DTI Analysis in AFNI

Does anyone have experience running DTI analysis in AFNI?
Species: pig!

Any help would be appreciated. Thank you, Kelly

Hi, Kelly-

<< Does anyone have experience running DTI analysis in AFNI? >>

→ Yes.
There is a fair amount of step-by-step documentation here, with commands/scripts:
Some of the lectures+PDFs here might be useful:
And finally, some more help on specific programs in AFNI:

<< Species: pig! >>

→ No. (Or, more accurately, I don’t…)
I would imagine some of the basic steps would be quite similar to humans (data conversion, alignment, tensor fitting, etc.). However, there might be some special flags/options to use in the TORTOISE preprocessing steps (see the first link above, “9.2.6. Preproc: TORTOISE”) for non-human brains; I believe that they recommend some specific settings for macaques and smaller mammals, for example.


If you want to move any results to a standard space or move atlas regions to the pig’s native space, there is apparently a pig brain template and atlas. Other than that, the method described here using TBSS points out the analysis is essentially otherwise unchanged from human brain DTI analysis.