Hi, Daniel
Thanks for your reply.
I am currently trying to align to macaque T1 images (has skull) so I can average them and improve SNR. I used the align_epi_anat.py.
align_epi_anat.py -dset1 dset1.nii.gz -dset2 dset2.nii.gz -master_dset2 dset2.nii.gz -suffix _al.nii.gz -dset1to2 -overwrite

The alignment was good and gave the dset1to2_mat.aff12.1D. The only problem is that the resulted file is a skull-stripped version and I want to keep the skull in the aligned image. So I planed to use 3dAllineate to directly transform the original image. I first obtained the inverse transformation from align_epi_anat.py
cat_matvec -ONELINE dset1to2_mat.aff12.1D -I > dset1to2_matINV.aff12.1D
I then used 3dAllineate and applied the inverse transformation
3dAllineate -input dset1.nii.gz -1Dparam_apply dset1to2_matINV.aff12.1D -master dset2.nii.gz -prefix dset1_al2.nii.gz -overwrite

However, the result looks completely wrong. It seems that the align_epi_anat.py step is correct but somehow I wrongly used the obtained transformation. Can you provide some insights here?

Thanks so much. I am sorry that I did not clearly describle the problem

ruyuan