[FieldTrip] MNE tutorial

Robin robince at gmail.com
Thu May 2 15:46:22 CEST 2013

By running from MNE suite:
mne_setup_mri --subject BON02 --mri T1

to create a COR.fif image from the Freesurfer output (including Talaraich
transformation) at least that COR.fir and the oct-6-src.fif mesh seem to
line up.

But now I am not sure which coordinate system they are in? (cordsys is
'neuromag' in fieldtrip) nor how to obtain the necessary inverse transform
from this space to the raw anatomy voxel space (so I can build the
transform from oct-6-src mesh to sensor space; I already have the transform
to take the original raw anatomy .img to the sensor coordinate system).



On Thu, May 2, 2013 at 1:04 PM, 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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