Recently I came across some issues using dsi studio to build a tractography of spinal cord of mice with in-vivo or ex-vivo scanning data. Here are some details.
1. in-vivo data were scanned in the axial direction, due to the phiological curve of mice(fig1), the center of axial figures cannot be align neatly on the same stright line. And thereafter the tracted fibers are segmented in different levels and not continuous(fig2). I'm wondering whether there are any ways to tract fibers along the orientation of phiological curve.
2.ex-vivo data were scanned in the sagittal direction. Tracts of fibers were found to curled and bent locally(fig3), which is inconsistent with the normal orientation of fibers. Why is that？How to fix this strange outcome.