[Mne_analysis] MNE source estimate analysis with multiple conditions

Wed May 31 08:36:38 EDT 2017

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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