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

Fri Aug 8 09:34:11 EDT 2014

Thanks Dan,

On Fri, Aug 8, 2014 at 3:27 PM, dgw <dgwakeman at gmail.com> wrote:

> IMO, oct-6 is severely decimated (only 2.75% of the points in the
> source space originally).

I agree. But what's the alternative? Do you compute inverse solutions on
the entire source space?

> I'm not sure that --loose 0.2 will
> accurately capture the range of orientations (especially dangerous if
> not using the cps). Plus by morphing on top of this coarse spacing
> with 20 smooth steps that ends up smoothing the result a lot. If you
> want to keep the analysis in the time domain, I would first explore
> the timecourses of the labels within the individuals to see what sort
> of pattern emerges (particularly with respect to their individual
> anatomy).

I was feeling that this is probably the way to go.

> As I said before it could be anatomical variability, but you
> may be able to correct for this if the whole label actually has a
> consistent orientation across participants (the current decimation (in
> combination with your other parameters), could be causing the sign
> flipping you are seeing). In that case simply adding cps "should"
> improve the situation.
>

I feel we should handle CPS a bit more verbosely, e.g. log whether it's
used or not when computing / applying inverse.

> Of course one "easy fix" is to just pick the peak frequency in the
> region/time you are interested in and average the power in that band
> (this will save you from the flipping issues, by removing phase).
>
>
indeed.

> HTH,
> D
>
> Aside:
> What would be "explicit" decimation? To me reducing the source space
> to oct-6 is decimation (how else could one decimate?).
>
>
forget about the wording. I simply expressed the fact that these are
parameters we normally don't touch.

> On Fri, Aug 8, 2014 at 9:06 AM, Denis-Alexander Engemann
> <denis.engemann at gmail.com> wrote:
> >
> >
> >
> > 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
> >> >> >
> >> >> > _______________________________________________
> >> >> > Mne_analysis mailing list
> >> >> > Mne_analysis at nmr.mgh.harvard.edu
> >> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >> >> >
> >> >> >
> >> >> > The information in this e-mail is intended only for the person to
> >> >> > whom
> >> >> > it is
> >> >> > addressed. If you believe this e-mail was sent to you in error and
> >> >> > the
> >> >> > e-mail
> >> >> > contains patient information, please contact the Partners
> Compliance
> >> >> > HelpLine at
> >> >> > http://www.partners.org/complianceline . If the e-mail was sent to
> >> >> > you
> >> >> > in
> >> >> > error
> >> >> > but does not contain patient information, please contact the sender
> >> >> > and
> >> >> > properly
> >> >> > dispose of the e-mail.
> >> >> >
> >> >> _______________________________________________
> >> >> Mne_analysis mailing list
> >> >> Mne_analysis at nmr.mgh.harvard.edu
> >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >> >
> >> >
> >> >
> >> > _______________________________________________
> >> > Mne_analysis mailing list
> >> > Mne_analysis at nmr.mgh.harvard.edu
> >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >> >
> >> >
> >> > The information in this e-mail is intended only for the person to whom
> >> > it is
> >> > addressed. If you believe this e-mail was sent to you in error and the
> >> > e-mail
> >> > contains patient information, please contact the Partners Compliance
> >> > HelpLine at
> >> > http://www.partners.org/complianceline . If the e-mail was sent to
> you
> >> > in
> >> > error
> >> > but does not contain patient information, please contact the sender
> and
> >> > properly
> >> > dispose of the e-mail.
> >> >
> >> _______________________________________________
> >> Mne_analysis mailing list
> >> Mne_analysis at nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >
> >
> >
> > _______________________________________________
> > Mne_analysis mailing list
> > Mne_analysis at nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >
> >
> > The information in this e-mail is intended only for the person to whom
> it is
> > addressed. If you believe this e-mail was sent to you in error and the
> > e-mail
> > contains patient information, please contact the Partners Compliance
> > HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to you
> in
> > error
> > but does not contain patient information, please contact the sender and
> > properly
> > dispose of the e-mail.
> >
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20140808/b037070b/attachment.html 