Hi, Brady-
So, the option to use to specify "left is left" should look like:
-left_is_left YES
The "-left_is_left LIL" in the help file is using LIL as a placeholder for either YES or NO. Please let me know if changing "LIL" to "YES" fixes your issue.
(For me, "-left_is_left LIL" behaved like "-left_is_left NO"---but I will make the code give an error if neither YES nor NO is provided as the option argument.)
And yes, the "left_is_left" value applies to both axial and coronal.
Re. sagittal images: "-left_is_posterior .." is a separate option to control that.
--pt