[Mne_analysis] MNE source estimate analysis with multiple conditions

Denis-Alexander Engemann denis.engemann at gmail.com
Tue Apr 11 13:18:59 EDT 2017
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But this way you will have a hard time interpreting your effect. Using dSPM
on each condition and then forming a contrast is also legitimate, as long
as you have a meaningful baseline. This would be dSPM(a) - dSPM(b).

Denis
On Tue, 11 Apr 2017 at 13:06, Marijn van Vliet <w.m.vanvliet at gmail.com>
wrote:

> 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
> >>
> >>
> >>
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