[Mne_analysis] Generating labels with mne_python

[Martin Luessi]

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
> 149 13th Street
> Charlestown, MA 02129
>
> Fax: +1 617 726-7422
>
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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