[FieldTrip] plotting dipoles on an anatomical mri

[IMALI THANUJA HETTIARACHCHI]

Dear Robert,

Thank you very much for the very quick reply and the explaining.

I am a bit struggling in the exact usage of ft_slice_plot function. I was trying to dig up on an example usage but was unable to find any.


What does exactly in the use ft_plot_slice(dat, ...) , dat argument stands for? Can you please explain me on how to plot a 2D slice using the function?



Thank you very much again.

Regards

Imali

From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Robert Oostenveld
Sent: Monday, 9 July 2012 6:02 PM
To: FieldTrip discussion list
Subject: Re: [FieldTrip] plotting dipoles on an anatomical mri

Dear Imali

The ft_sourceplot function was not designed to plot 3D data in combination with dipoles. If you use method=ortho, you can get the 3 intersections in the 3D volume at the location of the dipole.

For the best control over the details of the plot, which you need for your specific application of combining dipoles and volumetric data, I suggest that you look at the ft_plot_slice function. If you do three ft_plot_slice calls for the three orientations (x,y,z) at the location of the dipole and combine that with ft_plot_dipole, you will probably visualize the 3D relation between the two types of data the clearest.  Note that ft_plot_slice plots any slice in 3D, so you should use the 3D rotate option of the MATLAB figure.

best regards,
Robert


On 9 Jul 2012, at 9:26, IMALI THANUJA HETTIARACHCHI wrote:


Dear fieldTrip users,

I am doing a dipole fit with the ft_dipolefitting function and I can plot and visualize the results with ft_plot_dipole, further I also want to compare the results with a beamformer results so, I tried plotting the ft_dipolefitting results with ft_sourceplot. I cannot yet very well understand how ft_sourceplot works, I understand that the dipole should be assigned with some value but cannot figure out how to do this.

Can someone please give me some help in doing this? Following is the code I am using, where should I modify?

cfg = [];
cfg.location = dip_fitted.dip.pos;
cfg.method='ortho';
ft_sourceplot(cfg,mri)

where mri is the standard_mri.mat . I work in the MNI coordinates and my locations are in mm's.


Thank you very much in advance.

Kind regards
Imali

Imali Thanuja Hettiarachchi
PhD Candidate
Centre for Intelligent Systems research
Deakin University, Geelong 3217, Australia.
Email: ith at deakin.edu.au<mailto:ith at deakin.edu.au>
www.deakin.edu.au/cisr<http://www.deakin.edu.au/cisr>

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