Incorrect coordinates?

Robert Oostenveld r.oostenveld at FCDONDERS.RU.NL
Wed Oct 11 09:36:07 CEST 2006

Hi Jared,

On 10 Oct 2006, at 22:38, Jared Van Snellenberg wrote:
> I've been analyzing the output of BESA's multiple source beamformer
> (MEG
> data) using Fieldtrip, and it appears that there is a problem with the
> coordinate system. The results of volumewrite, when overlayed with
> the spm
> T1.img, appear to be substantially outside of the brain, and in oddly
> shaped patterns that suggest an error in assigning statical values
> to the
> correct coordinates.

I suspect a misalignment between your functional and anatomical data.

> mri=read_fcdc_mri('mri.img');

read_fcdc_mri does not do automatic alignment, but just returns the
data with the coordinate system as defined in the mri file.

Do you know what the coordinate system is to which the anatomical MRI
is aligned? I.e. where is the origin [0,0,0] in anatomical terms?

> for k=1:length(files)
>     src(k)=besa2fieldtrip([fdir filesep files(k).name]);
>     interp(k)=sourceinterpolate(sinterp_cfg,src(k),mri);
>     volume(k)=volumenormalise(norm_cfg,interp(k));
> end

And what is the coorrdinate system in which the functional source
data is described? I.e. at which location in the head would a dipole
at the coordinate [0 0 0] be?

For sourceinterpolate the two input arguments (functional +
anatomical data) should be defined w.r.t. the same coordinate system.

I suggest that you use sourceplot for debugging, e.g. something like

cfg =[]
cfg.funparameyter = 'pow'          % don't know how the functional
data in src is called, probably 'pow'
cfg.location      = 'interactive'  % or try [0 0 0]
sourceplot(cfg, src(1));           % there is no anatomy, only
functional data


cfg =[]
cfg.funparameyter = []             % no functional data, only anatomy
cfg.location      = 'interactive'  % or try [0 0 0]
sourceplot(cfg, mri);

that should give you both volumes (in seperate windows) and you can
compare whether they seem to be aligned. You could use the
volumerealign(*) function for manual realignment of the anatomical
MRI. Or you can use MRIcro. Also have a look at

I hope this helps.

*) that is a completely new function that was added yesterdays to
fieldtrip, hence you should fetch the latest version from ftp

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