Dear all,
Hope you are doing great and are safe and healthy! I want to ask a tractography question:
I am studying the connectivity of the subthalamic nucleus (STN) to the cortex in Parkinson’s Disease patients. I manually mask the STN for each patient using T2 images, but I want to create standard cortical masks.
I have ran BEDPOSTX, but the output is not clear to me (have I done registration? Linear? Non-linear?) In any case I do have transformation mat files. So in Probtrackx2:
-single mask —> STN (manually segmented in structural data)
-seed space is not diffusion
-transformation files: the structural to diffusion mat ( right?)
-surface —> reference image —> the T2 data (also tried diffusion, nodif brain, node brain mask, which I saw in some fora)
-targets —> the cortical standard masks
Still does not work… Do I need to do any registration first? And what? I’m not familiar with FLIRT or FNIRT.
Thank you very much in advance! 
Best wishes,
Barbara.