Hi Marina,

Nothing looks out of place in your commands to me.
Are you actually thresholding on sub-brick #1 in
the afni GUI?


For voxels that are 3 mm^3, there should be no
difference between a radius of 3.0 and one of 4.23.
They each imply NN=1 clustering (where voxels must
share a face). Since your GUI parameter is NN=2,
you must allow for sharing an edge, which means
using a radius of at least 3*sqrt(2) = 4.243. So
using 4.3 is appropriate.


To get an idea of how to fix the commands, use the
afni GUI. Use the '3dclust' button on the afni GUI
cluster report window to output a 3dclust command
(to the terminal window) that would create a cluster
report matching what is shown in the GUI.

Similarly, use the 'SaveMsk' button to output a
corresponding 3dclust command which would save the
actual mask dataset (exactly what you are trying to
do with 3dmerge). Use that command to either help
fix your current 3dmerge command, or better yet, to
replace it going forward.


What are those commands?

- rick