fit volume segment and sensors?

jan-mathijs schoffelen jan.schoffelen at DONDERS.RU.NL
Fri May 7 09:01:05 CEST 2010

Dear Marc,

It seems to me that there is an issue with the coordinate system in
which your original MRI is expressed. This could be related to the
order of the steps you take, so I would permute the order and see
whether this makes any difference at all (for me it usually works fine
as follows:)

First do a call to ft_volumerealign using your single subject's MRI.
This step should give you the transformation matrix from voxel to
headspace according to CTF's convention (which happens to be the same
as 4d).
Then do a segmentation of the output of ft_volumerealign, but note
that you should specify ctf.coordinates = 'ctf'.
Then you can proceed to create the single shell volume conductor model
(after checking whether the segmentation worked fine with respect to
the orientation etc of the resulting volumes; I believe there is some
documentation about this on the website) and plot the results.

Hopefully this helps,



On May 6, 2010, at 8:38 PM, Marc Recasens wrote:

> Hello,
> 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
> volumerealign.
> 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?
> <singleshell.jpg><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.

Dr. J.M. (Jan-Mathijs) Schoffelen
Donders Institute for Brain, Cognition and Behaviour,
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands
J.Schoffelen at
Telephone: 0031-24-3668063

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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