VAT calculation using the SimBio/Fieldtrip-model

[Mevluet]

Greetings to the group,
the models of Maedler 2012 or Kuncel 2008 work fine. I get the Volume of Activated Tissue (VAT) in the form of a circle. But there is no deformation of the circle, That should be like this right?

Matlab gives the following error message with the use of the model of SimBio/Fieldtrip (Horn 2017):

Statistics:
Input points: 18150
Input facets: 34599
Input segments: 37615
Input holes: 0
Input regions: 0

Mesh points: 49392
Mesh tetrahedra: 264581
Mesh faces: 542487
Mesh faces on exterior boundary: 26650
Mesh faces on input facets: 53010
Mesh edges on input segments: 42756
Steiner points on input facets: 3853
Steiner points on input segments: 5141
Steiner points inside domain: 23447

We have 26 regions and need to map these to tissue types.
Region 1 captured by grey matter.
Region 2 captured by grey matter.
Region 3 captured by white matter.
Region 4 captured by insulating material.
Region 5 captured by insulating material.
Region 6 captured by grey matter.
Region 7 captured by grey matter.
Region 8 captured by grey matter.
Region 9 captured by insulating material.
Region 10 captured by insulating material.
Region 11 captured by contact material.
Region 12 captured by grey matter.
Region 13 captured by insulating material.
Region 14 captured by contact material.
Region 15 captured by grey matter.
Region 16 captured by insulating material.
Region 17 captured by contact material.
Region 18 captured by insulating material.
Region 19 captured by grey matter.
Region 20 captured by grey matter.
Region 21 captured by contact material.
Region 22 captured by contact material.
Region 23 captured by grey matter.
Region 24 captured by white matter.
Region 25 captured by white matter.
Region 26 captured by white matter.
Index exceeds matrix dimensions.

Error in ea_genvat_horn (line 117)
tess = mesh.tet(:,1:4);

Error in ea_stimparams>stimulate_Callback (line 948)
[stimparams(1,side).VAT(el).VAT,volume]=feval(ea_genvat,elstruct(el).coords_mm,S,side,options,stimname,options.prefs.machine.vatsettings.horn_ethresh,handles.stimfig);

Error in gui_mainfcn (line 95)
feval(varargin{:});

Error in ea_stimparams (line 42)
gui_mainfcn(gui_State, varargin{:});

Error in
matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)ea_stimparams(‘stimulate_Callback’,hObject,eventdata,guidata(hObject))
Error while evaluating UIControl Callback.

How can I fix the problem? I think this model allows us to model the VTA with bipolar Stimulation. Other models uses monopolar Stimulation.

Best,
Mevlüt

[andreashorn]

Hi Mevlüt,

re the other models, please refer to their papers to better understand what they do.
Re our VTA model (which is still in beta version), it does matter which atlas you use to define the grey matter. Please also refer to the paper for specific questions first.
Some atlases lead to intersecting vertices in the meshing part and are thus not suited to define grey matter. The DISTAL Minimal atlas should work in most cases and gives a very precise definition of the grey matter of question – but of course this only works if the regions are the ones you’re interested in (they are STN, GP & RN).

Best, Andy

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