[Mne_analysis] Spatiotemporal cluster test in a subset of vertices

Tal Linzen tal.linzen at gmail.com
Mon Aug 18 07:52:08 EDT 2014
Search archives:

Thanks for your replies. Is this the right way to use spatial_exclude? I
think I might be missing something, because the clusters are *kind of* in
the ROI I would want them to be in but also spill out of the ROI:

        vertices = np.arange(5124)
        *excluded_vertices = vertices[~np.in1d(vertices, label.vertices)]*
        tris = mne.source_estimate.grade_to_tris(4)
        connectivity = mne.source_estimate.spatial_tris_connectivity(tris)
        clu = mne.stats.spatio_temporal_cluster_1samp_test(
            data, connectivity=connectivity, n_jobs=2,
            n_permutations=n_permutations, threshold=t_threshold,
            spatial_exclude=excluded_vertices)

Does anything jump out at you? Otherwise I can put my data somewhere online
and we can take a look together.

Thanks!

Tal


On Tue, Aug 12, 2014 at 7:55 AM, Denis-Alexander Engemann <
denis.engemann at gmail.com> wrote:

> Hi Tal,
>
> also have a look at this example (in combination wtih #1503):
>
> https://gist.github.com/dengemann/ea482183be869568412c
>
> Denis
>
>
> On Tue, Aug 12, 2014 at 1:16 AM, Eric Larson <larson.eric.d at gmail.com>
> wrote:
>
>> For now, you can use the `spatial_exclude` parameter of the clustering
>> functions to exclude all the source space vertices outside your label:
>>
>>
>> http://martinos.org/mne/stable/generated/mne.stats.spatio_temporal_cluster_1samp_test.html#mne.stats.spatio_temporal_cluster_1samp_test
>>
>> Denis also has some work going to make it easier:
>>
>> https://github.com/mne-tools/mne-python/pull/1503
>>
>> Eric
>>
>>
>>
>>  On Mon, Aug 11, 2014 at 4:05 PM, Tal Linzen <tal.linzen at gmail.com>
>> wrote:
>>
>>>  Hi all,
>>>
>>> How do I restrict the spatiotemporal cluster test to a label? I've been
>>> trying to work off of this example:
>>>
>>>
>>> http://martinos.org/mne/stable/auto_examples/stats/plot_cluster_stats_spatio_temporal.html
>>>
>>> And zeroed in on the following line as the line I'd probably want to
>>> modify:
>>>
>>> connectivity = spatial_tris_connectivity(grade_to_tris(5))
>>>
>>> But this is pretty opaque to me and I'm not sure what the next step
>>> would be.
>>>
>>> Thanks,
>>> Tal
>>>
>>> _______________________________________________
>>> Mne_analysis mailing list
>>> Mne_analysis at nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>
>>>
>>> The information in this e-mail is intended only for the person to whom
>>> it is
>>> addressed. If you believe this e-mail was sent to you in error and the
>>> e-mail
>>> contains patient information, please contact the Partners Compliance
>>> HelpLine at
>>> http://www.partners.org/complianceline . If the e-mail was sent to you
>>> in error
>>> but does not contain patient information, please contact the sender and
>>> properly
>>> dispose of the e-mail.
>>>
>>>
>>
>> _______________________________________________
>> Mne_analysis mailing list
>> Mne_analysis at nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20140818/1e4199bb/attachment.html 


More information about the Mne_analysis mailing list