Hi, Sondos-

I think by "cat"ing the text file, that is like adding lots of arguments after the option name, which confuses the parser and so it doesn't recognize -refset as an option name.

In any case, the program is not meant to be used in that manner. You should enter the name of a single data set (which can have multiple volumes) after each of the "-inset" and "-refset" options. Those sets much have the same grid space, so that they can be compared voxelwise.

For individual comparisons, the files will have to be analyzed one-by-one. You can loop over the name of files for this inset, for example. If you are familiar with tcsh syntax, this could be done with, say:

set allfiles = `ls SOME_DIR/*HEAD`
foreach vv ( $allfiles )
     set bb = `3dinfo -prefix_noext $vv`
    3dMatch -inset $vv    \
              -refset /Users/sondos/Desktop/dualreg_40subj_output3/merged_Yeo_40sub_standardSpace_matchingZscore.nii.gz  \
              -mask /Users/sondos/Desktop/dualreg_40subj_output3/maskALL.nii.gz \
              -in_min 0 \
              -prefix 3dMatch_40sub_$bb
end

(This matches some fo the output files prefix with each input file's name.)

--pt