Hi Peter,
I ran 3dmerge with the parameters given by the 3dclust or savemask, without using the -dxyz=1, and it worked. It did give me the same two clusters I saw on afni gui.
Thanks a lot for your help. I still would like to know why 3dclust and savemask reads the resolution of my file incorrectly (as I mentioned in my last email). There was some mistake in what I copied in the last email. See below for the correct information.
Best,
Marina
++ 3dclust command:
3dclust -1Dformat -nosum -1dindex 1 -1tindex 1 -2thresh -2.924 2.924 -dxyz=1 1.44 33 /local/mridata/True_and_False_Memory/Analyses/Conjunction_CR12FA56_and_CR12HiConfiProportionalHit_17Subjects_3x3_2only_ExclusivelyMasked_wTvalue_Wholebrain+tlrc.HEAD
++ Writing mask dataset ./Clust_mask+tlrc.BRIKand_CR12HiConfiProportionalHit_17Subjects_3x3_2only_Exc + 3dclust -1Dformat -nosum -1dindex 1 -1tindex 1 -2thresh -2.924 2.924 -dxyz=1 -savemask Clust_mask 1.44 33 /local/mridata/True_and_False_Memory/Analyses/Conjunction_CR12FA56_and_CR12HiConfiProportionalHit_17Subjects_3x3_2only_ExclusivelyMasked_wTvalue_Wholebrain+tlrc.HEAD
