hi Christine
I tried this out and found the same problem--if I gave:
3dBlurInMask -FWHM 8 -input epi+tlrc -prefix blur_test -mask test_mask+tlrc
the output dataset is the blurred EPI data within the mask and 0 everywhere else.
for the moment, I think you could use a 3dcalc command to get what you want (the original data everywhere outside the mask and blurred data in the mask) like so:
3dcalc -a your_original_epi_data -b your_blurred_data -c your_mask -expr 'iszero(c) * a + b'
hope this helps
James