[Mne_analysis] Overlaying multiple labels on a surface in mne_analyze

[Stephen Politzer-Ahles]

Thanks, I'll give that a shot!



Stephen Politzer-Ahles
New York University, Abu Dhabi
Psychology Department
http://files.nyu.edu/spa268/public


On Tue, Aug 13, 2013 at 6:43 PM, Eric Larson <larson.eric.d at gmail.com>wrote:

> Hey Steve,
>
> In mne-python, you can load your label using 'label = mne.read_label(...)'
> and then just use the 'label.smooth(...)' method -- it will do exactly what
> you want, namely fill in a label so it becomes contiguous if it was
> produced on a decimated surface. If the label was produced on fsaverage, 2
> smoothing steps should be enough (although it will look jagged so 3-5 might
> look better), otherwise you might need more. Drawing labels in PySurfer is
> then as easy as doing brain.add_label(label, color='r', alpha=0.5), because
> it has been coded to understand mne-python Label objects. One of the
> options for "add_label" is to use outlines. PySurfer then also has a
> brain.save_image() method to save the image. This makes scripting figures
> easy, if you're into that. This is the pipeline I've adopted recently with
> seemingly nice results.
>
> Eric
>
>
>
> On Tue, Aug 13, 2013 at 7:23 AM, Stephen Politzer-Ahles <
> politzerahless at gmail.com> wrote:
>
>> Hi Eric,
>>
>> Thanks for the feedback. Is it also possible to draw labels in PySurfer?
>> The reason I ask is because I have some funky labels (labels which were
>> defined on a decimated source space instead of a Freesurfer surface, so
>> when I plot them they show up as a bunch of disconnected points rather than
>> as nice contiguous areas), so I was hoping to just draw labels around them
>> to make nicer-looking plots; but to keep them from overlapping with
>> neighboring labels, I would probably need to be able to overlay a few at
>> once. (I tried doing this in Freesurfer by turning my labels into an
>> annotation and plotting the annotation, but I've been running into issues
>> with that pipeline, so I thought I'd try it in MNE instead.)
>>
>> Best,
>> Steve
>>
>>
>>
>> Stephen Politzer-Ahles
>> New York University, Abu Dhabi
>> Psychology Department
>> http://files.nyu.edu/spa268/public
>>
>>
>> On Tue, Aug 13, 2013 at 6:07 PM, Eric Larson <larson.eric.d at gmail.com>wrote:
>>
>>> I have not found a way to do it in mne_analyze, but it is quite easy in
>>> PySurfer.
>>>
>>> Best,
>>> Eric
>>>  On Aug 13, 2013 1:32 AM, "Stephen Politzer-Ahles" <
>>> politzerahless at gmail.com> wrote:
>>>
>>>> Hi,
>>>>
>>>> Is it possible to overlay multiple layers at the same time (ideally in
>>>> different colors) on a surface in mne_analyze?
>>>>
>>>> Thanks,
>>>> Steve
>>>>
>>>>
>>>> Stephen Politzer-Ahles
>>>> New York University, Abu Dhabi
>>>> Psychology Department
>>>> http://files.nyu.edu/spa268/public
>>>>
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