Hi Nick and Dan,
Thanks for your expedite reply.
The anat_fs_al.nii is aligned properly with the following command only after updating AFNI to the latest version.
3dAllineate -1Dmatrix_apply anat_fs_brain_al_mat.aff12.1D -prefix anat_fs_al.nii anat_fs.nii
Both '3drefit -deoblique anat_fs_al.nii' and '3drefit -deoblique anat_fs.nii' do not work.
I recall that I updated the AFNI package in May 23 2014. What are changes in the binaries between the version on May 23 and the latest version so as to make it work?
Thank you so much for your help.
Phoebe.
