set RT_data = '/private/automount/Volumes/afni/var/www/html/pub/dist/edu/2005_10_milwaukee/Actions/DF'
3dUniformize -prefix ./df_spgr1_uni -anat $RT_data/DFSPGR_1+orig. -auto_clip
3dUniformize -prefix ./df_spgr2_uni -anat $RT_data/DFSPGR_2+orig. -auto_clip
3dvolreg -base df_spgr1_uni+orig. -prefix df_spgr2_alnd_1_uni -cubic df_spgr2_uni+orig.
3dMean -prefix df_spgr_avg df_spgr1_uni+orig. df_spgr2_alnd_1_uni+orig.
3dmerge -1blur_fwhm 12 -prefix df_spgr_avg_bl12 df_spgr_avg+orig.
#determine threshold by hand, in afni with colormap thresholding
3dcalc -a df_spgr_avg_bl12+orig. -expr 'step(a-25)' -prefix df_spgr_avg_bl12_manualmask
#fill a few holes by hand in Draw ROI plugin
#pad the volume with 1 slice all around
3dZeropad -R 1 -L 1 -I 1 -S 1 -A 1 -P 1 -prefix df_spgr_avg_bl12_manualmask_zp df_spgr_avg_bl12_manualmask+orig.
#create isosurface
IsoSurface -isoval 1 -o_ply df_spgr_avg_bl12_manualmask_zp -input df_spgr_avg_bl12_manualmask_zp+orig.
#a spec file of isosurface
quickspec -tn Ply df_spgr_avg_bl12_manualmask_zp.ply -spec df_spgr_avg_bl12_manualmask_zp.spec
#smooth surface
SurfSmooth -spec df_spgr_avg_bl12_manualmask_zp.spec -surf_A df_spgr_avg_bl12_manualmask_zp -Niter 12 -met NN_geom -surf_out df_spgr_avg_bl12_manualmask_zp_sm.ply
#check it out