Problem using mne_analyze

✉️ Mailing List Archive (read-only)
1

Hi,

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. 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

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!

Peter
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2

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

3

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

4

Thank you for the responses! I moved on to the viewer, but quickly
encountered another problem. After I set the LAP, Nasion, and RAP, and then
click 'align using fiducials' nothing seems to happen. No coordinate
transformation matrix appears. If I make the digitizer data visible again,
it is no closer to the scalp surface. Any thoughts on what I could be doing
wrong? Sorry for all the questions!

Peter