Hi Ranjan-
This is definitely possible in AFNI. As Daniel mentioned, the easiest thing to do would be to set the -master_epi. So a command like this would perform the alignment between anatomical and functional datasets (including removing motion correction and doing slice timing adjustments) while also putting the two datasets on the same grid (here being the size of the anatomical data:
align_epi_anat.py \
-anat anatFile+orig. \
-epi functionalFile+orig. \
-epi_base 0 \
-master_epi anatFile+orig. \
-epi2anat \
-big_move
You may need to play with having -big_move on or off or even try -giant_move depending on how far apart your two datasets start.
Edited 1 time(s). Last edit at 03/26/2015 04:57PM by Peter Molfese.