Thanks, Paul for the detailed explanation.

I'm using Version AFNI_18.0.05.

I followed your steps for aligning the anatomical image to the standard template. But it threw an error in the warping. Below I have given the afni proc file for the same along with the error message.

#########afni_proc #############

afni_proc.py -subj_id 004 \
-blocks despike tshift align tlrc volreg blur mask scale regress \
-copy_anat 004_SurfVol.nii \
-anat_follower_ROI aaseg anat aparc.a2009s+aseg.nii \
-anat_follower_ROI aeseg epi aparc.a2009s+aseg.nii \
-anat_follower_ROI FSvent epi 001_vent.nii \
-anat_follower_ROI FSWe epi 002_wm.nii \
-anat_follower_erode FSvent FSWe \
-dsets Rest.nii \
-tcat_remove_first_trs 3 \
( -tlrc_base MNI152_T1_2009c+tlrc \
-tlrc_NL_warp \
-volreg_align_to MIN_OUTLIER \
-volreg_align_e2a \ ) (you want me to remove these steps since the warping is happening in the below steps )
-volreg_tlrc_warp -tlrc_base /home/naren123/abin/MNI152_2009_template_SSW.nii.gz \
-tlrc_NL_warp \
-tlrc_NL_warped_dsets \
anatQQ.-base.nii \
anatQQ.-base.aff12.1D \
anatQQ.-base_WARP.nii \
-regress_ROI_PC FSvent 3 \
-regress_anaticor_fast \
-regress_anaticor_label FSWe \
-regress_bandpass 0.01 0.1 \
-regress_apply_mot_types demean deriv \
-regress_RSFC \
-regress_est_blur_epits \
-regress_est_blur_errts \
-regress_run_clustsim no
##########ends here #####

################## error while executing the commands #######################

cat_matvec -ONELINE anatQQ.-base_WARP.nii anatQQ.-base.aff12.1D

Fatal Signal 11 (SIGSEGV) received
mri_read_double_ascii
THD_read_dvecmat
cat_matvec
Bottom of Debug Stack
** AFNI version = AFNI_18.0.05 Compile date = Jan 13 2018
** [[Precompiled binary linux_ubuntu_16_64: Jan 13 2018]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.

############### command line message ends here ###############

For more clarity, I have attached the procedure file also.

############### proc file ###############
# warp the volreg base EPI dataset to make a final version
cat_matvec -ONELINE \
anatQQ.-base.aff12.1D \
CSRI004_SurfVol_al_junk_mat.aff12.1D -I > mat.basewarp.aff12.1D

3dNwarpApply -master anatQQ.-base+tlrc -dxyz 3.5 \
-source vr_base_min_outlier+orig \
-nwarp "anatQQ.-base_WARP.nii mat.basewarp.aff12.1D" \
-prefix final_epi_vr_base_min_outlier

# create an anat_final dataset, aligned with stats
3dcopy anatQQ.-base+tlrc anat_final.$subj

# record final registration costs
3dAllineate -base final_epi_vr_base_min_outlier+tlrc -allcostX \
-input anat_final.$subj+tlrc |& tee out.allcostX.txt

# -----------------------------------------
# warp anat follower datasets (affine)

# catenate all transformations
cat_matvec -ONELINE \
anatQQ.-base_WARP.nii \
anatQQ.-base.aff12.1D > warp.all.anat.aff12 (here it threw an error)

################ ends here #################

Secondly, as you mentioned rightly regarding the censoring and RSFC, we have decided not to include censoring since we are using bandpass.
It would be good if you incorporate '3dLombScargle' and '3dAmpToRSFC' soon in the afni_proc file.

Thanks & regards
-Korann