[Mne_analysis] Generating labels with mne_python

[Luke Bloy]

Thank you both for the help. I got it working reasonably well.

I might throw together an example, and send it to the list, if i get some
time.

Thanks again,
Luke


On Wed, Aug 7, 2013 at 4:58 PM, Eric Larson <larson.eric.d at gmail.com> wrote:

> 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
>> >>
>> >>
>> >>
>> >> _______________________________________________
>> >> Mne_analysis mailing list
>> >> Mne_analysis at nmr.mgh.harvard.edu
>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>> >>
>> >
>> >
>> > --
>> > 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
>> >
>> >
>> > 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.
>> >
>> >
>> >
>>
>>
>> --
>> 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
>> _______________________________________________
>> Mne_analysis mailing list
>> Mne_analysis at nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20130809/674ad7a0/attachment.html