Step by Step Guide
Diffusion tensor fitting
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
Probabilistic model fitting
- Make sure you have run all the steps above (diffusion tensor fitting)
Run BEDPOSTX to fit a non-tensor model used for tractography and registration (allow 15 hours).
Register your nodif_brain images to standard space using the FDT Gui.
- Create target masks to be used for tractography.
Run PROBTRACKX to isolate tracts of interest.
Use Fslview to check the output of probtrackx makes sense anatomically.
Use probtrackx results to determine probability of connections between regions or to create masks for comparing other diffusion values of interest.