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

[Alexandre Gramfort]

hi Laetitia,

this is extremely weird.

did you inspect the values inside the stc? maybe plot an histogram?

plt.hist(stc.data.ravel())

did you reconstruct only in a label?

Alex


On Thu, Nov 10, 2016 at 3:46 PM, Laetitia Grabot
<laetitia.grabot at gmail.com> wrote:
>
> 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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