Hi Jeremy,

I think 3dfractionize is the way to go, though you should probably
be using the -warp option, too. The dataset for that option should
be the one (anatomical, presumably) that you used to go from orig
space to tlrc space.

The -vote (or -preserve) is necessary so that your mask values stay
uninterpolated.

So assuming that anat+tlrc contains the transformation from orig
space to tlrc space for mask+tlrc, then your command might be:

3dfractionize -template 3d+t+orig -input mask+tlrc \
-warp anat+tlrc -vote -clip 0.2

That would produce mask+orig, having the same grid as 3d+t+orig.

Then you could use programs such as 3dmaskdump or 3dmaskave to
produce time-series from your mask.

- rick