[FieldTrip] fit volume segment and sensors

"Jörn M. Horschig" jm.horschig at donders.ru.nl
Mon Dec 9 11:54:14 CET 2013

Dear Sara,

the procedure described on the FT-page is tailored towards data gathered 
from CTF data just because we happen to have a CTF-system here. Since 
you have itab-data, the coordinate system of your sensors (gradiometers) 
is not in ctf-space. Some more information on the different coordinate 
systems can be found here:

Your first step needs to be to coregister the gradiometer information 
with the MRI. Afaik, ft_volumerealign will then also take care of the 
coordinate system then (or, more precisely, return the appropriate 
transformation). See also here

If I remember correctly, this will not change the coordinate system of 
the gradiometers, but adjust the transformation matrix of the MRI 
instead. You do not need to be in CTF-space, you just need to make sure 
that all your data are in the same coordinate-system. Once you got that, 
it should work.  For example, for EEG source reconstruction you can stay 
in MNI-space all the time. Dealing with these transformation between 
coordinate systems is some nasty job, so take care you do it correctly 
and e.g. not get confused by neurological and radiological convention
And note that there is also ft_convert_coordsys for transformation, but 
I am not sure whether that works for gradiometers, yet. I think this all 
just works for volumes. I hope this works for you.


s.rombetto at cib.na.cnr.it wrote:
> Dear Fieldtrippers
> I 'm trying to perform source analysis on MEG data.
> I use an AtB system (usually it is described as 'itab' in fieldtrip)
> First I have preprocessed my data and I have calculated the cross 
> spectral density matrix
> Then I have constructed the forward model
>  mri = ft_read_mri('Subject01.mri');
> cfg = [];
> cfg.write      = 'no';
> cfg.coordsys   = 'ctf';
> [segmentedmri] = ft_volumesegment(cfg, mri);
> and segmented the brain surface:
> cfg = [];
> cfg.method = 'singleshell';
> vol = ft_prepare_headmodel(cfg, segmentedmri);
> With the command ft_read_sens I have also read the sensors positions.
> Before going on I have checked the results plotting the volume and the 
> sensors using the commands
> vol = ft_convert_units(vol,'cm');
> sens = ft_read_sens(rawdataname);
> figure
> ft_plot_sens(sens, 'style', '*b');
> hold on
> ft_plot_vol(vol);
> and I have noticed that the result is wrong because the volume soesn't 
> fit the sensors as shown in the attachment
> Moreover, following some topics in the mailing list I have used
> ft_determine_coordsys(mri)
> ft_determine_coordsys(vol)
> ft_determine_coordsys(sens)
> and I have found that the coordinate systems are diffeerent.
> As far as I understand I should use the ctf coordinate system to 
> perform the source analysis. But even if I try to specify this 
> coordinate system it did not work.
> Any suggestion to solve this problem?
> Kind regards
> -------------------------
>  Dott.ssa Sara Rombetto
>  Istituto di Cibernetica
>  "E. Caianiello"
>  Via Campi Flegrei, 34
>  80078 Pozzuoli (NA)
>  Italy
>  mob +39 3401689815
>  tel +39 0818675361
>  fax +39 0818675128
> --------------------------
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Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
FieldTrip Development Team

P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands

E-Mail: jm.horschig at donders.ru.nl
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Web: http://www.ru.nl/donders

Visiting address:
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