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Dear reader, In addition to my previous message, I found out that the script works fine when the coordinates do not include negative values (45 works, but -45 doesn't). A bit surprising to me is that if I run the fslmaths command outside of the script, negative values won't work either: fslmaths $outim -mul 0 -add 1 -roi 16 1 20 1 30 1 0 1 -mul 1 -add $outim $outim fslmaths $outim -mul 0 -add 1 -roi 14 1 17 1 10 1 0 1 -mul 2 -add $outim $outim fslmaths $outim -mul 0 -add 1 -roi 27 1 45 1 5 1 0 1 -mul 3 -add $outim $outim provides me with 3 clusters in one file, however, fslmaths $outim -mul 0 -add 1 -roi 16 1 20 1 30 1 0 1 -mul 1 -add $outim $outim fslmaths $outim -mul 0 -add 1 -roi -14 1 17 1 10 1 0 1 -mul 2 -add $outim $outim fslmaths $outim -mul 0 -add 1 -roi 27 1 -45 1 5 1 0 1 -mul 3 -add $outim $outim gives me one cluster as the other 2 clusters are not calculated because of their negative values. I hope you might have some suggestions how to solve this. Thank you. Kind regards, Liza