If you look at the "3dcalc -help" documentation [afni.nimh.nih.gov], you'll find (under "COORDINATES and PREDEFINED VALUES") a discussion of the predefined variables "x", "y", and "z". If you don't define "x" with a "-x dataset" option, then "x" in the expression refers to the voxel x coordinate (mutatis mutandum for "y" and "z"). Thus, you could do something brutal like

3dmaskdump -mask mm+orig -noijk '3dcalc( -a dset+orig -datum float -expr x)' \
'3dcalc( -a dset+orig -datum float -expr y)' \
'3dcalc( -a dset+orig -datum float -expr z)' dset+orig

This would calculate temporary datasets on-the-fly (using the little known command line 3dcalc() input option) with x,y,z in the voxels, and then dump them to stdout.

Of course, simpler (for you) would be for us to add a "-xyz" option to 3dmaskdump.c, but this solution is simpler for me.

The "-mask mm+orig" option to 3dmaskdump will pick out the voxels where the mask dataset "mm+orig" is nonzero. If you don't input any mask dataset, 3dmaskdump will dump out the ASCII data for all voxels - this is usually humungous. Without seeing your command line and the sequence of operations you're performing, I can't give any further diagnosis. Read the output of "3dmaskdump -help" [afni.nimh.nih.gov] carefully. I know it's terse, but that's all the documentation there is (or is likely to be).

bob cox