Incorrect coordinates?

Jared Van Snellenberg jaredvs at GMAIL.COM
Wed Oct 11 19:16:47 CEST 2006


Hi Robert,

Thanks very much, it looks like you're right. While plotting the src data
just came up with an empty image, BESA is supposed to output coordinates
according to the Talairach atlas, so [0 0 0] should be on the anterior
commisure. Plotting the structural MRI shows that [0 0 0] is clearly
*not*on the AC, so it needs to be realigned. I'll try volumerealign
now.

-Jared


On 10/11/06, Robert Oostenveld <r.oostenveld at fcdonders.ru.nl> wrote:
>
> 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
>
> and
>
> 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
> http://www2.ru.nl/fcdonders/fieldtrip/doku.php?
> id=fieldtrip:documentation:frequently_asked_questions#how_are_the_differ
> ent_head_and_mri_coordinate_systems_defined
>
> I hope this helps.
> Robert
>
> *) that is a completely new function that was added yesterdays to
> fieldtrip, hence you should fetch the latest version from ftp
>



--
Jared Van Snellenberg
Social Cognitive Affective Neuroscience Unit
http://scan.psych.columbia.edu
(212) 854-7858 p
(212) 854-3609 f
Department of Psychology, Columbia University
406 Schermerhorn Hall
1190 Amsterdam Avenue, Mail Code 5501
New York, NY 10027
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