yea, it's not Nifti files. As I converted files to AFNI format and still getting the same issue.
Afni version is : linux_openmp_64: Jul 1 2014
afni_proc.py -subj_id $sub \
-script $scrpt_file -scr_overwrite -out_dir $out_dir \
-blocks tshift align tlrc volreg blur mask scale regress \
-copy_anat $anat_file \
-tcat_remove_first_trs $TR \
-tshift_opts_ts -tpattern $pattern \
-dsets \
$epi_file \
-align_opts_aea -cost lpa \
-tlrc_base MNI_avg152T1+tlrc \
-volreg_align_to last \
-volreg_align_e2a \
-volreg_tlrc_warp \
-blur_to_fwhm \
-blur_size 4 \
-blur_in_automask \
-regress_stim_times \
$stim_dir/only_${task}_vis.1D \
$stim_dir/only_${task}_nv.1D \
-test_stim_files yes \
-regress_stim_labels \
${task}_vis ${task}_nv \
-regress_basis \
'BLOCK(30,1)' \
-regress_censor_motion 0.5 \
-regress_opts_3dD \
-tout \
-regress_make_ideal_sum sum_ideal.1D \
-regress_est_blur_epits \
-regress_est_blur_errts
