fit volume segment and sensors?

Marc Recasens recasensmarc at GMAIL.COM
Thu May 6 20:38:40 CEST 2010


I'm new in Fieldtrip and I find myself needed of some help :)
I'm currently analysing some MEG data (4D-Neuroimaging, Magnes 2500WH) and
trying to create a Single-Shell headmodel using a segmented mri.
. I've read all the documentation on FT website but I'm still stuck. The
volume never fits in the correct position inside the sensor helmet.

First of all, I create a segmented MRI  using Analyse images (.img'), and
the segmentation is performed using:
cfg.coordinates  = 'spm';
cfg.template     = 'C:\...\MATLAB\R2007a\toolbox\spm2\templates\T1.mnc';
segmentedmri = ft_volumesegment (cfg, mri);
segmentedmri.anatomy = mri.anatomy;    <--- I use that for posterior

Then, I do a volumerealign by selecting manually the fiducial points (Nas,
Lpa, Rpa), as I actually don't have fiducials on the MRI scans.
cfg.method = 'realignfiducial';
cfg.fiducial.nas = Nas;  <--- (I get this from headshape.fid)
cfg.fiducial.lpa = Lpa;
cfg.fiducial.rpa = Rpa;
segmented_r = ft_volumerealign (cfg, segmentedmri);

Finally I create a volume through the ft_prepare_singleshell (cfg,
segmented_r) function and plot it.
I have the fiducials or head position coils and the scalp registered by
means of a Polhemus digitizer..
Though the segment via ft_sourceplot (doing the: segment.avg.pow =
segment.gray+...) looks right, the headmodelplot shows that the volume and
the headshape don't fit.

Is there any possibility to realign the segmented mri according either to
the headshape points either to the MEG fiducials? I'm afraid the answer is
no in both cases (as the MRI  and MEG coordinates are different). I tried to
realign the segment interactively by selecting the positions where the coils
in the MRI should be... but as the picture shows, it doesn't fit.
am I doing something wrong or skipping some important step?
Is it possible to transform MRI coordinate system to MEG-head coordinate
system? Would it help?

[image: singleshell.jpg][image: singleshell2.jpg]
I attach a picture of what i've managed to do till now!

Thanks for all!!!

Marc Recasens
Tel.: +34 639 24 15 98

The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also and
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