Hi-
A few quick questions:
1) are you using afni_proc.py, or doing something separately?
2) What is the output of:
afni_system_check.py -check_all
?
3) What is the output of:
3dinfo -n4 -o3 -orient -prefix deoblw_pb06.shellgame_26.r02.Cd3MP+orig shellgame_26.BrainExtractionBrain.nii.gz
4) what "other" EPI are you using that makes things OK?
--pt