Great, thanks for the advice, after also changing the ownership of ~/.afni I was able to successfully run the command:

tcsh @update.afni.binaries -package macos_10.12_local -do_extras

And the suma -update env command also successfully ran.

I have now moved on to installing R, and have run into another error. I installed R3.5.3 and confirmed I can open and run R from the terminal, but I receive the following error when running the command:

sudo rPkgsInstall -pkgs ALL
updating R_LD_LIBRARY_PATH ...

oo Warning:
Failed to load R_io.so with this error message:

Error in dyn.load(ll) :
unable to load shared object '/Users/amy/abin/R_io.so':
dlopen(/Users/amy/abin/R_io.so, 6): Library not loaded: /sw/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libR.dylib
Referenced from: /Users/amy/abin/R_io.so
Reason: Incompatible library version: R_io.so requires version 3.6.0 or later, but libR.dylib provides version 3.5.0
Calls: source ... withVisible -> eval -> eval -> set_R_io -> dyn.load
Execution halted

I do have another version of R installed in a different enviornment, is this causing the problem?