Salut, Clem--

For the first question about passing skullstrip opts to align_epi_anat.py, I think the following would work (note the 2nd line of options for "-align_opts_aea .."; the first line is just kinda standard stuff which is secondary for your question at hand):

-align_opts_aea -cost lpc+ZZ -giant_move  \
            -epi_strip 3dSkullStrip -skullstrip_opts -monkey   \

That created this align_epi_anat.py command in the proc* script:

# ================================= align ==================================
# for e2a: compute anat alignment transformation to EPI registration base
# (new anat will be intermediate, stripped, FT_anat_ns+orig)
align_epi_anat.py -anat2epi -anat FT_anat+orig                      \
       -save_skullstrip -suffix _al_junk                            \
       -epi vr_base_min_outlier+orig -epi_base 0                    \
       -epi_strip 3dAutomask                                        \
       -cost lpc+ZZ -giant_move -check_flip -epi_strip 3dSkullStrip \
       -skullstrip_opts -monkey                                     \
       -volreg off -tshift off

so it looks like that is working how you would want? Well, now I notice that there are 2 "-epi_strip .." commands, and from looking at the history of the files created, it seems like 3dAutomask is still used, oddly. I will have to check with Daniel about this.

To this question: "It seems to me that having a bad SkullStrip generates lots of problems for the co-registration?" well, severe inhomogeneity or odd brightness patterns in the EPI can cause lots of problems for alignment; it is possible that changing the cost function might help. Could you post an image of your EPI, as an example? The details likely matter for deciding what to do here...

--pt