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:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/fatcat_prep/main_toc.html
Some of the lectures+PDFs here might be useful:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/educational/bootcamp_recordings.html#supplementary-lectures
And finally, some more help on specific programs in AFNI:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/FATCAT/main_toc.html
<< 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.
–pt
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.
https://www.sciencedirect.com/science/article/pii/S0165027017304351?via%3Dihub