Hi Rick,
thanks for the advice!
This is the output of afni -ver
Version AFNI_2011_12_21_1014
[[Precompiled binary linux_xorg7_64: Sep 30 2013]]
Following your input, I played around with the filenames a bit, and I don't get the error anymore:
anatomy=VMR.ss+orig
tlrc_anatomy=VMR.ss+tlrc
epi=EPI+tshift+moco+wrap+orig
align_epi_anat.py -epi $base_folder/$data_folder/EPI+tshift+moco+wrap+mask+orig -anat $base_folder/$anat_folder/$anatomy -epi_base 0 -epi2anat -anat_has_skull no -epi_strip None -volreg off -tshift off -edge -suffix _algn -overwrite -rat_align -verb 0 -tlrc_apar $base_folder/$anat_folder/$tlrc_anatomy
It seems that AFNI didn't like that I tried to use the normalized version of the tlrc-ed anatomy.
Unfortunately however, the alignment of the EPI to the tlrc anatomy is completly off.
I have also tried to use Align_centers first, and then supply the (inverse) of that matrix as -pre_matrix to align_epi_anat.py, but with no success.
Caspar