Hi, Steph-

While that blog is useful, a full processing description, from DICOM conversion through tracking, and including distortion correction with the recommended TORTOISE tools (also freely available from NIH, [tortoise.nibib.nih.gov]) is available from here:
[afni.nimh.nih.gov]

There are descriptions of outputs, and each program generates automatic QC images along the way, too. That goes hand-in-glove with the FATCAT_DEMO2 in AFNI, available via running:

@Install_FATCAT_DEMO2

It is the same data set as processed in that tutorial, with a full script (parts of which are segmented in the tutorial pages).

The above pipeline is for data acquired with dual phase encoding: one set of DWIs with phase encoding say, in the anterior->posterior direction, and another set of the same DWIs with the phase encoding in the opposite, posterior->anterior direction. That facilitates EPI (AKA B0 inhomogeneity) distortion correction, accomplished with the DR_BUDDI tool in TORTOISE. If you don't have that, you can slightly modify the script.

--pt