Hi, Shana-

I'm not quite understanding what data you have available after running FS. Typically, there is a directory (let's call it DDD) that contains subdirectories such as "label/", "mri/", "scripts/", etc. Then, to convert everything to AFNI+SUMA, you could just run something like this:

@SUMA_Make_Spec_FS                            \
    -NIFTI                                    \
    -fspath DDD                \
    -sid    SSS

where SSS will be prefix used in naming convert files like the "SurfVol" dset. This will generate a new subdirectory in DDD called SUMA/, which will contain the AFNI+SUMA outputs.

Do you *not* have a main directory like DDD?

Re. "-use_mgz": I have never used this option, so I am not exactly sure of its purpose actually... Can I ask why you want to use that? Looking at the @SUMA_Make_Spec_FS help file, under the "-NIFTI" option, which you are also using, please note the last line copied here:

-NIFTI :Produce files in exchangeable formats. With this option
           :COR volumes are no longer used and output volumes
           :and surfaces are in alignment with the original 
           :volume used to create the surface. All volumes are
            written out NIFTI format, and all surfaces are
            in GIFTI format.

            This option is incompatible with -neuro or -use_mgz

So, it looks like having -NIFTI and -use_mgz would be conflicting options

I believe that something quite close to the first command posted in this reply ("@SUMA_Make_Spec_FS ...") would make it possible to do 3dLME, etc. analysis, so perhaps that would be worth trying?

Re. 12000 subjects (!!!!), wow! Ummm, I guess it would be computer-RAM dependent, I don't know.

--pt