Dear Qunxi,
the output of `summarize_clusters_stc’ is a bit poorly documented (I’ve opened a pull request for it to be fixed in future versions of MNE).
The output is as follows:
out : instance of SourceEstimate
A summary of the clusters. The first time point in this SourceEstimate
object is the summation of all the clusters. Subsequent time points
contain each individual cluster. The magniture of the activity
corresponds to the length the cluster spans in time (in samples).
So it is perfectly reasonable to create labels from the clusters. However, you do not need to take the mean across the time points or anything like that. Also, thresholding does not do what you want. Instead, this should work:
stc = summarize_clusters_stc(clu, p_thre, tstep=tstep,
tmin=tmin, vertices=fsave_vertices,
subject='fsaverage')
lh_labels, rh_labels = mne.stc_to_label(stc, src=src, smooth=True,
subjects_dir=subjects_dir, connected=True)
The labels look bigger than the clusters as visualised with stc.plot(…), because the plotting functions applies its own thesholding. Try to visualise it without any thresholding by doing this:
b = stc.plot(hemi=‘both’, subject=subject, subject_dir=subject_dir)
b.scale_data_colormap(0, stc.data.mean(), stc.data.max(), True)
Let me know if you have further questions.
Marijn.
--
Marijn van Vliet
w.m.vanvliet at gmail.com
> On 11 Aug 2016, at 19:09, 董群喜 <dongqunxi at gmail.com> wrote:
>
> Dear all,
>
> For you easier understanding my problem, I made a gist and paste the critical codes in the following link:
> https://gist.github.com/dongqunxi/daca753366c592927ff789c03aa6ed0b
> Thanks, looking forward to your response.
>
> Best wishes,
> Qunxi Dong
>
> 2016-08-11 17:52 GMT+02:00 董群喜 <dongqunxi at gmail.com>:
> Dear All,
>
> Recently, I am trying to make functional labels from a group of subjects.
> I first refer the 2sample clustering scripts. I get some significant clusters and derive the source estimates.
> if I apply 'stc_to_label' to make functional labels directly, the size of the functional labels is too large.
> I also try to use percentile of 95 to restrict the size, but I can not explain what the actual meaning
> of this threshold.
> Can someone give me some tips?
> Thanks a lot!
>
> Best wishes,
> Qunxi Dong
>
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