[Mne_analysis] Fwd: smooth parameter in morph_data: default to change?

Laetitia Grabot laetitia.grabot at gmail.com
Thu Nov 10 09:46:24 EST 2016
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2016-11-10 15:29 GMT+01:00 dgw <dgwakeman at gmail.com>:

> Hi Laetitia,
>
> I think it would be best to take a step back and see how you got these
> results. I have a number of questions.
>
> 1. How did you produce the individual result? This looks very odd to
> me (it seems to only show activity in very narrow strips, which is
> unusual).
>

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)

>
> 2. Have you checked the FreeSurfer segmentation and labels to
> fsaverage? (The data seem to be rotated somehow).
>
>
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.


> 3. Can you provide an abbreviated version the code you used to produce
> this affect?
>

For the stc smooth=1, I run the line :
stc_fs = mne.morph_data(subject, 'fsaverage', stc, fsave_vertices, 1,
SUBJECTS_DIR, n_jobs=3)

For the stc smooth=None, I run the line :
stc_fs = mne.morph_data(subject, 'fsaverage', stc, fsave_vertices, None,
SUBJECTS_DIR, n_jobs=3)



>
> Thanks!
> d
>
> On Thu, Nov 10, 2016 at 9:15 AM, Laetitia Grabot
> <laetitia.grabot at gmail.com> wrote:
> >
> > Dear MNE-users,
> >
> > I would like to draw your attention on the importance of the smooth
> > parameter used to morph a source estimate from an individual's brain to
> an
> > average brain (fsaverage). By default, this parameter is set to None and
> the
> > doc precised that, in this case, the smooth parameter is automatically
> > defined to fill the surface with non-zeros value. Yet, it happen to me
> that
> > the produced source estimates are sometimes unreliable.
> >
> > I attached snapshot where you can see data (here PSD) in the visual
> cortex
> > (nativeBrain). These data are correctly morphed into fsaverage brain when
> > the smooth parameter is set to 1. However, the source estimate created
> with
> > smooth=None does not make sense.
> >
> > Maybe it would be better than the default parameter is set to 1 and not
> to
> > None, or at least that a warning informs which smooth parameter was
> finally
> > used.
> >
> > Best,
> > Laetitia
> >
> >
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