Hi Peter,

1)For slow_surf_clustsim.py I used the -on_surface yes flag as below. In doing so do I also need to enter in a mask of cortical thickness or is this taken into account with this being a surface tool. Traditionally with 3dClustSim we would enter in a mask to define which volumes we want to calculate for.


slow_surf_clustsim.py -save_script surf.sim -on_surface yes -uvar blur 8.8 -uvar spec_file fsaverage/SUMA/fsaverge_lh.spec -uvar surf_vol fsaverage/SUMA/fsaverage_SurfVol+orig

2) For the output of slow_surf I get the following in a terminal:

p-value thresholds : 0.1 0.05
z-score thresholds: 1.28 1.64
maximum cluster areas: 1701.08 1152.53

quick.alpha.vals.py -niter 1000 cluster.results/z.max.area.0.05


When using the quck.alpha command I see that for 0.05 (second column alpha corrected) it corresponds to 643mm^3.

I believe the 643mm^3 is the correct value to use for alpha=0.05 but I wanted to see if the 1.64 T threshold from the terminal output is correct? Usually in 3dClustsim it will have the corresponding p value and clustersize for a p value initial threshold. In this case my alpha of 0.05 corresponds to a clustersize of 643mm^3 but at which input p threshold?


3) Finally on SurfClust does this command make sense?
I found something similar on a post but I'm not sure what -rmm -1 does.

SurfClust -spec fsaverage_lh.spec -surf_A lh.pial.asc -input '~/Group_Gender_Results/Lthickness.niml.dset[9]' 0 -thresh 1.64 -amm2 1151 -rmm -1 -out_roidset -prefix test


Thanks,
Ajay



Edited 1 time(s). Last edit at 04/27/2016 12:38PM by AjaySK.