[FieldTrip] MNE tutorial

[Bruno L. Giordano]

Hi Robin,

I had a similar problem during the field trip course. In my case I found
out that one set of coordinates was in mm and then other in m, so I just
had to multiply one set of coordinates.

Another thing you should be aware of is that you can segment your
anatomical using procedures other than the default ones. For example, Spm12
has new, better procedures. Importing an already prepared segmentation in
ft requires some hacking, but if you are interested I can tell you how as
soon as I get a decent internet connection.

Finally, remember that the single shell model is not that great. You should
prepare a better volume conduction model.

    Bruno
On May 2, 2013 8:05 AM, "Robin" <robince at gmail.com> wrote:

> Running the full Freesurfer reconstruction pipeline (without the hybrid
> skull stripping and Talaraich alignment on the fieldtrip side) appears to
> have been successful.
>
> However, when I try to continue with the tutorial I find that my volume
> and source grid don't line up (even before any issues converting to sensor
> space):
>
> Figure: http://imgur.com/uo9uPUc (code below)
>
> Does anyone have any idea what could be wrong?
>
> What coordinate system is the sub-oct-6-src.fif file in (created by MNE
> suite)?
> If it is in talairach coordinates, how do I load the Talairach aligned
> image from the Freesurfer pipeline? (is it orig.mgz? I also tried nu.mgz)
>
> Do I need to manually include the transform from transform/talairach.xfm?
> To include that can I use it directly as mri.transform in fieldtrip or do I
> need to multiply it by the existing mri.transform which is there when
> loading the raw anatomy scan (.img)? Come to think of it what does that
> transform represent?
>
> Sorry if these are not fieldtrip questions but I am trying to follow the
> fieldtrip MNE tutorial so I was hoping someone might know.
>
> Thanks
>
> Robin
>
> % load freesurfer image
> mri_fs_tal = ft_read_mri(fullfile(fs_dir, sub.code, 'mri', 'orig.mgz'));
> mri_fs_tal = ft_convert_units(mri_fs_tal, 'cm');
> % load MNE grid% computed with mne_setup_source_space --ico -6
> bnd = ft_read_headshape(fullfile(fs_dir, sub.code, 'bem', [sub.code '-oct-6-src.fif']), 'format', 'mne_source');
> sourcespace = ft_convert_units(bnd, 'cm');
> % Volume conduction model
> cfg = [];cfg.coordsys = 'spm';cfg.output = {'brain'};
> seg = ft_volumesegment(cfg, mri_fs_tal);
> cfg = [];cfg.method = 'singleshell';
> vol = ft_prepare_headmodel(cfg, seg);
> % Check volume conduction
> figure; hold on
> ft_plot_vol(vol, 'facecolor', 'none'); alpha 0.5;
> ft_plot_mesh(sourcespace, 'edgecolor', 'none'); camlight
>
> On Wed, May 1, 2013 at 5:41 PM, Robin robince at gmail.com wrote:
>
> I am trying to run through the MNE tutorial here:
>
> http://fieldtrip.fcdonders.nl/tutorial/minimumnormestimate
>
> Unfortunately after the volumetric processing in freesurfer my
> intermediate result looks wrong.
>
> I have followed the steps (including interactive alignment to
> Talairach) according to the tutorial. I wondered if anyone has any
> idea what could be wrong, or could point to some more possible
> diagnostic commands to run?
>
> The original Subject01.mgz file seems to have been saved correctly.
> But if I load the orig.mgz created with:
> mri_convert -c -oc 0 0 0 Subject01masked.mgz orig.mgz
> and plot it with ft_sourceplot it has the same offset and upside down
> position as the final incorrectly segments freesurfer image. Could
> this indicate a problem?
>
> Thanks for any help,
>
> Cheers
>
> Robin
>
>
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