Hi Rick,
I have followed these steps to align the epi dataset to the template (TT_N27+tlrc) using 3dQwarp. But, it seems the non-linear transformation does not work. Not only the output epi is not aligned with the template, its shape is stretched in a strange way.
The anatomical I get as the output from 3dQwarp is very very well aligned with the template. But, when I apply the affine and the non-linear transformation to the original skull-stripped anatomical (which has been aligned with the epi dataset), it results in a dataset which is misaligned and mishapen in ways that are similar to case I did this with epi, as mentioned above.
I have tried to do this every which way and I cannot figure out what is wrong.
-Kausar