afni.nimh.nih.gov

Hi Daniel,

It looks like you use this instead of the default skull-stripping method? Then the final output is a Qwarped, skull-stripped brain aligned to a template that can later be used to align the EPI to?

I have a question regarding your script:

In your command "align_epi_anat.py -dset1 ${based}_un+orig -dset2 $template -giant_move -suffix _al2template \
-dset1_strip None -dset2_strip None -master_dset1 BASE", what does BASE refer to here, anatomy or the standard?

Thanks,

Danny