Agent 007-

That is a good question. I think the resolution of the SEM differences is this (I am using the AFNI_data6/afni/func_slim* dset for running this--we can compare notes on the same data): your 3dclust command is "2thresh", or simple 2sided testing, and your 3dClusterize command is "bisided".

Keeping this 3dclust command constant:

3dclust -nosum -no_1Dformat -1dindex 5 -1tindex 6 -2thresh -2.8 2.8 -NN2 33 func_slim+orig.

... if I run the "bisided" case, results differ:

3dClusterize -nosum -no_1Dformat -idat 5 -ithr 6 -bisided -2.8 2.8 -NN 2 -clust_nvox 33 -inset func_slim+orig.

... but if I run 3dClusterize as "2sided" to match the 3dclust command:

3dClusterize -nosum -no_1Dformat -idat 5 -ithr 6 -2sided -2.8 2.8 -NN 2 -clust_nvox 33 -inset func_slim+orig.

then the tables appear to be the exact same to me. Please check if that sorts our your difference, as well (and this might resolve other issues there...).

The difference between 2sided and bisided is important: the thresholding is the same, but in "bisided", clusters are only formed between voxels with effects of the same sign; in 2sided, positive and negative voxels that happen to be adjoining will clump together. It is hard to see how "bisided" would not generally be the clusterizing rule of choice.

Re. your question about the Mean values: wow, I never noticed that. Looking in the code, there is actually a switch that the "Mean" actually is the "|Mean|" by default (that is, the absolute value). If you use the option "-noabs", then you will see the signed Mean.
To be honest, the reason for this is mysterious. I kind of think we should change this default (3dClusterize is just copying 3dclust here, and 3dclust is oooold, as you might notice, with really tough syntax to use). Thanks very much for bringing up this point---I will reply back about this anon.

Re. "bursting" the clusters to separate files: there is no tool for that, so looping over values with 3dcalc would be the way to do it. In general, using subbrick selectors on datasets (e.g., Clust_mask+tlrc"<3>") for given commands is often a pretty efficient way to go (not requiring lots of separate files). Do you have a particular use case in mind for applying individual ROIs?

--pt



Edited 2 time(s). Last edit at 04/29/2021 11:55AM by ptaylor.