afni.nimh.nih.gov

It would help if you gave the names of some of the "invisible files".

AFNI-readable datasets are stored in files whose names end in .HEAD or .nii or .nii.gz -- you won't see the other files in the directory in the AFNI GUI.

Files with names ending in .1D are text files with columns of numbers -- these are visible in the AFNI GUI, but not as 3D datasets to visualize.