[Mne_analysis] Problem using mne_analyze

[Peter Glynn]

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

On Thu, Sep 22, 2011 at 9:25 AM, Matti Hamalainen
<msh at nmr.mgh.harvard.edu>wrote:

>
> 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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> > Mne_analysis at nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >
> >
>
>
>
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