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thank you for your suggestions and offer to skype! I think I will just plot the structures, store it as .fig and then load it to plot my contacts subsequently into this 3d figure with the usual MATLAB plotting function because we need them to be colored according to a separate dependent variable. The X-Cut view sometimes looks a bit strange (not all nuclei are displayed), I will probably just generate the outlines of the structures in Inkscape once I have the 2D views of the plot.
Thank you very much for the detailed answer! I will follow your advice and check some of the positions in slicer.
is there any heuristic on how to determine the exact vertical position of the most ventral contact of the electrodes? On our CT scans the single contacts are sometimes not very clearly visible. The heuristic I am using now is: I shift the trajectory down until there is nothing visible anymore in the transversal view, and then go up a few steps again (usually about 4) until it is clearly visible but mostly still smaller in diameter than the dorsal contacts.
The diameter size seems to vary quite a lot and depend on the quality of the CT. Would you recommend to stick to one certain number of steps for each reconstruction?
I also noticed that saving the manual reconstruction does not work if the “Rotate 3D” button is activated. That was the reason why my manual corrections weren’t saved once before – it would be great if you could enable this, or otherwise point it out in the manual so that nobody else will stumble over it.