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http://www.grahamwideman.com/gw/brain/afni/alldocs_afni.htm
Assume we have the following 3d data sets.~
4 T1W 3Ds(T1-1,T1-2,T1-3,T1-4)~
2 T2*W 3Ds(T2-1,T2-2)~
Scan order: T1-1 T2-1 T2-2 T1-2 T1-3 T1-4~
1.Registration among T1s, here registrate to T1-2
T1-1>T1-2<T1-3
<T1-4
2.Registration among T2*s
T2-1>T2-2
3.Registration between T1ave and T2*ave
T1ave<T2ave
AFNI commands: 3dvolreg, 3dAllineate 3dcopy　3dAFNItoNIFTI　(3dAFNItoANALYZE)~
*Processing steps: [#i487baa6]
**Make NIFTI files [#b758ffde]
human3d 3d.t1-1 -F~
...~
human3d 3d.t2-2 -F~
** Registration among T1s [#d8d385ea]
3dvolreg -verbose -dfile param_t1_12 -base 3d.t1-2.nii -prefix 3d.t1-1reg 3d.t1-1.nii~
3dvolreg -verbose -dfile param_t1_32 -base 3d.t1-2.nii -prefix 3d.t1-3reg 3d.t1-3.nii~
3dvolreg -verbose -dfile param_t1_42 -base 3d.t1-2.nii -prefix 3d.t1-4reg 3d.t1-4.nii~
### You should check param files here ###
3dcopy 3d.t1-2.nii 3d.t1-2~
cat 3d.t1-1reg+orig.BRIK 3d.t1-2+orig.BRIK 3d.t1-3reg+orig.BRIK 3d.t1-4reg+orig.BRIK > 3d.t1all+orig.BRIK~
mstat 3d.t1all+orig.BRIK 4 -ave~
cp 3d.t1-1reg+orig.HEAD 3d.t1all+orig-ave.HEAD~
**Registration among T2*s [#k84acc4f]
3dvolreg -verbose -dfile param_t2_12 -base 3d.t2-2.nii -prefix 3d.t2-1reg 3d.t2-1.nii~
### You should check param files here ###~
3dcopy 3d.t2-2.nii 3d.t2-2~
mapcal 3d.t2-1reg+orig.BRIK ave 3d.t2-2+orig.BRIK 3d.t2ave+orig.BRIK~
cp 3d.t2-1reg+orig.HEAD 3d.t2ave+orig.HEAD~
**Registration between T1ave and T2*ave [#tf51084f]
3dAllineate -verb -warp shift_rotate -base 3d.t1ave+orig -source 3d.t2ave+orig -prefix 3d.t2ave_reg~
mapcal 3d.t2ave+orig.BRIK lt 0.05 mask.sdt~
mapcal 3d.t2ave+orig.BRIK + mask.sdt 3d.t2avethre+orig.sdt~
mapcal 3d.t1ave+orig-ave.BRIK / 3d.t2avethre+orig.sdt 3d.t1t2ave+orig.BRIK~
cp 3d.t2-2+orig.HEAD 3d.t1t2ave+orig.HEAD~
3dAFNItoNIFTI -prefix result 3d.t1t2ave+orig~
(3dAFNItoANALYZE -orient LPI result 3d.t1-4reg+orig)~
~
### Removing skull ###
### Removing skull ###~
3dSkullStrip -input 3d.t1t2ave+orig -prefix 3d.t1t2_noskull~
~
(*)If you find some part of the brain is missing or too much sandy noise outside of the brain, you need to adjust the threshold value manually for "mapcal 3d.t2ave+orig.BRIK lt 0.05 mask.sdt".~