Thanks for your help. I'm sharing your suggested solution here:
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if I convert your input file to be floats instead of scaled shorts, then I don't get an error:
$ 3dcalc -a rs_map+tlrc -expr 'a' -prefix rs_map_FLOAT -float
$ 3dROIMaker -inset rs_map_FLOAT+tlrc. -inflate 2 -prefix TEST2 -skel_thr 0.2 -skel_stop -thresh 1 -wm_skel subject_FA+tlrc
++ Value of threshold is: 1.000000
++ GM map is done.
++ GMI map is done.
I'm not precisely sure why this is. I'll look into the 3dROIMaker's innards and see if I can make this not happen, but for the moment, a quick fix for you is to turn your data set into floats with 3dcalc.
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