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= Step by Step Guide =
== Diffusion tensor fitting ==
 * [[InitialProcessing|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 [[BET/StepByStep|brain extraction]] on the nodif scan
 * Run [[FDT/UserGuide#DTIFIT|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 [[FDT/UserGuide#DTIFIT|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 [[FDT/UserGuide#BEDPOSTX|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/UserGuide#Registration|FDT]] Gui.
 * Create target masks to be used for tractography.
 * Run [[FDT/UserGuide#ProbtrackX|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.