[Mne_analysis] Problem using mne_analyze

[Matti Hamalainen]

Hello Peter,

The *warning* message is not serious. The mri volume viewer (View/Show MRI viewer...) still works. However, transformation from MRI (Surface RAS) to Talairach coordinates will not be available. The "sample" subject reconstruction is so old that the mgz format was not invented yet.

- Matti


On Sep 22, 2011, at 9:05 AM, Alexandre Gramfort wrote:

> Hello Peter,
> 
>> I am new to MNE (and linux) and I am running through the sample data set for
>> practice. Everything seemed to be working fine until I had to use
>> mne_analze. I loaded the digitizer data from the sample_audvis_raw.fif file,
>> and got a message saying that 146 digitizer points had been loaded from the
>> file. But nothing was brought up in the gui besides this message, so I'm not
>> sure this step worked completely.
> 
> yes so far so good.
> 
>> When I went to load the inflated surface,
>> a message appears in the gui saying "No data loaded" and the following
>> appears in the terminal window:
>> 
>> Loading surface
>> /home/pglynn/Desktop/SampleData/subjects/sample/surf/lh.inflated ...
>> Quad file : nvert = 154409 nquad = 154430
>>         Warning : zero size triangle # 40062
>>         Triangle and vertex normals and neighboring triangles...[done]
>>         Vertex neighbors...[done]
>>         Distances between neighboring vertices...[926574 distances done]
>>         Warning: 6 vertices had incorrect number of distinct neighbors
>> (fixed).
>> Loading surface
>> /home/pglynn/Desktop/SampleData/subjects/sample/surf/rh.inflated ...
>> Quad file : nvert = 150548 nquad = 150574
>>         Triangle and vertex normals and neighboring triangles...[done]
>>         Vertex neighbors...[done]
>>         Distances between neighboring vertices...[903438 distances done]
>>         Warning: 6 vertices had incorrect number of distinct neighbors
>> (fixed).
>> Warning : /home/pglynn/Desktop/SampleData/subjects/sample/mri/T1.mgz does
>> not exist or is not readable
> 
> are you sure that this mri volume is at this location on your hard disk?
> 
> For the next you need to go in View > Show viewer
> 
> then options and click on digitizer data.
> 
>> Any ideas as to what the problem is? When would the T1.mgz file have been
>> generated/modified? Was my download incomplete from the beginning? Any help
>> would be much appreciated! Thanks!
> 
> hope this helps
> 
> if you want the new sample dataset preprocessed that will be coming
> with the new release of MNE:
> 
> ftp://surfer.nmr.mgh.harvard.edu/pub/data/MNE-sample-data-processed.tar.gz
> 
> Alex
> 
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