[Mne_analysis] pick orientation, MNE, dSPM and group analyses

[Hari Bharadwaj]

Hi Denis,
   With the orientation fixed, is it the across vertex (within a parcel for a give subject) or the across subject averaging that is reducing the dSPMs? Also, is the data some kind of event related response where you'd expect the peaks across subjects to along in time? I ask because the signed estimates when not aligned across subjects (in time) could go down quite a bit when you average across subjects...the "mis-alignment" could also simply come from the possibility the polarity is not the same across subjects, i.e., though the peaks are around the same time, for some subjects the peaks are negative and for some positive (both in vertex by vertex grand-averaging case ..or the label wise average for each subject separately case)

Hari 

> On Aug 8, 2014, at 8:26 AM, Denis-Alexander Engemann <denis.engemann at gmail.com> wrote:
> 
> Hi Dan,
> 
> 
>> On Thu, Aug 7, 2014 at 9:45 PM, dgw <dgwakeman at gmail.com> wrote:
>> Hi Denis,
>> 
>> This effect can be influenced by a lot of variables. I would say
>> anatomical variability is a huge one but there are tons of factors
>> which affect just that:
>> 
>> Did you decimate? (I guess you must have to morph, but how severely
>> did you decimate?)
> 
> I think I did not explicitlly decimate. Simply a 20 steps morpch from subject to fsaverage.
>  
>> Are you using --loose, or --loosevar
>> What parameters with those
> 
> our default, loose=0.2 
>  
>> Did you use cps?
> 
> I'm actually not sure whether Python takes the cps into account / where / when / 
>  
>> I suspect the morphing will also influence this, but that is easy to
>> check (and wise to do see how the labels morph back on the
>> individual's surface?).
> 
> Yeah, or compute the grand ave time series based on time courses extracted from unorphed stcs.
>  
>> Though as long as you have FreeSurfer quality
>> scans, I don't expect the segmentation to be an issue. What if any
>> smoothing did you do (at each stage)?
> 
> see above
>  
>> HTH,
>> D
> 
> more imporatanlty, does all this actually matter at all if the SNR seems to be ok.
>  
> Denis
> 
>> 
>> On Thu, Aug 7, 2014 at 11:25 AM, Denis-Alexander Engemann
>> <denis.engemann at gmail.com> wrote:
>> > Dear list,
>> >
>> > I'm currently comparing group grand averages in a set of functional labels
>> > which are derived from the PALS B12 Brodmann parcellation. These were then
>> > used with subjects' stcs after morphing to fsaverage.
>> > Now I'm really struck that with surface orientation AND mean flipping the
>> > minima and maxima, even for dSPM shrink to values below 1 while the expected
>> > temporal dynamics are preserved. In the 'wild', that is, *before* averaging,
>> > the signed dSPMS are between -7 and 8, just as the free-orientation dSPM
>> > maxima are around 8 --- *after*  --- averaging.
>> >
>> > I'm wondering whether this could be a result of the morphing, the anatomical
>> > variability, or even the segmentation quality.
>> >
>> > Any hint would be appreciated.
>> >
>> > Denis
>> >
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