foreach infile(GLM.cbucket)
@auto_tlrc -rmode NN -dxyz 2
-suffix _at
-apar Anatomical_reg_AlndExp_ns_at+tlrc
-input “$infile”+orig

When the input file is “”$infile"+orig" file, the output is named “$infile”_at+TLRC, by default.
However, when the input file is “”$infile".nii.gz"file, the output is named “”$infile"_at.nii.
Is it right? Do different output formats affect data content?

If you type:

3dinfo -space -av_space FILENAME

on either of those files, you will see that they are marked internally as being a special, “non-original” space. The NIFTI file name doesn’t show that explicitly, but it is marked in the header info internally for the file.

From the 3dinfo help, these properties are showing you:

-space: dataset's space
-av_space: AFNI format's view extension for the space

These things relate to AFNI’s use of templates and atlas information, with the “whereami” function-- being able to jump around to locations marked in atlases, or to be able to estimate one’s location with respect to known atlases.