Peter,
Thanks for such a quick reply.
First in order to get the affine and non-linear transformations, I use 3dQwarp:
3dAllineate -prefix anat_SSA -base TT_N27+tlrc \
-source anat_SS+orig -twopass -cost lpa \
-1Dmatrix_save anat_SSA.aff12.1D \
-autoweight -fineblur 3 -cmass
3dQwarp -prefix anat_SSAQ -duplo -useweight -blur 3 \
-base TT_N27+tlrc -source anat_SSA+tlrc
where
anat_SS+orig ----> skull-stripped anatomical which has been aligned with epi
Then, I use this affine and non-linear transformations on the epi dataset:
3dNwarpApply -source epi+orig \
-nwarp 'anat_SSAQ_WARP+tlrc anat_SSA.aff12.1D' \
-master NWARP \
-prefix epi_AQ
The epi was passed through volume registration before this step. I have also tried this with and without '-master' and '-newgrid' options. All of this seems to produce exactly the same results.
I don't know how to check for the versions of binaries for a specific program, but I typed in 'afni -ver' and this is the output:
Version AFNI_2011_12_21_1014
[[Precompiled binary linux_openmp_64: Oct 18 2013]]
-Kausar