Rick- I run 2 scripts- 3TafniNew, and then 3Tafni2. Both scripts are below:

----------3TafniNew-----------

#!/bin/csh -f

#THIS SCRIPT IS FOR SINGLE SESSION REGISTRATION WITH 3T DATA

#Setup Variables

#>>>ENTER THE DIRECTORY LOCATION OF DATA
set File = '/data/phase3/t_cc20020728'

#>>>ENTER THE START AND END PLANES FOR THE EPI DATA
set Left = '75.9L'
set Right = '84.1R'

#>>>ENTER THE START AND END PLANES FOR THE STRUCTURAL (HIGH RESOLUTION) DATA
set HiRes_L = '90.8L'
set HiRes_R = '93.7R'

#>>>ENTER THE SESSION NUMBER FOR THE SUBJECT
set Session = '2'

#>>>ENTER THE SERIES NUMBER FOR THE HI RESOLUTION SCAN
set Series = 003

set Dir = 'afni'
#set Dir = 'afni2'
set TR = 4000
set Nslice = 32
set Ntime = 297
#set Ntime = 267

cd $File

#CREATE AFNI DIRECTORY

cd $File
test -d $Dir || mkdir $Dir
cd raw
#cd raw1

#RECONSTRUCT P FILES USING RECONLX AND REMOVE THE FIRST TIME POINT

reconlx -swap P* im
rm -f im_*.001
rm -f im_*.002
rm -f im_*.003

#CREATE BRIK FOR EPI DATA

to3d -epan -prefix E$Session -session ../$Dir -time:tz $Ntime $Nslice $TR 'alt+z' -xFOV 120S-120I -yFOV 120P-120A -zSLAB $Left-$Right im*

#rm -rf im*

#ZERO PAD COMMAND FOR 1 ADDITIONAL SLICE

#3dZeropad -R 1 -prefix ../$Dir/EPad$Session ../$Dir/E$Session'+orig'
#mv ../$Dir/E$Session'+orig.BRIK' ../$Dir/E$Session'nopad+orig.BRIK'
#mv ../$Dir/E$Session'+orig.HEAD' ../$Dir/E$Session'nopad+orig.HEAD'
#mv ../$Dir/EPad$Session'+orig.BRIK' ../$Dir/E$Session'+orig.BRIK'
#mv ../$Dir/EPad$Session'+orig.HEAD' ../$Dir/E$Session'+orig.HEAD'

#CREATE BRIK FOR STRUCTURAL DATA

cd ../struct


tar -xvf *.tar

# cd */*/$Series
cd */$Series

# to3d -spgr -2swap -prefix S -session ../../../../$Dir -xFOV 120A-120P -yFOV 120S-120I -zSLAB $HiRes_L-$HiRes_R I.*
to3d -spgr -2swap -prefix S$Session -session ../../../$Dir -xFOV 120A-120P -yFOV 120S-120I -zSLAB $HiRes_L-$HiRes_R I.*

#2D IMAGE REGISTRATION

# cd ../../../../$Dir
cd ../../../$Dir

2dImReg -input E$Session'+orig' -base 4 -prefix 2dimreg -dprefix 2dmotion

#3D VOLUME REGISTRATION WITH NO DETRENDING

3dvolreg -verbose -clipit -prefix E$Session'reg' -base '2dimreg+orig[4]' -dfile 3dmotion.1D 2dimreg+orig

#3D VOLUME REGISTRATION WITH DETRENDING

3dTshift -slice 0 -prefix detr -rlt+ 2dimreg+orig

3dvolreg -verbose -clipit -prefix E$Session'reg_detr' -base 'detr+orig[4]' -dfile 3dmotion_detr.1D detr+orig

rm 2dimreg*
rm detr+orig*



I use the zeropad command in 3Tafni2:
--------------3Tafni2----------------

#!/bin/csh -f

#THIS SCRIPT IS FOR SESSION >1 of MULTI-SESSION REGISTRATION WITH 3T DATA

#Setup Variables

#>>>ENTER THE DIRECTORY LOCATION OF DATA
set File = '/data/phase3/t_cc20020728'

#>>>ENTER THE DIRECTORY LOCATION OF SESSION 1 FOR THE SUBJECT set Parent = '/data/phase3/t_cc20020714/2afni/'

#>>>ENTER THE START AND END PLANES FOR THE EPI DATA
set Left = '75.9L'
set Right = '84.1R'

#>>>ENTER THE START AND END PLANES FOR THE STRUCTURAL DATA
set HiRes_L = '90.8L'
set HiRes_R = '93.7R'

#>>>ENTER THE SESSION NUMBER FOR THE SUBJECT
set Session = '2'

#>>>ENTER THE SLICE WIDTH OF THE PARENT STRUCTURAL DATA
# IF DIFFERENT FROM THIS SESSION AND PUT # SIGN IN FRONT OF OPTION A BELOW # IF SLICE WIDTH IS THE SAME PUT # SIGN IN FRONT OF OPTION B BELOW set Regrid = 1.5

#>>>ENTER THE SERIES NUMBER FOR THE HI RESOLUTION SCAN
set Series = 003

set Dir = '2afni'
#set Dir = '2afni2'
set TR = 4000
set Nslice = 32
set Ntime = 297
#set Ntime = 267

#CREATE AFNI DIRECTORY

cd $File
test -d $Dir || mkdir $Dir
cd raw
#cd raw1

#RECONSTRUCT P FILES USING RECONLX AND REMOVE THE FIRST THREE TIME POINTS

reconlx -swap P* im
rm -f im_*.001
rm -f im_*.002
rm -f im_*.003

#CREATE BRIK FOR EPI DATA

rm ../$Dir/E$Session*

to3d -epan -prefix E$Session -session ../$Dir -time:tz $Ntime $Nslice $TR 'alt+z' -xFOV 120S-120I -yFOV 120P-120A -zSLAB $Left-$Right im*

rm -rf im*

#ZERO PAD COMMAND FOR 1 ADDITIONAL SLICE

3dZeropad -R 1 -prefix ../$Dir/E$Session ../$Dir/EPad$Session'+orig'

# CREATE BRIK FOR STRUCTURAL DATA

cd ../struct

tar -xvf *.tar

# cd */*/$Series
cd */$Series

rm ../../../$Dir/S$Session*

# to3d -spgr -2swap -prefix S -session ../../../../$Dir -xFOV 120A-120P -yFOV 120S-120I -zSLAB $HiRes_L-$HiRes_R I.*

to3d -spgr -2swap -prefix S$Session -session ../../../$Dir -xFOV 120A-120P -yFOV 120S-120I -zSLAB $HiRes_L-$HiRes_R I.*

cd ../../../$Dir
pwd

# OPTION A - COMPUTE STRUCTURAL TRANSFORMATION WITH NO REGRID

#3dvolreg -twopass -twodup -clipit -zpad 4 -base $Parent'S1+orig' -prefix S$Session'reg' S$Session'+orig'

#3dvolreg -twopass -twodup -clipit -zpad 4 -base $Parent'S+orig' -prefix S$Session'reg' S$Session'+orig'

#OPTION B - COMPUTE STRUCTURAL TRANSFORMATION WITH REGRID

3dZregrid -dz $Regrid -prefix regrid S$Session'+orig'

3dvolreg -twopass -twodup -clipit -zpad 4 -base $Parent'S1+orig' -prefix S$Session'reg' regrid+orig

rm regrid*


#2D IMAGE REGISTRATION

# cd ../../../../$Dir
# cd ../../../$Dir

rm 2dimreg+orig.*
2dImReg -input E$Session'+orig' -base 4 -prefix 2dimreg -dprefix 2dmotion


#3D VOLUME REGISTRATION WITH NO DETRENDING

3dvolreg -verbose -clipit -base '2dimreg+orig[4]' -rotparent S$Session'reg+orig' -gridparent $Parent'E1reg+orig' -prefix E$Session'reg' -dfile 3dmotion.1D 2dimreg+orig

#3D VOLUME REGISTRATION WITH DETRENDING

3dTshift -slice 0 -prefix detr -rlt+ 2dimreg+orig

3dvolreg -verbose -clipit -base 'detr+orig[4]' -rotparent S$Session'reg+orig' -gridparent $Parent'E1reg_detr+orig' -prefix E$Session'reg_detr' -dfile 3dmotion_detr.1D detr+orig

rm 2dimreg+orig*
rm detr+orig*