[FieldTrip] MNE tutorial

[Robin]

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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