I did the testing just now after donwloading latest version of AFNI.

I start with *.hdr and *.mri files and used to3d command to change it in NIFTI format.

to3d -spgr -prefix .....anat.nii to make anatomy files. But during this step, I received these messages:
[Outliers are defined as in program 3dToutcount. ]
[Outliers early in an EPI time series may be due to ]
[the longitudinal magnetization equilibration effect.]
[Other causes are subject movement, scanner problems,]
[or anything that makes a time series look irregular.]
[ 3dToutcount -save outnam dataset | 1dplot -stdin ]
[can be used to make a dataset 'outnam' that marks ]
[outlier voxels; see 3dToutcount -help for details. ]

I was geting them before too, so I just ignored them.

after this step, I do Skullstripping...