<div dir="ltr"><br><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Aug 8, 2014 at 3:38 PM, dgw <span dir="ltr"><<a href="mailto:dgwakeman@gmail.com" target="_blank">dgwakeman@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="">On Fri, Aug 8, 2014 at 9:34 AM, Denis-Alexander Engemann<br>
<<a href="mailto:denis.engemann@gmail.com">denis.engemann@gmail.com</a>> wrote:<br>
> Thanks Dan,<br>
><br>
> On Fri, Aug 8, 2014 at 3:27 PM, dgw <<a href="mailto:dgwakeman@gmail.com">dgwakeman@gmail.com</a>> wrote:<br>
>><br>
>> IMO, oct-6 is severely decimated (only 2.75% of the points in the<br>
>> source space originally).<br>
><br>
><br>
> I agree. But what's the alternative? Do you compute inverse solutions on the<br>
> entire source space?<br>
<br>
</div>I often do, but you could always try with ico 5 (higher numbers than<br>
that make more work, by breaking morphing), to keep it simple and<br>
still have morphing.<br>
<div class="HOEnZb"><div class="h5"><br></div></div></blockquote><div><br></div><div>If only all this wouldn't be that impractical wrt to resources consumption ...</div><div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="HOEnZb"><div class="h5">
><br>
>><br>
>> I'm not sure that --loose 0.2 will<br>
>> accurately capture the range of orientations (especially dangerous if<br>
>> not using the cps). Plus by morphing on top of this coarse spacing<br>
>> with 20 smooth steps that ends up smoothing the result a lot. If you<br>
>> want to keep the analysis in the time domain, I would first explore<br>
>> the timecourses of the labels within the individuals to see what sort<br>
>> of pattern emerges (particularly with respect to their individual<br>
>> anatomy).<br>
><br>
><br>
> I was feeling that this is probably the way to go.<br>
><br>
>><br>
>> As I said before it could be anatomical variability, but you<br>
>> may be able to correct for this if the whole label actually has a<br>
>> consistent orientation across participants (the current decimation (in<br>
>> combination with your other parameters), could be causing the sign<br>
>> flipping you are seeing). In that case simply adding cps "should"<br>
>> improve the situation.<br>
><br>
><br>
> I feel we should handle CPS a bit more verbosely, e.g. log whether it's used<br>
> or not when computing / applying inverse.<br>
><br>
>><br>
>> Of course one "easy fix" is to just pick the peak frequency in the<br>
>> region/time you are interested in and average the power in that band<br>
>> (this will save you from the flipping issues, by removing phase).<br>
>><br>
><br>
> indeed.<br>
><br>
>><br>
>> HTH,<br>
>> D<br>
>><br>
>> Aside:<br>
>> What would be "explicit" decimation? To me reducing the source space<br>
>> to oct-6 is decimation (how else could one decimate?).<br>
>><br>
><br>
> forget about the wording. I simply expressed the fact that these are<br>
> parameters we normally don't touch.<br>
><br>
><br>
>><br>
>> On Fri, Aug 8, 2014 at 9:06 AM, Denis-Alexander Engemann<br>
>> <<a href="mailto:denis.engemann@gmail.com">denis.engemann@gmail.com</a>> wrote:<br>
>> ><br>
>> ><br>
>> ><br>
>> > On Fri, Aug 8, 2014 at 3:01 PM, dgw <<a href="mailto:dgwakeman@gmail.com">dgwakeman@gmail.com</a>> wrote:<br>
>> >><br>
>> >> On Fri, Aug 8, 2014 at 8:26 AM, Denis-Alexander Engemann<br>
>> >> <<a href="mailto:denis.engemann@gmail.com">denis.engemann@gmail.com</a>> wrote:<br>
>> >> > Hi Dan,<br>
>> >> ><br>
>> >> ><br>
>> >> > On Thu, Aug 7, 2014 at 9:45 PM, dgw <<a href="mailto:dgwakeman@gmail.com">dgwakeman@gmail.com</a>> wrote:<br>
>> >> >><br>
>> >> >> Hi Denis,<br>
>> >> >><br>
>> >> >> This effect can be influenced by a lot of variables. I would say<br>
>> >> >> anatomical variability is a huge one but there are tons of factors<br>
>> >> >> which affect just that:<br>
>> >> >><br>
>> >> >> Did you decimate? (I guess you must have to morph, but how severely<br>
>> >> >> did you decimate?)<br>
>> >> ><br>
>> >> ><br>
>> >> > I think I did not explicitlly decimate. Simply a 20 steps morpch from<br>
>> >> > subject to fsaverage.<br>
>> >><br>
>> >> How did you map the full ~300,000 vertices from each participant to<br>
>> >> fsaverage without decimating?<br>
>> >><br>
>> ><br>
>> > As I said, not *explcitly*, it's the an oct 6 source space that we<br>
>> > usually<br>
>> > recommend as default.<br>
>> ><br>
>> >><br>
>> >><br>
>> >> ><br>
>> >> >><br>
>> >> >> Are you using --loose, or --loosevar<br>
>> >> >> What parameters with those<br>
>> >> ><br>
>> >> ><br>
>> >> > our default, loose=0.2<br>
>> >> ><br>
>> >> >><br>
>> >> >> Did you use cps?<br>
>> >> >><br>
>> >> ><br>
>> >> > I'm actually not sure whether Python takes the cps into account /<br>
>> >> > where<br>
>> >> > /<br>
>> >> > when /<br>
>> >> ><br>
>> >> >><br>
>> >> >> I suspect the morphing will also influence this, but that is easy to<br>
>> >> >> check (and wise to do see how the labels morph back on the<br>
>> >> >> individual's surface?).<br>
>> >> ><br>
>> >> ><br>
>> >> > Yeah, or compute the grand ave time series based on time courses<br>
>> >> > extracted<br>
>> >> > from unorphed stcs.<br>
>> >> ><br>
>> >> >><br>
>> >> >> Though as long as you have FreeSurfer quality<br>
>> >> >> scans, I don't expect the segmentation to be an issue. What if any<br>
>> >> >> smoothing did you do (at each stage)?<br>
>> >> >><br>
>> >> ><br>
>> >> > see above<br>
>> >> ><br>
>> >> >><br>
>> >> >> HTH,<br>
>> >> >> D<br>
>> >> >><br>
>> >> ><br>
>> >> > more imporatanlty, does all this actually matter at all if the SNR<br>
>> >> > seems<br>
>> >> > to<br>
>> >> > be ok.<br>
>> >> ><br>
>> >> > Denis<br>
>> >> ><br>
>> >> >><br>
>> >> >> On Thu, Aug 7, 2014 at 11:25 AM, Denis-Alexander Engemann<br>
>> >> >> <<a href="mailto:denis.engemann@gmail.com">denis.engemann@gmail.com</a>> wrote:<br>
>> >> >> > Dear list,<br>
>> >> >> ><br>
>> >> >> > I'm currently comparing group grand averages in a set of<br>
>> >> >> > functional<br>
>> >> >> > labels<br>
>> >> >> > which are derived from the PALS B12 Brodmann parcellation. These<br>
>> >> >> > were<br>
>> >> >> > then<br>
>> >> >> > used with subjects' stcs after morphing to fsaverage.<br>
>> >> >> > Now I'm really struck that with surface orientation AND mean<br>
>> >> >> > flipping<br>
>> >> >> > the<br>
>> >> >> > minima and maxima, even for dSPM shrink to values below 1 while<br>
>> >> >> > the<br>
>> >> >> > expected<br>
>> >> >> > temporal dynamics are preserved. In the 'wild', that is, *before*<br>
>> >> >> > averaging,<br>
>> >> >> > the signed dSPMS are between -7 and 8, just as the<br>
>> >> >> > free-orientation<br>
>> >> >> > dSPM<br>
>> >> >> > maxima are around 8 --- *after* --- averaging.<br>
>> >> >> ><br>
>> >> >> > I'm wondering whether this could be a result of the morphing, the<br>
>> >> >> > anatomical<br>
>> >> >> > variability, or even the segmentation quality.<br>
>> >> >> ><br>
>> >> >> > Any hint would be appreciated.<br>
>> >> >> ><br>
>> >> >> > Denis<br>
>> >> >> ><br>
>> >> >> > _______________________________________________<br>
>> >> >> > Mne_analysis mailing list<br>
>> >> >> > <a href="mailto:Mne_analysis@nmr.mgh.harvard.edu">Mne_analysis@nmr.mgh.harvard.edu</a><br>
>> >> >> > <a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a><br>
>> >> >> ><br>
>> >> >> ><br>
>> >> >> > The information in this e-mail is intended only for the person to<br>
>> >> >> > whom<br>
>> >> >> > it is<br>
>> >> >> > addressed. If you believe this e-mail was sent to you in error and<br>
>> >> >> > the<br>
>> >> >> > e-mail<br>
>> >> >> > contains patient information, please contact the Partners<br>
>> >> >> > Compliance<br>
>> >> >> > HelpLine at<br>
>> >> >> > <a href="http://www.partners.org/complianceline" target="_blank">http://www.partners.org/complianceline</a> . If the e-mail was sent to<br>
>> >> >> > you<br>
>> >> >> > in<br>
>> >> >> > error<br>
>> >> >> > but does not contain patient information, please contact the<br>
>> >> >> > sender<br>
>> >> >> > and<br>
>> >> >> > properly<br>
>> >> >> > dispose of the e-mail.<br>
>> >> >> ><br>
>> >> >> _______________________________________________<br>
>> >> >> Mne_analysis mailing list<br>
>> >> >> <a href="mailto:Mne_analysis@nmr.mgh.harvard.edu">Mne_analysis@nmr.mgh.harvard.edu</a><br>
>> >> >> <a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a><br>
>> >> ><br>
>> >> ><br>
>> >> ><br>
>> >> > _______________________________________________<br>
>> >> > Mne_analysis mailing list<br>
>> >> > <a href="mailto:Mne_analysis@nmr.mgh.harvard.edu">Mne_analysis@nmr.mgh.harvard.edu</a><br>
>> >> > <a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a><br>
>> >> ><br>
>> >> ><br>
>> >> > The information in this e-mail is intended only for the person to<br>
>> >> > whom<br>
>> >> > it is<br>
>> >> > addressed. If you believe this e-mail was sent to you in error and<br>
>> >> > the<br>
>> >> > e-mail<br>
>> >> > contains patient information, please contact the Partners Compliance<br>
>> >> > HelpLine at<br>
>> >> > <a href="http://www.partners.org/complianceline" target="_blank">http://www.partners.org/complianceline</a> . If the e-mail was sent to<br>
>> >> > you<br>
>> >> > in<br>
>> >> > error<br>
>> >> > but does not contain patient information, please contact the sender<br>
>> >> > and<br>
>> >> > properly<br>
>> >> > dispose of the e-mail.<br>
>> >> ><br>
>> >> _______________________________________________<br>
>> >> Mne_analysis mailing list<br>
>> >> <a href="mailto:Mne_analysis@nmr.mgh.harvard.edu">Mne_analysis@nmr.mgh.harvard.edu</a><br>
>> >> <a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a><br>
>> ><br>
>> ><br>
>> ><br>
>> > _______________________________________________<br>
>> > Mne_analysis mailing list<br>
>> > <a href="mailto:Mne_analysis@nmr.mgh.harvard.edu">Mne_analysis@nmr.mgh.harvard.edu</a><br>
>> > <a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a><br>
>> ><br>
>> ><br>
>> > The information in this e-mail is intended only for the person to whom<br>
>> > it is<br>
>> > addressed. If you believe this e-mail was sent to you in error and the<br>
>> > e-mail<br>
>> > contains patient information, please contact the Partners Compliance<br>
>> > HelpLine at<br>
>> > <a href="http://www.partners.org/complianceline" target="_blank">http://www.partners.org/complianceline</a> . If the e-mail was sent to you<br>
>> > in<br>
>> > error<br>
>> > but does not contain patient information, please contact the sender and<br>
>> > properly<br>
>> > dispose of the e-mail.<br>
>> ><br>
>> _______________________________________________<br>
>> Mne_analysis mailing list<br>
>> <a href="mailto:Mne_analysis@nmr.mgh.harvard.edu">Mne_analysis@nmr.mgh.harvard.edu</a><br>
>> <a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a><br>
><br>
><br>
><br>
> _______________________________________________<br>
> Mne_analysis mailing list<br>
> <a href="mailto:Mne_analysis@nmr.mgh.harvard.edu">Mne_analysis@nmr.mgh.harvard.edu</a><br>
> <a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a><br>
><br>
><br>
> The information in this e-mail is intended only for the person to whom it is<br>
> addressed. If you believe this e-mail was sent to you in error and the<br>
> e-mail<br>
> contains patient information, please contact the Partners Compliance<br>
> HelpLine at<br>
> <a href="http://www.partners.org/complianceline" target="_blank">http://www.partners.org/complianceline</a> . If the e-mail was sent to you in<br>
> error<br>
> but does not contain patient information, please contact the sender and<br>
> properly<br>
> dispose of the e-mail.<br>
><br>
_______________________________________________<br>
Mne_analysis mailing list<br>
<a href="mailto:Mne_analysis@nmr.mgh.harvard.edu">Mne_analysis@nmr.mgh.harvard.edu</a><br>
<a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a><br>
</div></div></blockquote></div><br></div></div>