[Mne_analysis] Generating labels with mne_python

Tue Sep 3 12:48:46 EDT 2013

hi Luke,

FYI the pull request is now merged. See:

https://github.com/mne-tools/mne-python/pull/730

your example is now reproduced with this script:

https://github.com/mne-tools/mne-python/blob/master/examples/inverse/plot_label_from_stc.py

Best,
Alex

On Sat, Aug 24, 2013 at 4:40 PM, Alexandre Gramfort
<alexandre.gramfort at telecom-paristech.fr> wrote:
> Hi Luke,
>
> thanks for sharing. I've simplified a bit the example and opened a pull request:
>
> https://github.com/mne-tools/mne-python/pull/730
>
> You can follow the progress there.
>
> Alex
>
>
> On Fri, Aug 23, 2013 at 11:19 PM, Luke Bloy <luke.bloy at gmail.com> wrote:
>> Hi Everyone,
>>
>> I put together a quick example of generating labels in case others end up
>> with a similar problem.
>>
>> Enjoy.
>> Luke
>>
>>
>> On Fri, Aug 9, 2013 at 2:34 PM, Luke Bloy <luke.bloy at gmail.com> wrote:
>>>
>>> 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
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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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>>>>> Mne_analysis mailing list
>>>>> Mne_analysis at nmr.mgh.harvard.edu
>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>>
>>>>
>>>
>>
>>
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