I am having a related problem with 3dSkullStrip, despite having just re-installed gsl (and making sure that the PATH is included). This seems to have started when I updated the AFNI binaries around the 16th of November:
3dSkullStrip: error while loading shared libraries: libgsl.so.0: cannot open shared object file: No such file or directory
** ERROR: Could not strip skull
** ERROR - script failed
@auto_tlrc -base TT_N27+tlrc -input 167-MA-1_s2_t1_mprage_sag_1mm_strip+orig -no_ss -suffix NONE -init_xform CENTER
Suffix not used.
if: Expression Syntax.