[FieldTrip] segmentation problem with Neuromag

[Elena Orekhova]

Dear Fieldtrip users and developers,

I would like to start using Fieldtrip for the source analysis of the MEG data, but
I  have some problem with mri segmentation using  Neuromag-306 .fif MRI file.

I do:
1) import .fif, (Coordinate alignment was already done in Neuromag).
mriname = 'NEUROMAGxxx.fif'
[mri] = ft_read_mri(mriname)
cfg  = [];
ft_sourceplot(cfg,mri);

***** attachment: mri.jpg ******

2) do segmentation
cfg                = [];
cfg.template       = 'T1.nii'; %spm8
cfg.coordsys       = 'neuromag';
cfg.write          = 'no';
cfg.name           = 'temp';
cfg.interactive    = 'yes';
[segmentedmri]     = ft_volumesegment(cfg, mri)

3) plot the original and segmented mri
cfg                = [];
test.dim = [512  512 180];
test               = segmentedmri;
test.avg.pow       = test.gray+test.white;
test.anatomy       = mri.anatomy;
cfg.funparameter   = 'avg.pow';
cfg.interactive    = 'yes';
ft_sourceplot(cfg,test);

***** attachment : mri_segmented.jpg ******


Apparently, there is a displacement of the segmented mri image. It seems also that the  segmented mri  is bigger then the original mri.
The similar (although not the same) picture is observed when I do coordinate alignment in the MNE and use the /sets/CORxxx.fif saved from the MNE sohtware.
I have seen some discussions on this topic, but I have not found the solution.

Should I   swap x and y coordinates? How can I do it?

I would be most grateful for help!

Elena

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