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

[Denis-Alexander Engemann]

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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