Hi Rick,
So I have found that the "-1tindex" option is essential for 3dmerge to work with a subbrick.
For example,
3dmerge -prefix X -1tindex 1 -1thresh # -1clust # # anova+tlrc"[12,13]"
are different from
3dmerge -prefix X -1thresh # -1clust # # anova+tlrc"[12,13]"
Although both cases deal with a string "[subbricks]" and defaults are printed to be dindex = 0 and tindex = 1, the upper one with the "-1tindex" only produced the correct clusters. So I guess the -1tindex in 3dmerge is the only case that works? Would you please check on this?
Thank you!