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

[dgw]

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?


>
>>
>> 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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