I just noticed that you have made some changes to the 3dClustSim function. I appreciate that you improve the functionality in AFNI, and have some feature requests.
It would be nice if you can select the distance type (NN1, NN2, NN3), if you are only interested in one of them.
It would be nice if you can select the thresholding type (one-sided, two-sided, bi-sided), if you are only interested in one of them.
It would also be nice if you can specify the voxel-wise threshold as a z-score, in addition to a p-value threshold. So something like
3dClustSim -mask mask.nii -fwhmxyz 6 6 6 -athr 0.05 -zthr 2.3, similar to
3dClustSim -mask mask.nii -fwhmxyz 6 6 6 -athr 0.05 -pthr 0.01
The reason for this is that the 3dclust function wants the threshold as a "regular" value, and not as a p-value, and it would be nice if you can use the same threshold as for the 3dClustSim function (an alternative is to add -pthresh for 3dclust)
3dclust -1noneg -1thresh 2.3 -dxyz=1 1.01 10 brik.nii
