[Mne_analysis] Comparison of brain responses under three different conditions?

Sun Dec 21 09:45:00 EST 2014

Hi Denis,

Are you sure that the sphericity correction is implemented by f_twoway_rm?
I tested it with data where the assumption of sphericity is violated. I
calculated p values with Statistica and corrected them using the
lower-bound estimate, Greenhouse-Geisser correction and the Huynh-Feldt
correction. However, the p-values given by f_twoway_rm were equal with the
uncorrected values I calculated with Statistica. I used f_twoway_rm as:

[f,p]=f_twoway_rm(data,factor_levels=[2,3])

where data is hemisphere*sesion ANOVA table.

-Maria

2014-12-21 15:08 GMT+02:00 Denis-Alexander Engemann <
denis.engemann at gmail.com>:

>
>
> 2014-12-21 14:00 GMT+01:00 Maria Hakonen <maria.hakonen at gmail.com>:
>
>> Hi,
>>
>> Is it that when I have hemisphere*session ANOVAs, I can use f_twoway_rm,
>> and this gives the corrected values?
>>
>
> with correction=True
>
>
>> Should one-way ANOVA be used in the cases where I am not interested in
>> hemisperic asymmetry? Is there any function for one way ANOVA that gives
>> sphericity corrected values?
>>
>>
> A one-way ANOVA is currently not implemented. But you can just look at the
> relevant main effect. Should be equivalent.
>
>
>> -Maria
>>
>> 2014-12-21 14:21 GMT+02:00 Denis A. Engemann <denis.engemann at gmail.com>:
>>
>>> Hi Maria,
>>>
>>> On 21 Dec 2014, at 12:51, Maria Hakonen <maria.hakonen at gmail.com> wrote:
>>>
>>> Hi Denis,
>>>
>>> Should I use two-way ANOVA if I also want to compare hemispheres, i.e.
>>> have a 2*3 (hemisphere*session) ANOVA table?
>>>
>>>
>>> Sounds like the repeated measures anova is what you want to do here
>>> indeed. I just realized the sphericity correction is actually implemented
>>> by our code. So that should fly. Checkout the correction parameter.
>>>
>>>
>>> I would need to do group level analysis.
>>>
>>> -Maria
>>>
>>>
>>> 2014-12-21 12:38 GMT+02:00 Denis-Alexander Engemann <
>>> denis.engemann at gmail.com>:
>>>
>>>> Hi Maria,
>>>>
>>>> 2014-12-21 10:18 GMT+01:00 Maria Hakonen <maria.hakonen at gmail.com>:
>>>>
>>>>> Hi all,
>>>>>
>>>>> I would need to find the time intervals where there are statistically
>>>>> significant differences between MEG responses measured under three
>>>>> different conditions.  I study the responses by comparing the mean values
>>>>> in steps of 200 ms between the range of 400-2400 ms. I would like to do
>>>>> this for responses from several brain areas. What could be the best way to
>>>>> compare the mean values of the tree responses?
>>>>>
>>>>>
>>>> Single subject or group level?
>>>> For single subject a standard F-test would be appropriate. For groups a
>>>> oneway repeated measures ANOVA, if I understand your design correctly
>>>> (simply 3 different conditions).
>>>>
>>>>
>>>>> I have planned to try f_twoway_rm in a loop. However, when rmANOVA is
>>>>> used, sphericity test is needed, and if the assumption of sphericity is
>>>>> violated, p values need to be corrected. Is there any function for this in
>>>>> Python (e.g. Mauchly's sphericity test and Greenhouse-Geisser test)?
>>>>>
>>>>>
>>>> Note that this only needed if you have more than 2 factors with more
>>>> than two levels. Currently this is not implemented in our stats code. The
>>>> other questions is why you need a 2-way test for 3 conditions. I probably
>>>> did not fully understand your design.
>>>>
>>>> Denis
>>>>
>>>>
>>>>> Many thanks already in advance!
>>>>>
>>>>> Regards,
>>>>> Maria
>>>>>
>>>>> _______________________________________________
>>>>> Mne_analysis mailing list
>>>>> Mne_analysis at nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>>>
>>>>>
>>>>> The information in this e-mail is intended only for the person to whom
>>>>> it is
>>>>> addressed. If you believe this e-mail was sent to you in error and the
>>>>> e-mail
>>>>> contains patient information, please contact the Partners Compliance
>>>>> HelpLine at
>>>>> http://www.partners.org/complianceline . If the e-mail was sent to
>>>>> you in error
>>>>> but does not contain patient information, please contact the sender
>>>>> and properly
>>>>> dispose of the e-mail.
>>>>>
>>>>>
>>>>
>>>> _______________________________________________
>>>> Mne_analysis mailing list
>>>> Mne_analysis at nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>>
>>>>
>>>> The information in this e-mail is intended only for the person to whom
>>>> it is
>>>> addressed. If you believe this e-mail was sent to you in error and the
>>>> e-mail
>>>> contains patient information, please contact the Partners Compliance
>>>> HelpLine at
>>>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>>> in error
>>>> but does not contain patient information, please contact the sender and
>>>> properly
>>>> dispose of the e-mail.
>>>>
>>>>
>>> _______________________________________________
>>> Mne_analysis mailing list
>>> Mne_analysis at nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom
>>> it is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>> in error
>>> but does not contain patient information, please contact the sender and
>>> properly
>>> dispose of the e-mail.
>>>
>>>
>>> _______________________________________________
>>> Mne_analysis mailing list
>>> Mne_analysis at nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom
>>> it is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>> in error
>>> but does not contain patient information, please contact the sender and
>>> properly
>>> dispose of the e-mail.
>>>
>>>
>>
>> _______________________________________________
>> Mne_analysis mailing list
>> Mne_analysis at nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20141221/982bf7d4/attachment.html 