Hi canbe,
thanks for your nice words. I fear I don’t understand what you want to do. Diffusion tensor images (you made with FSL) should be suitable for FSL. Then usually .nii images are 3D (or 4D) but usually not 2D.
Lead-DBS is mainly for reconstructing DBS electrodes. You can in theory use Lead Connectome to perform whole-brain fiber tracking and then investigate connectivity from DBS electrodes to other regions. However, this process is poorly documented and most people that know how to do this currently lack the time to write nice tutorials about it.
Best, Andy
