Hey afni folks,

I am attempting to use 3dSkullStrip rather than 3dAutomask for anatomical to epi alignment, via

-align_opts_aea -cost lpc+ZZ -epi_strip 3dSkullStrip

When I check the proc script produced, the align section shows the align_epi_anat.py call contains both -epi_strip options, the default (first) and my request - but looking in the script output file, only 3dAutoMask is used to produce the 'skull stripped' epi,

3dAutoMask -apply_prefix ./__tt_vr_base_ts_rs_ns ./__tt_vr_base_ts_rs+orig

I can imagine a work around (skull strip the epi, and use that as a the volreg target) but I wanted to bring this to your attention. Perhaps I have done something wrong in the way that it is called, by placing the -epi_strip call last?

Thanks!