Getting dipole orientations

ArndMeiser · November 21, 2019, 2:03pm

Hello everyone,

I am currently trying to simulate dipoles in an MRI-volume, meaning I want to control both position and orientation. From the headmodel (a 3ShellSphere) I get the grid positions of the source onto which I want to place the dipole. All neccessary information seem to be in the structure that results from Process->Sources->Dipole scanning (Location, Amplitude, etc.) but the information I need, being the orientation of the dipole only seems to be displayed in the window 'Dipole Info' when klicking on the dipole in the GUI. Is there a way to retrieve these values?

Thanks in advance!

Francois · November 22, 2019, 12:08pm

Dipole orientation is derived from the field "Amplitude", which gives you for each dipole the amplitude along the three axes.

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/gui/panel_dipoles.m#L850


      
          pointSize = ctrl.jSliderDipSize.getValue;

          lineWidth = 1.5*(ctrl.jSliderTailWidth.getValue/10);

          

          % ===== DISPLAY GROUPS =====

          % Get number of different groups

          for iGroup = 1:length(dipGroups)

              % Get all the dipoles of this group

              iDipGroup = find(dipGroupTag == dipGroups(iGroup));

              % Get dipole locations

              Loc = [sDipoles(iDipGroup).Loc];

              % Compute dipole orientations (normalized amplitude)

              Orient = [sDipoles(iDipGroup).Amplitude];

              normAmp = sqrt(sum(Orient.^2,1));

              Orient = Orient ./ repmat(normAmp,3,1) .* 0.02;

              % Get color

              iColor = mod(dipGroups(iGroup)-1, size(ColorTable,1)) + 1;

              

              % Loop added to be able to track each dipole inpendently

              for i = 1:length(iDipGroup)

                  % Plot point

                  line(Loc(1,i), Loc(2,i), Loc(3,i), ...

Does it help?

ArndMeiser · November 25, 2019, 2:35pm

Thanks a lot, that is what I was looking for!

ArndMeiser · December 2, 2019, 1:28pm

One more question: I have a dipole file as a result from "Dipole scanning" that I can plot on a cortex with scalp. Now I want to add electrode locations (EEG) . When trying this, I get the error

error
There seems to be some information missing in the dipole file. Any ideas? The channelFile is definetly ok.

Thank you in advance,

Arnd

Francois · December 2, 2019, 5:58pm

Bug fixed: https://github.com/brainstorm-tools/brainstorm3/commit/82f9234ce78dfb055e4283805a5422e3fa4134df

Please update Brainstorm and try again.

Thanks for reporting the issue

ArndMeiser · December 3, 2019, 9:25am

Thank you very much!