[Mne_analysis] (no subject)

[Alexandre Gramfort]

hi Yuval,

> I am new to MNE and did not succeed to get things to work yet
> at the moment two things hold me:
> 1. mne_analyze open in a strange way. it is a narrow window with all the
> areas piled one over the other. there is little room to display anything
> this way (the surface of the head cannot be enlarged to cover more than
> 1cm). buttons also seem not to be displayed as meant to. I can however load
> and display headshape + MRI and realign. I am running ubutnu Pangolin 64bit.
> did anyone encountered such a problem?

how did you setup MNE?

did you actually source mne_setup_sh as explain on the website? or did you
manually set your PATH ?

you should do something like:

export MNE_ROOT=..
source $MNE_ROOT/bin/mne_setup_sh

at least if you use bash.

> 2. I work on 4D data after conversion to fif (thanks, Denis). after running
> freesurfer I align the MRI to the digitized headshape with mne_analyze and
> save MRI set and the transformation matrix. I then follow this pipeline:

how did you convert the 4d file? python or the mne C command?

maybe Denis can help you on this.

Alex

> mne_watershed_bem --atlas
> mne_setup_source_space --ico -6 --overwrite
> mne_setup_forward_model --homog --surf --ico 4
> mne_do_forward_solution --spacing oct-6 mindist --overwrite --meas
> 'subject1.fif' --megonly
> I get the following message:
>
> mne_forward_solution version 2.9 compiled at Jan  6 2011 02:25:30
> Source space                 :
> /usr/local/freesurfer/subjects/maor1/bem/maor1-oct-6-src.fif
> MRI -> head transform source : ./maor-trans.fif
> Measurement data             : maor.fif
> BEM model                    :
> /usr/local/freesurfer/subjects/maor1/bem/maor1-5120-bem.fif
> Accurate field computations
> Do computations in head coordinates.
> Free source orientations
> Destination for the solution : ./maor-oct-6-fwd.fif
> Reading /usr/local/freesurfer/subjects/maor1/bem/maor1-oct-6-src.fif...
> Read 2 source spaces a total of 8196 active source locations
> Coordinate transformation: MRI (surface RAS) -> head
>  0.000000  0.951057  0.309017   18.33 mm
> -1.000000 -0.000000  0.000000   -3.00 mm
>  0.000000 -0.309017  0.951057   43.46 mm
>  0.000000  0.000000  0.000000     1.00
> MEG -> head coordinate transformation not found.
> Forward computation failed (see above)
>
> I found a similar report here:
> https://mail.nmr.mgh.harvard.edu/pipermail//mne_analysis/2012-April/001003.html
> but I did not see a solution there.
>
> Thanks
> Yuval
>
>
> --
>
> Dr .Harpaz
>
> BIU MEG lab
>
>
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