[Mne_analysis] Alternatives to mne_analyze for drawing functional ROIs

[Victoria Sharpe]

Hi, Matti,

This is what happens:

First, I load the inflated brain for fsaverage as a surface. Then, I go to
overlayManager and load my averaged stc (the average of the binary stcs for
each participant that I made in mne_make_movie). I choose either "apply" or
"ok" or "show" (I've tried them all with no difference in success) in the
overlayManager and the stc is overlaid on the fsaverage brain. However,
there does not appear to be a way to change the timepoint (between 150 and
350 ms), so I go back to the overlayManager. A sliding time scale has
appeared in the overlayManager (that was not there before), but before I
can use it, mne_analyze crashes.

I've also tried loading my stc before loading the fsaverage surface, but
mne_analyze doesn't like this either--it doesn't show the overlay or the
surface. I've also tried loading one of the individual participants'
stcs--no change.

I'm using Yosemite.

Best,

Tori


Date: Fri, 11 Dec 2015 06:54:16 +0200
From: Matti Hamalainen <msh at nmr.mgh.harvard.edu>
Subject: Re: [Mne_analysis] Alternatives to mne_analyze for drawing
        functional ROIs
To: Discussion and support forum for the users of MNE Software
        <mne_analysis at nmr.mgh.harvard.edu>
Message-ID: <4E393E80-DB00-4ACE-82F2-407030332249 at nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="us-ascii"


Hi Tori,

Can you explain the exact circumstances when this happens? I am using
mne_analyze quite successfully on my Mac.
Also, which Mac OSX version are you using?

- Matti


> On Dec 10, 2015, at 11:06 PM, Victoria Sharpe <vs1666 at nyu.edu> wrote:
>
> Dear List,
>
>
> This is a two-part question, which I'll preface by saying that I've been
attempting to use mne_analyze  to draw functional ROIs based on the
averaged left hemisphere stc for a group of subjects. Stcs were made using
mne_make_movie and averaged with mne_average_estimates. However, mne keeps
crashing, usually when I  open the overlayManager. I get this error message:
>
> error: xp_attach_gl_context returned: 2
> Ignoring Xlib error: error code 0 request code 150
> Segmentation fault
>
>
> So, my first question is whether there is a fix for this. I've already
updated XQuartz, which did not fix the problem.
>
> My second question is whether there is an alternative for drawing
functional ROIs that wouldn't require using mne_analyze. Perhaps an
implementation in MNE Python?
>
>
>
> Any help would be appreciated.
>
> Best,
>
> Tori
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> Mne_analysis at nmr.mgh.harvard.edu
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