<div dir="ltr"><div class="gmail_extra"><br><div class="gmail_quote">2016-11-10 15:29 GMT+01:00 dgw <span dir="ltr"><<a href="mailto:dgwakeman@gmail.com" target="_blank">dgwakeman@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Laetitia,<br>
<br>
I think it would be best to take a step back and see how you got these<br>
results. I have a number of questions.<br>
<br>
1. How did you produce the individual result? This looks very odd to<br>
me (it seems to only show activity in very narrow strips, which is<br>
unusual).<br></blockquote><div><br></div><div>The data are PSD (zscore relative to baseline) at the stimulation frequency of a black and white stimulus and my aim was to create a retinotopic map so, in that respect, the present map does not seem odd (and I use a small smoothing parameter in mne_analyze visualization, like 5 i think) </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<br>
2. Have you checked the FreeSurfer segmentation and labels to<br>
fsaverage? (The data seem to be rotated somehow).<br>
<br></blockquote><div><br></div><div>I'm not sure I get your point, which data seems rotated? The one for smooth=1 or smooth=None? See attached the same data in the native brain space, they fit well with the fsaverage data for smooth=1.</div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
3. Can you provide an abbreviated version the code you used to produce<br>
this affect?<br></blockquote><div><br></div><div>For the stc smooth=1, I run the line :</div><div>stc_fs = mne.morph_data(subject, 'fsaverage', stc, fsave_vertices, 1, SUBJECTS_DIR, n_jobs=3)</div><div><br></div><div>For the stc smooth=None, I run the line :</div><div>stc_fs = mne.morph_data(subject, 'fsaverage', stc, fsave_vertices, None, SUBJECTS_DIR, n_jobs=3)</div><div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<br>
Thanks!<br>
d<br>
<div><div class="gmail-h5"><br>
On Thu, Nov 10, 2016 at 9:15 AM, Laetitia Grabot<br>
<<a href="mailto:laetitia.grabot@gmail.com">laetitia.grabot@gmail.com</a>> wrote:<br>
><br>
> Dear MNE-users,<br>
><br>
> I would like to draw your attention on the importance of the smooth<br>
> parameter used to morph a source estimate from an individual's brain to an<br>
> average brain (fsaverage). By default, this parameter is set to None and the<br>
> doc precised that, in this case, the smooth parameter is automatically<br>
> defined to fill the surface with non-zeros value. Yet, it happen to me that<br>
> the produced source estimates are sometimes unreliable.<br>
><br>
> I attached snapshot where you can see data (here PSD) in the visual cortex<br>
> (nativeBrain). These data are correctly morphed into fsaverage brain when<br>
> the smooth parameter is set to 1. However, the source estimate created with<br>
> smooth=None does not make sense.<br>
><br>
> Maybe it would be better than the default parameter is set to 1 and not to<br>
> None, or at least that a warning informs which smooth parameter was finally<br>
> used.<br>
><br>
> Best,<br>
> Laetitia<br>
><br>
><br>
</div></div>> ______________________________<wbr>_________________<br>
> Mne_analysis mailing list<br>
> <a href="mailto:Mne_analysis@nmr.mgh.harvard.edu">Mne_analysis@nmr.mgh.harvard.<wbr>edu</a><br>
> <a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" rel="noreferrer" target="_blank">https://mail.nmr.mgh.harvard.<wbr>edu/mailman/listinfo/mne_<wbr>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" rel="noreferrer" target="_blank">http://www.partners.org/<wbr>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>
______________________________<wbr>_________________<br>
Mne_analysis mailing list<br>
<a href="mailto:Mne_analysis@nmr.mgh.harvard.edu">Mne_analysis@nmr.mgh.harvard.<wbr>edu</a><br>
<a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" rel="noreferrer" target="_blank">https://mail.nmr.mgh.harvard.<wbr>edu/mailman/listinfo/mne_<wbr>analysis</a><br>
</blockquote></div><br></div></div>