[Mne_analysis] Generating labels with mne_python

[Eric Larson]

FYI, the branch for PySurfer to handle mne-python's label objects has
actually already been merged, the linked PR is for a different (much
bigger) can of worms... you should be able to do Brain.add_label(label)
once you've loaded

If you don't want to deal with the private _find_clusters functions, you
should also be able to use the standard statistical clustering functions,
but just use a dummy stat_fun (instead of e.g., ttest_1samp). If you can't
figure it out, give me a shout and I can probably write a few lines of code
for it.

Eric



On Wed, Aug 7, 2013 at 12:50 PM, Martin Luessi
<mluessi at nmr.mgh.harvard.edu>wrote:

> Hi Luke,
>
> On 08/07/13 15:40, Luke Bloy wrote:
> > Thanks Martin,
> >
> > What's the best way to expose mne.stats._find_clusters to my code. I'd
> > rather not fiddle with ../stats/__init.py if I can avoid it.
>
> use
>
> from mne.stats.cluster_level import _find_clusters
>
> what I wrote below (mne.stats._find_clusters) doesn't work because the
> function is not directly visible from mne.stats. Also, not that the
> leading "_" indicates that this is a "private function", i.e., it is
> only used internally in MNE-Python and the API may change from one
> release to the next without notification. But this code is fairly
> stable, so this shouldn't be a problem.
>
> Also, I forgot to answer your second question. You currently have to
> save the label as a file to show it in PySurfer. There is work in the
> pipeline to make it possible to pass labels directly, see:
>
> https://github.com/nipy/PySurfer/pull/53
>
> Best,
>
> Martin
>
>
> > Luke
> >
> > -----Original Message-----
> > From: Martin Luessi [mailto:mluessi at nmr.mgh.harvard.edu]
> > Sent: Wednesday, August 07, 2013 2:24 PM
> > To: Luke Bloy
> > Cc: mne_analysis at nmr.mgh.harvard.edu
> > Subject: Re: [Mne_analysis] Generating labels with mne_python
> >
> > Hi Luke,
> >
> > MNE-Python currently doesn't have a function that does exactly what you
> > want, but it should be possible to put something together to get the
> desired
> > result. I would do something like this:
> >
> > 1) Use mne.spatial_src_connectivity to get a connectivity matrix that
> > describes the neighbor relations in source space. The "src" parameter is
> the
> > source space, e.g., "inv['src']", where inv is your inverse operator.
> >
> > 2) Use mne.stats._find_clusters and pass in "stc.data[:, idx]" where idx
> > selects a single time point. This function will return a list of clusters
> > (connected components)
> >
> > 3) For each cluster, generate a SourceEstimate using the original source
> > space (so stc_cluster.vertices is the same as in stc). Set the data of
> > stc_cluster to all-zero except inside the cluster (use e.g. 1.0). Pass
> > stc_cluster to mne.stc_to_label to generate a Label from it. Save the
> > labels, add it to a list, etc.
> >
> > I hope this helps,
> >
> > Martin
> >
> > On 08/07/13 13:57, Luke Bloy wrote:
> >> Hi all,
> >>
> >> I am interested in generating a label from an stc. What I would like
> >> is to be able to supply a seed and a threshold, and to get as output a
> >> label consisting of the source points  connected to the seed and above
> >> threshold. Basically I'd like to be able to compute connected
> >> components on stcs. Has this been implemented? If not could someone
> >> maybe help me out by pointing to how I could get neighborhood
> >> information from the src space? Alternatively, can someone think of a
> >> way to combine thresholding stc.data with mne.label.grow_label to do
> what
> > I want?
> >>
> >> A second easier question. Is there an simple way to show labels on a
> >> pysurfer plot. At the moment I'm generating the label, then saving it
> >> to disk and using 'brain.add_label' to load the label from disk. Is
> >> there a more straight forward way that I'm missing.
> >>
> >> Thanks
> >>
> >> Luke
> >>
> >>
> >>
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> >>
> >
> >
> > --
> > Martin Luessi, Ph.D.
> >
> > Research Fellow
> >
> > Department of Radiology
> > Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General
> > Hospital Harvard Medical School
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> >
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> --
> Martin Luessi, Ph.D.
>
> Research Fellow
>
> Department of Radiology
> Athinoula A. Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> Harvard Medical School
> 149 13th Street
> Charlestown, MA 02129
>
> Fax: +1 617 726-7422
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