Megan,
> 1) Can the -ACF option be used with small volumes? i.e. are there any issues in using -ACF and -oksmallmask together?
3dClustSim -ACF should be fine with a small mask as long as you can justify the small volume correction approach.
> 2) We are interested in running 3dClustSim and 3dFWHMx in two ROIs- the bilateral amygdala and the vmPFC.
> Can all three (counting left and right amygdala as separate ROIs) be run in the same 3dClustSim command? Or
> does this lead to miscalculations of smoothness and cluster size? If there is an issue, would it still be present if
> only running the left and right amygdala (excluding vmPFC)? Essentially we're wondering if issues are produced
> if you have discontiguous ROI masks.
To avoid any potential issues, you can estimate the ACF values based on the whole brain instead of those few small regions.
Gang
