Hi Sarah,

Unfortunately, the data that you uploaded doesn't have any
difference between the 3dclust and 3dmerge output. Maybe
that was under different circumstances.

The GUI output that is there looks like it was clustered at a
higher threshold than the 3dmerge result (the minimum non-zero
value in the dataset is 10, not the 7 of the 3dmerge result).

I ran the cluster plugin with the same parameters (thresh 7,
radius 5mm, min volume 1160 ul), and it is also identical with
the 3dmerge output. So I'm not seeing any differences here.

---

So two things cross my mind here (besides just being careful
with the cluster parameters). One is that if you are using
the warp-on-demand dataset via the afni GUI, then you might
be careful about putting multiple subject anatomies in that
same directory. I believe that afni would apply the orig->tlrc
transformation from the first anatomical dataset found in the
directory. But there is only 1 transformation that is correct.
My suggestion here is to apply adwarp to whichever sub-brick
you want to work with; it is less error prone than through the
GUI.

The other note is the warning about Identical ID codes. That
is a mistake on the part of 3dclust (but it should not cause
you any trouble, besides the irritating warning). I'll fix
it.

---

If you are able to point to a difference between the 3dmerge
and 3dclust output, I would still be interested in seeing it.
If you think I have missed some point(s), please let me know.

- rick