afni.nimh.nih.gov

Thanks, Paul for assisting on a regular basis.

After updating AFNI to a new version, now things are fine. One sincere suggestion from my side is that why don't you people incorporate @SSwarper along with afni proc in example 11 and since eg. 11 does not do the intended job properly. So it would be helpful for others if you could club @SSwarper and example 11 together.

I also attached the normalization results after using the @SSwarper function along with codes.

@SSwarper          \
        -input  SubjID-Structural.nii       \
        -base   MNI152_2009_template_SSW.nii.gz        \
        -subid  SubjID \

afni_proc.py -subj_id SubjID \
	-blocks despike tshift align tlrc volreg blur mask scale regress \
	-copy_anat anatSS.SubjID.nii \
	-anat_has_skull no \
	-anat_follower anat_w_skull anat SubjID_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 \
	-align_opts_aea -giant_move -cost lpc+ZZ -check_flip \
	-volreg_tlrc_warp -tlrc_base /home/naren123/abin/MNI152_2009_template_SSW.nii.gz \
	-tlrc_NL_warp \
      	-tlrc_NL_warped_dsets \
         	anatQQ.SubjID.nii \
         	anatQQ.SubjID.aff12.1D \
         	anatQQ.SubjID_WARP.nii \
	-volreg_align_to MIN_OUTLIER \
	-volreg_align_e2a \
	-volreg_tlrc_warp \
	-mask_epi_anat yes \
	-regress_motion_per_run \
	-regress_ROI_PC FSvent 3 \
	-regress_make_corr_vols aeseg FSvent \
	-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

Thanks, Rick for helping at the right time.

Regards
-Korann