You could use

3dDeconvolve -stuff input+orig 2>&1 | tee 3dDeconvolve.log
(if you're using bash)

or

3dDeconvolve -stuff input+orig |& tee 3dDeconvolve.log
(if you're using tcsh)

which would save all the screen output to a file 3dDeconvolve.log in the current directory. If you don't care about seeing the output on the screen and only want the file, you could use the simpler

3dDeconvolve -stuff input+orig >& 3dDeconvolve.log

where in this case it doesn't matter if you're using bash or tcsh.