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

[Denis-Alexander Engemann]

On Fri, Aug 8, 2014 at 3:01 PM, dgw <dgwakeman at gmail.com> wrote:

> On Fri, 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.
>
> How did you map the full ~300,000 vertices from each participant to
> fsaverage without decimating?
>
>
As I said, not *explcitly*, it's the an oct 6 source space that we usually
recommend as default.


>
> >
> >>
> >> 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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