[Mne_analysis] mne_analyze Xmsh_error_popup: "Please load the main surfaces first"

Björn Herrmann herrmann.b at gmail.com
Thu Mar 10 14:07:44 EST 2016
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Hi Alex, Tristan and others,

my problem was indeed that I did not run this

. $MNE_ROOT/bin/mne_setup_sh

Running this did the trick. It seems at my previous institute it was
initialized automatically, so i did not think of it. Awesome. Tristan
seems to have posted it on the MNE list by now.
Thank you for your help. I really appreciate it.
I can finally move on with my data analysis.
Bjorn




-----------------------------------------------------------------
Bjorn,

do you see something like this :

http://martinos.org/mne/dev/manual/gui/analyze.html#the-main-window

when starting mne_analyze ?

If not you're not setting up the mne environment properly.

A


>
> ----------------
>
> Hi Björn,
>
> Does the inflated surface show up in the mne_analyze window? Is there
> any information in the terminal?
>
> Thanks
> d
>
>
> On Wed, Mar 2, 2016 at 1:27 PM, Björn Herrmann <herrmann.b at gmail.com> wrote:
>> Hello members,
>>
>> I found a problem in the list's archives which I have as well (I
>> copied it below). Tristan described it in detail (see below), so I
>> won't repeat it here (problem to open the viewer in mne_analyze). I
>> followed Alex's suggestion using the sample data set, but the problem
>> remains. I use the newest MNE version (Tristan seemed to have used an
>> older one) on a new Ubuntu Linux 64bit. Maybe one of you has a
>> solution? Currently, I cannot co-register the MRI and MEG.
>> Thank you for any help.
>>
>>
>> Björn
>>
>> -----------------
>>
>> hi Tristan,
>>
>> do you have the same problem when trying using the MNE sample data?
>>
>> https://mne-tools.s3.amazonaws.com/datasets/MNE-sample-data-processed.tar.gz
>>
>> if this works make sure your respect the layout of the anatomical
>> files on disk for your subjects.
>>
>> Let us know how it goes.
>>
>> Alex
>>
>>
>> On Tue, Mar 1, 2016 at 8:48 AM, Nakagawa Tristan T
>> <nakagawa-t at ifrec.osaka-u.ac.jp> wrote:
>>> Hi,
>>>
>>> I am trying to coregister my MEG and T1 images, but I am stuck at
>>> aligning the coordinate frameworks:
>>> http://martinos.org/mne/stable/manual/cookbook.html#aligning-coordinate-frames
>>>
>>> I successfully created the surface models with mne_setup_source_space
>>> and mne_watershed_bme and linked them,
>>> created a forward model with mne_setup_forward_model,
>>>
>>> And when opening mne_analyze, I get a list of Surfaces to be loaded for
>>> the subject (inflated being pre-marked).
>>> When loading any surface by pressing ok, The loading dialog closes with
>>> no error.
>>>
>>> However, the Viewer gives the above mentioned error and doesn't open.
>>> ShowMRIViewer works, but when trying to open the viewer I get the error
>>> above.
>>>
>>> I can load digitizer points. I use mne_analyze version 2.56 on ubuntu
>>> linux x64.
>>>
>>> Thanks for any help,
>>>
>>> Tristan
>>>
>>> --
>>> Tristan T. Nakagawa, Ph.D.
>>> Laboratory for Brain-Immune Interaction,
>>> iFReC, Osaka University
>>> 3-1 Yamadaoka, Suita, Osaka, Japan
>>> Tel: 0668789710
>>> Office: CiNet R 2B6-2
>>> http://seymourlab.com
>>
>
>
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