afni.nimh.nih.gov

Drew, before you upload the data, try this:
Instead of:
3dAllineate -1Dmatrix_apply mot.func2struc.tlrc.aff12.1D -input rawdata+orig -prefix rawdata.mot.func2struc

Use:
3dWarp -matvec_in2out mot.func2struc.tlrc.aff12.1D \
-prefix rawdata.mot.func2struc_i2o \
rawdata+orig
and just for the hell of it also try:
3dWarp -matvec_out2in mot.func2struc.tlrc.aff12.1D \
-prefix rawdata.mot.func2struc_o2i \
rawdata+orig

3dWarp is the program that should be used to apply generic affine xforms.

cheers,
z