[Mne_analysis] MNE source estimate analysis with multiple conditions

[Marijn van Vliet]

Hi Liam,

yes, exactly!

Marijn.

> On 11 Apr 2017, at 03:49, Lyam Bailey <Lyam.Bailey at dal.ca> wrote:
> 
> Dear Marijin,
> 
> Thanks for your help! I think I see what you're saying, but just to clarify, does MNE(cond1-cond2) refer to source estimates generated from (evoked cond1 - evoked cond2)?
> 
> 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 Marijn van Vliet <w.m.vanvliet at gmail.com>
> Sent: Friday, April 7, 2017 12:43:03 PM
> To: mne_analysis at nmr.mgh.harvard.edu
> Subject: Re: [Mne_analysis] MNE source estimate analysis with multiple conditions
>  
> Dear Lyam,
> 
> the reason why you see a difference between MNE(cond1) - MNE(cond2) and MNE(cond1 - cond2) is because of the dipole orientations. The source estimate only retains the magnitude of the dipoles. See here for some more information about what is going on:
> https://4006-1301584-gh.circle-artifacts.com/0/home/ubuntu/mne-python/doc/_build/html/auto_tutorials/plot_dipole_orientations.html
> 
> When using fixed orientations, there should not be any difference. When using loose orientations (the default), MNE(cond1 - cond2) is in my opinion the correct way.
> 
> regards,
> Marijn.
> 
> On 04/06/2017 06:42 PM, Lyam Bailey wrote:
>> Dear MNE users,
>> 
>> I am analysing surface-based source estimates computed from evoked MEG data. I would like to extract peak amplitude times from source estimates of the difference between two experimental conditions (exp. and control), and as far as I can tell there are two approaches to this. One is to calculate the difference prior to computing source estimates (i.e: exp. evoked - control evoked) and then compute source estimates (.stc) based on the returned array. Another is to generate source estimates for each condition, and then subtract the returned stc files (exp.stc - control.stc) Unfortunately, these two approaches yield slightly different results (I suspect this is due to noise generated by the .stc subtraction) - so which would be most prudent? Alternatively, is there a different (more robust) approach that I could use?
>> 
>> Thanks in advance for any help!
>> 
>> Regards,
>> Lyam
>> 
>> 
>> ---------------------------------------------------------
>> Lyam Bailey, BSc.
>> Graduate Student
>> Department of Psychology & Neuroscience
>> Dalhousie University
>> 
>> 
>> 
>> _______________________________________________
>> 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.