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Thanks a lot Robert, now I get it!<br>
Best,<br>
Ulrich<br>
<br>
<br>
On 07.02.2012 11:34, Robert Oostenveld wrote:
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<title>Re: [FieldTrip] Defining cfg.neighbourdist at source level</title>
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<p><font size="2">Dear Ulrich<br>
<br>
On 1 Feb 2012, at 13:44, Pomper, Ulrich wrote:<br>
<br>
> Dear Robert and Stephan,<br>
> Thank you for your replies.<br>
> I guess I use what Robert called the 'regular' 3D grid,
but I'm not quite sure.<br>
...<br>
> ldf =<br>
><br>
> xgrid: [-65 -58 -51 -44 -37 -30 -23 -16 -9 -2 5
12 19 26 33 40 47 54 61 68]<br>
> ygrid: [-107 -100 -93 -86 -79 -72 -65 -58 -51 -44
-37 -30 -23 -16 -9 -2 5 12 19 26 33 40 47 54 61 68 75]<br>
> zgrid: [-52 -45 -38 -31 -24 -17 -10 -3 4 11 18 25
32 39 46 53 60 67 74 81]<br>
> dim: [20 27 20]<br>
> pos: [10800x3 double]<br>
...<br>
><br>
> In any case, I still don't quite understand how to
calculate the neighbours to each voxel.<br>
<br>
Yes, you are using a regular 3D grid with dipole positions
that are placed at the center of a large number of voxels
which jointly fill a cube that spans the head. Just like an
MRI.<br>
<br>
If you look in ldf.pos you will see all positions. Those
positions form a 20x27x20 regular grid, with the x-, y, and
z-values according to xgrid/ygrid/zgrid. You have a grid
spacing of 7mm in each direction.<br>
<br>
The first positions is [-65 -107 -52] and its neighbours are
the grid points that are 7mm to the right, top and front. Just
think of it as<br>
functional_data = rand(20, 27, 20)<br>
i.e. a cube. It is clear for each voxel what the neighbours
are.<br>
<br>
FieldTrip makes use of vectorization, i.e. the 3d matrix with
the functional data can also be represented by MATLAB as a
vector.<br>
functional_data = functional_data(:)<br>
What you then get is a vector of length 10800, i.e. matching
all the [x y z] positions as they are specified in ldf.pos.<br>
<br>
> By saying that the "neighbours are trivial to find and
you do not have to specify a structure", do you mean that I
don't need to define the cfg.neighbours property at all (given
that I do use a regular 3D grid)?<br>
<br>
correct.<br>
<br>
Robert<br>
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