3dClustSim, ACF option and discontiguous ROIs

AFNI Message Board
1

Hello AFNI community,

I have two questions regarding the new (11/2016) installation of 3dClustSim.

  1. Can the -ACF option be used with small volumes? i.e. are there any issues in using -ACF and -oksmallmask together?

  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.

Thank you very much,
Megan

2

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.

  1. 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.

3

Certainly the ACF parameters should be estimated from the whole brain residuals – it is very not a good idea to estimate them from a small region.

Otherwise the normal caveat about small volume correction are still present – were the ROIs selected via some unbiased reasoning?

Another option to consider, if it applies to your situation, is the new 3dttest++ -Clustsim option, with the appropriate mask.

4

Thank you very much for your answers. The ROIs are chosen a priori based on prior literature and our hypotheses so I believe it should be ok to utilize them for small volume ROI analyses. And I will look into the new 3dttest++ -Clustsim option thank you!