[Mne_analysis] Expand Labels

Eric Larson larson.eric.d at gmail.com
Sat Apr 11 19:40:45 EDT 2020
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Perhaps one of these will do it?

https://mne.tools/dev/generated/mne.grow_labels.html
https://mne.tools/dev/generated/mne.Label.html#mne.Label.smooth

Eric


On Fri, Apr 10, 2020 at 5:37 PM Geller, Jason <jason-geller at uiowa.edu>
wrote:

>         External Email - Use Caution
>
> Hi!
>
> I am trying to expand soruce labels to make them a little bigger. Is there
> an easy way to do this in MNE?
>
> Thanks,
>
> Jason
>
>
>
> > On Apr 10, 2020, at 11:00 AM, mne_analysis-request at nmr.mgh.harvard.edu
> wrote:
> >
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> > Today's Topics:
> >
> >   1. Question about permutation testing (Dirk van Moorselaar)
> >   2. Re: Question about permutation testing (Eric Larson)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Fri, 10 Apr 2020 15:12:05 +0200
> > From: Dirk van Moorselaar <dirkvanmoorselaar at gmail.com>
> > Subject: [Mne_analysis] Question about permutation testing
> > To: mne_analysis at nmr.mgh.harvard.edu
> > Message-ID: <2865A9FD-02A0-4A96-9CAF-4BC415C2678D at gmail.com>
> > Content-Type: text/plain; charset="us-ascii"
> >
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> >
> > Dear MNE users,
> >
> > I have a question about using permutation tests to compare decoding
> accuracy across time between two conditions. Specifically, I am interested
> to see whether these conditions not only differ during stimulus
> presentation, but also already in anticipation of a new (search) display. I
> have a within subject design so I am running the following code
> >
> > t_obs, clusters, cluster_pv, H0 =
> mne.stats.permutation_cluster_1samp_test(X_1 - X_2)
> >
> > If I then inspect the results, I get significant clusters during
> stimulus presentation (which is nice. However, there are  no significant
> anticipatory clusters, even though numerically the conditions clearly
> differ.
> > Interestingly, I am able to make these anticipatory clusters significant
> if instead of analysing the whole time course, I limit the permutation test
> to the anticipatory window. I assume that this is the case because the
> anticipatory cluster is smaller than the reactive cluster????
> >
> > My question is whether this is a valid approach, and if not whether
> there is another alternative way to still show that the conditions already
> differ before stimulus processing.
> >
> > Thanks in advance,
> >
> > Dirk van Moorselaar
> >
> >
> >
> >
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Fri, 10 Apr 2020 09:42:23 -0400
> > From: Eric Larson <larson.eric.d at gmail.com>
> > Subject: Re: [Mne_analysis] Question about permutation testing
> > To: Discussion and support forum for the users of MNE Software
> >       <mne_analysis at nmr.mgh.harvard.edu>
> > Message-ID:
> >       <
> CAGu2niXPm+nAXyXX-rzpK3XCd8uEZvg2SU55KPF-o2B5Q15oAg at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> >        External Email - Use Caution
> >
> >>
> >> If I then inspect the results, I get significant clusters during
> stimulus
> >> presentation (which is nice. However, there are  no significant
> >> anticipatory clusters, even though numerically the conditions clearly
> >> differ.
> >> Interestingly, I am able to make these anticipatory clusters significant
> >> if instead of analysing the whole time course, I limit the permutation
> test
> >> to the anticipatory window. I assume that this is the case because the
> >> anticipatory cluster is smaller than the reactive cluster????
> >>
> >
> > The `step_down_p` is meant to deal with this case. Basically it runs the
> > clustering, and if it finds any clusters below the step_down_p threshold
> > (usually 0.05 is a good choice), it cuts those data points out of the
> > analysis and redoes the permutation test. This prevents the first cluster
> > from dominating the H0 values, increasing sensitivity to smaller but
> still
> > valid effects.
> >
> > My question is whether this is a valid approach, and if not whether there
> >> is another alternative way to still show that the conditions already
> differ
> >> before stimulus processing.
> >>
> >
> > It seems reasonable, but keep in mind that interpreting
> > cluster spatio-temporal locations from tests is considered problematic
> (see
> > the bottom of this section in our stats tutorial
> > <
> https://mne.tools/dev/auto_tutorials/discussions/plot_background_statistics.html#clustering
> >,
> > and the linked Fieldtrip tutorial
> > <
> http://www.fieldtriptoolbox.org/faq/how_not_to_interpret_results_from_a_cluster-based_permutation_test/
> >).
> > A potential workaround is to use TFCE (see the stats tutorial), though it
> > will take longer to run.
> > <
> http://www.fieldtriptoolbox.org/faq/how_not_to_interpret_results_from_a_cluster-based_permutation_test/
> >
> >
> > Eric
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