[Mne_analysis] MNE source estimate analysis with multiple conditions

Wed May 31 09:46:49 EDT 2017

hi,

in this example the sign flip is not applied to epochs but
to vertices in the labels. What this figure:

https://martinos.org/mne/stable/_images/sphx_glr_plot_compute_mne_inverse_epochs_in_label_002.png

shows you is that you can equivalently apply the sign flip on evoked or on
epochs and then average.

In all examples the sign flip is not data dependent.

Alex

On Wed, May 31, 2017 at 2:36 PM, Lin Wang <wanglinsisi at gmail.com> wrote:

> Hi Alex,
>
> Thanks for the clarification.
>
> As far as I understand, the sign flip can be used to avoid signal
> cancellation when averaging signed values. This cancellation could come
> from averaging within ROIs or across trials/subjects.
> In the tutorial (https://martinos.org/mne/stable/auto_examples/inverse/
> plot_compute_mne_inverse_epochs_in_label.html?highlight=make%20inverse),
> you demonstrated how flipping signs affects the trial-average results.
>
> Then do we need to worry about the signs when averaging across subjects?
> Or do I misunderstand something?
>
> One further questions is whether we need to flip the sign during the
> cluster-based statistical analysis and during ANOVA within ROI.
>
> Thanks for your help!
>
> Lin
>
> On Wed, May 31, 2017 at 2:13 AM, Alexandre Gramfort <
> alexandre.gramfort at telecom-paristech.fr> wrote:
>
>> hi Lin,
>>
>> the label_sign_flip is used to average time courses within a label
>> in order to avoid signal cancellations.
>>
>> Alex
>>
>> On Tue, May 30, 2017 at 6:54 PM, Lin Wang <wanglinsisi at gmail.com> wrote:
>>
>>> Hi everyone,
>>>
>>> I have a followup question regarding the group level contrast: Do I need
>>> to apply mne.label_sign_flip before averaging the activaitons across all
>>> subjects?
>>>
>>> I used "fixed=False, loose=0.2" to get the inverse solution, then I
>>> defined "pick_ori="normal"" when applying the inverse solution to the
>>> evoked difference (evoked1 - evoked2) for each subject.
>>>
>>> I'm wondering if I should flip the signs when averaging the activations
>>> across subjects.
>>>
>>> Thanks for the help!
>>>
>>> Lin
>>>
>>>
>>>
>>> On Tue, Apr 18, 2017 at 10:55 AM, Lyam Bailey <Lyam.Bailey at dal.ca>
>>> wrote:
>>>
>>>> Thanks Andy!
>>>>
>>>>
>>>> ---------------------------------------------------------
>>>>
>>>> Lyam Bailey, BSc.
>>>>
>>>> Graduate Student
>>>> Department of Psychology & Neuroscience
>>>> Dalhousie University
>>>>
>>>> ------------------------------
>>>> *From:* mne_analysis-bounces at nmr.mgh.harvard.edu <
>>>> mne_analysis-bounces at nmr.mgh.harvard.edu> on behalf of Andrew R.
>>>> Dykstra <andrew.dykstra at uni-heidelberg.de>
>>>> *Sent:* Monday, April 17, 2017 8:08:15 PM
>>>>
>>>> *To:* Discussion and support forum for the users of MNE Software
>>>> *Subject:* Re: [Mne_analysis] MNE source estimate analysis with
>>>> multiple conditions
>>>>
>>>>
>>>> Hi Lyam,
>>>>
>>>>
>>>> See here:
>>>>
>>>> http://martinos.org/mne/dev/generated/mne.epochs.equalize_ep
>>>> och_counts.html
>>>>
>>>>
>>>> HTH,
>>>>
>>>> Andy
>>>>
>>>> On 2017-04-17 06:04 PM, Lyam Bailey wrote:
>>>>
>>>> I suppose we could equalise the number of epochs per condition, in
>>>> theory (although I'm not familiar with the best way to do this). Basically
>>>> the unequal epoch numbers arose due to problems during data collection,
>>>> whereby a few random trials were lost in almost every subject.
>>>>
>>>>
>>>> Regards
>>>>
>>>> Lyam
>>>>
>>>>
>>>> ---------------------------------------------------------
>>>>
>>>> Lyam Bailey, BSc.
>>>> Graduate Student
>>>> Department of Psychology & Neuroscience
>>>> Dalhousie University
>>>>
>>>> ------------------------------
>>>> *From:* mne_analysis-bounces at nmr.mgh.harvard.edu
>>>> <mne_analysis-bounces at nmr.mgh.harvard.edu>
>>>> <mne_analysis-bounces at nmr.mgh.harvard.edu> on behalf of
>>>> Denis-Alexander Engemann <denis.engemann at gmail.com>
>>>> <denis.engemann at gmail.com>
>>>> *Sent:* Monday, April 17, 2017 4:40:11 PM
>>>> *To:* Discussion and support forum for the users of MNE Software
>>>> *Subject:* Re: [Mne_analysis] MNE source estimate analysis with
>>>> multiple conditions
>>>>
>>>> Does your experimental logic allow you to equalize the number of epochs
>>>> per conditions or do you have some rare events by design?
>>>>
>>>> Denis
>>>>
>>>> On Mon, Apr 17, 2017 at 11:30 AM Lyam Bailey <Lyam.Bailey at dal.ca>
>>>> wrote:
>>>>
>>>>> Hi Alex,
>>>>>
>>>>>
>>>>> Thanks for the tip! I'm glad you mentioned this because as it happens,
>>>>> I don't have the same number of epochs for each condition. Can you suggest
>>>>> a work around?
>>>>>
>>>>>
>>>>> Regards
>>>>>
>>>>> Lyam
>>>>>
>>>>>
>>>>> ---------------------------------------------------------
>>>>>
>>>>> Lyam Bailey, BSc.
>>>>> Graduate Student
>>>>> Department of Psychology & Neuroscience
>>>>> Dalhousie University
>>>>>
>>>>> ------------------------------
>>>>> *From:* mne_analysis-bounces at nmr.mgh.harvard.edu <
>>>>> mne_analysis-bounces at nmr.mgh.harvard.edu> on behalf of Alexandre
>>>>> Gramfort <alexandre.gramfort at telecom-paristech.fr>
>>>>> *Sent:* Tuesday, April 11, 2017 6:31:55 PM
>>>>> *To:* Discussion and support forum for the users of MNE Software
>>>>>
>>>>> *Subject:* Re: [Mne_analysis] MNE source estimate analysis with
>>>>> multiple conditions
>>>>> > This would be dSPM(a) - dSPM(b).
>>>>>
>>>>> tiny detail: this will only be true if the two conditions have the
>>>>> same number of epochs averaged in each condition.
>>>>>
>>>>> Alex
>>>>> _______________________________________________
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