, 2019 8:17 AM
>> *To:* Discussion and support forum for the users of MNE Software <
>> mne_analysis at nmr.mgh.harvard.edu>
>> *Subject:* Re: [Mne_analysis] mne.minimum_norm.compute_source_psd
>>
>>
>> External Email - Use Caution
>>
>> The total time I have considered is 574 seconds so how it is related to
>> 1025 time points.
>>
>> On Wed, Sep 25, 2019 at 8:46 PM Daniel McCloy <dan.mccloy at gmail.com>
>> wrote:
>>
>> External Email - Use Caution
>>
>> It is the number of time points.
>>
>> On September 25, 2019 2:27:52 AM PDT, Vivek Sharma <
>> vivek.sharma1510 at gmail.com> wrote:
>>> External Email - Use Caution
>>>
>>> In continuation of the above thread, I unable to understand what does
>>> 1025
>>> mean in data shape.
>>> <SourceEstimate | 8064 vertices, subject : Collin, tmin : 0.0 (ms),
>>> tmax
>>> : 100000.0 (ms), tstep : 97.65625 (ms),
>>> *data shape : (8064, 1025)>*
>>>
>>>
>>> On Fri, Jun 14, 2019 at 4:33 PM Vivek Sharma
>>> <vivek.sharma1510 at gmail.com>
>>> wrote:
>>>
>>>> Thank You.
>>>>
>>>> On Wed, Jun 12, 2019 at 11:53 AM Alexandre Gramfort <
>>>> alexandre.gramfort at inria.fr> wrote:
>>>>
>>>>> External Email - Use Caution
>>>>>
>>>>> hi,
>>>>>
>>>>> this function hacks a SourceEstimate object : stc_psd to store PSDs.
>>> So
>>>>> what you read
>>>>> with time:
>>>>>
>>>>> <SourceEstimate | 8064 vertices, subject : Collin, tmin : 0.0
>>> (ms),
>>>>> tmax : 100000.0 (ms), tstep : 97.65625 (ms), data shape : (8064,
>>> 1025)>
>>>>>
>>>>> should be:
>>>>>
>>>>> <SourceEstimate | 8064 vertices, subject : Collin, fmin : 0.0
>>> (Hz),
>>>>> fmax : 100000.0 (mHz), fstep : 97.65625 (mHz), data shape : (8064,
>>> 1025)>
>>>>>
>>>>> HTH
>>>>> Alex
>>>>>
>>>>> _______________________________________________
>>>>> Mne_analysis mailing list
>>>>> Mne_analysis at nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>>
>>>>
>>>>
>>>> --
>>>> Vivek Sharma
>>>>
>>>
>>>
>>> --
>>> Vivek Sharma
>>
>> _______________________________________________
>> Mne_analysis mailing list
>> Mne_analysis at nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>
>>
>>
>> --
>> Vivek Sharma
>> _______________________________________________
>> Mne_analysis mailing list
>> Mne_analysis at nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
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>
> Message: 2
> Date: Fri, 27 Sep 2019 04:05:30 +0530
> From: Vivek Sharma <vivek.sharma1510 at gmail.com>
> Subject: Re: [Mne_analysis] mne.minimum_norm.compute_source_psd
> To: Discussion and support forum for the users of MNE Software
> <mne_analysis at nmr.mgh.harvard.edu>
> Message-ID:
> <CAKzh67FKy0ShTSUCEO496cZF7K-7QJbzNT6fmKC_7=KVY6v31Q at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> External Email - Use Caution
>
> Hi,
> Thanks for the information.
>
> On Fri, Sep 27, 2019 at 12:00 AM Dan McCloy <dan.mccloy at gmail.com> wrote:
>
>> External Email - Use Caution
>>
>> Ah, Victor is right. Sorry Vivek for giving you the wrong advice; I
>> looked only at the repr of the object, which had a tmin, tmax, and tstep; I
>> didn't dig through the example that got you there.
>>
>> On Thu, Sep 26, 2019 at 3:30 AM Victor Ferat <victor.ferat at fcbg.ch> wrote:
>>
>>> External Email - Use Caution
>>>
>>> It should be the number of frequencies.
>>> For each source (8064) you have 1025 values of power density, one per
>>> frequency . (frequencies ranging from 0 Hz to 100Hz with 97.65625mHz step).
>>> This tutorial
>>> <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>
>>> should help you understand how it works ( especially the last plot)
>>>
>>>
>>> Best,
>>> Victor
>>> ------------------------------
>>> *From:* mne_analysis-bounces at nmr.mgh.harvard.edu <
>>> mne_analysis-bounces at nmr.mgh.harvard.edu> on behalf of Vivek Sharma <
>>> vivek.sharma1510 at gmail.com>
>>> *Sent:* Thursday, September 26, 2019 8:17 AM
>>> *To:* Discussion and support forum for the users of MNE Software <
>>> mne_analysis at nmr.mgh.harvard.edu>
>>> *Subject:* Re: [Mne_analysis] mne.minimum_norm.compute_source_psd
>>>
>>>
>>> External Email - Use Caution
>>>
>>> The total time I have considered is 574 seconds so how it is related to
>>> 1025 time points.
>>>
>>> On Wed, Sep 25, 2019 at 8:46 PM Daniel McCloy <dan.mccloy at gmail.com>
>>> wrote:
>>>
>>> External Email - Use Caution
>>>
>>> It is the number of time points.
>>>
>>> On September 25, 2019 2:27:52 AM PDT, Vivek Sharma <
>>> vivek.sharma1510 at gmail.com> wrote:
>>>> External Email - Use Caution
>>>>
>>>> In continuation of the above thread, I unable to understand what does
>>>> 1025
>>>> mean in data shape.
>>>> <SourceEstimate | 8064 vertices, subject : Collin, tmin : 0.0 (ms),
>>>> tmax
>>>> : 100000.0 (ms), tstep : 97.65625 (ms),
>>>> *data shape : (8064, 1025)>*
>>>>
>>>>
>>>> On Fri, Jun 14, 2019 at 4:33 PM Vivek Sharma
>>>> <vivek.sharma1510 at gmail.com>
>>>> wrote:
>>>>
>>>>> Thank You.
>>>>>
>>>>> On Wed, Jun 12, 2019 at 11:53 AM Alexandre Gramfort <
>>>>> alexandre.gramfort at inria.fr> wrote:
>>>>>
>>>>>> External Email - Use Caution
>>>>>>
>>>>>> hi,
>>>>>>
>>>>>> this function hacks a SourceEstimate object : stc_psd to store PSDs.
>>>> So
>>>>>> what you read
>>>>>> with time:
>>>>>>
>>>>>> <SourceEstimate | 8064 vertices, subject : Collin, tmin : 0.0
>>>> (ms),
>>>>>> tmax : 100000.0 (ms), tstep : 97.65625 (ms), data shape : (8064,
>>>> 1025)>
>>>>>>
>>>>>> should be:
>>>>>>
>>>>>> <SourceEstimate | 8064 vertices, subject : Collin, fmin : 0.0
>>>> (Hz),
>>>>>> fmax : 100000.0 (mHz), fstep : 97.65625 (mHz), data shape : (8064,
>>>> 1025)>
>>>>>>
>>>>>> HTH
>>>>>> Alex
>>>>>>
>>>>>> _______________________________________________
>>>>>> Mne_analysis mailing list
>>>>>> Mne_analysis at nmr.mgh.harvard.edu
>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Vivek Sharma
>>>>>
>>>>
>>>>
>>>> --
>>>> Vivek Sharma
>>>
>>> _______________________________________________
>>> Mne_analysis mailing list
>>> Mne_analysis at nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>
>>>
>>>
>>> --
>>> Vivek Sharma
>>> _______________________________________________
>>> Mne_analysis mailing list
>>> Mne_analysis at nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>
>> _______________________________________________
>> Mne_analysis mailing list
>> Mne_analysis at nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
>
>
> --
> Vivek Sharma
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