[Mne_analysis] Overlaying multiple labels on a surface in mne_analyze

[Luke Bloy]

Hi Eric,

 

What's the best way to install pysurfer to get this label ability. I've been
using the version the gets installed via pip. But that is pysurfer 0.3.1 is
there a newer release that has this change. Should I just grab the master
branch from git hub and install from source? How stable is the master
branch?

 

Thanks.

Luke

 

From: mne_analysis-bounces at nmr.mgh.harvard.edu
[mailto:mne_analysis-bounces at nmr.mgh.harvard.edu] On Behalf Of Eric Larson
Sent: Tuesday, August 13, 2013 10:44 AM
To: Stephen Politzer-Ahles
Cc: mne_analysis at nmr.mgh.harvard.edu
Subject: Re: [Mne_analysis] Overlaying multiple labels on a surface in
mne_analyze

 

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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