Step by Step Guide

Diffusion tensor fitting

• Initial processing

• Create bvecs and bvals (may be made automatically from conversion to NIFTI, or may need to obtain them from scanner console/operator separately)

• Make sure that files are named correctly (data, nodif_brain_mask, bvecs, bvals)

• Identify and extract a nodif (b=0) scan

• Run brain extraction on the nodif scan

• Run DTIFIT (easiest from GUI, but can be done from command line too)

• Check that the orientation of the diffusion vectors in FSLView are anatomically correct (in all three views)

• Run Topup for distortion correction

• Run Eddy correction (includes motion correction)

• Run DTIFIT again

  • Check that the directions viewed in FSLView are anatomically correct