[FieldTrip] beamformer results smaller than brain

[Gio Piantoni]

Hi Akiko,

Your headmodel looks pretty good and your beamformer plot seems to
cover most of the gray matter.

However, it's good to check the location of your dipoles in respect to
your headmodel. For example, you can plot the .pos field of your
leadfield. Something like:

ft_plot_mesh(bnd(3), 'facealpha', .5)
hold on
plot3(lead.pos(:,1), lead.pos(:,2), lead.pos(:,3), '.')

It might well be that your grid is too coarse and some dipoles just
happen to be over the edge of the brain. Remember that your
"beamformer_result.png" is just an interpolation of the values of this
dipole grid.

You can either try to make your grid more refined (but remember that
your computation time will significantly increase). Or you can
manipulate the way dipoles are considered inside or outside the brain
with "inwardshift" for ft_prepare_leadfield (although I'd advise
against using a negative value as some dipoles might really end up
outside of your brain mesh, with some numerical instabilities).
Another option (the easiest) is to nudge your grid by, say, a few
millimeters, so that the parietal dipoles will be just inside the
brain mesh.

HTH,

Gio

-- 
Giovanni Piantoni, MSc
Dept. Sleep & Cognition
Netherlands Institute for Neuroscience
Meibergdreef 47
1105 BA Amsterdam (NL)

+31 20 5665492
gio at gpiantoni.com
www.gpiantoni.com

On Thu, Mar 29, 2012 at 00:22, Akiko Ikkai <akiko.ikkai at gmail.com> wrote:
> Hi Fieldtrip users,
>
> I'm hoping that someone could give me advice on segmentation and beamformer
> on EEG data. I have EEG data set based on 128 channel cap. Thanks to the
> help I got in mid-Feb, I'm now able to create a decent
> segmentation (seg_results image attached) and volume conduction model.
> However, when I run beamformer based on these models, resulting beamforming
> image is often smaller than the brain (beamformer_result attached).
> Particularly posterior parietal and occipital map is NaN.
>
> I have tried going back to segmentation and expanded brain by using imdilate
> after ft_volumesegment such as:
>
> newbrain = imdilate(seg2.brain,strel_bol(1)); % seg2.brain is original brain
> tissue from segmentation
>
> seg2.brain = newbrain;
>
> seg2.seg = seg2.scalp + seg2.skull*3 + seg2.brain*6;
>
> and run ft_prepare_mesh_new on seg2. Of course, I have to make sure there is
> no intersect between different tissue types, so using imdilate has
> limitation.
>
> Could someone explain why this shrinkage might be happening, and how I could
> fix it?
>
> Thanks in advance! Akiko
>
> --
> Akiko Ikkai, Ph.D.
> Postdoctoral Fellow
> Department of Psychological and Brain Sciences
> Johns Hopkins University
> Ames Hall, 3400 N. Charles St.
> Baltimore, MD 21218
>
>
>
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