And seems @SUMA_AlignToExperiment works when I test this :

@SUMA_AlignToExperiment -exp_anat ortho+orig. -surf_anat ~/subjects/FIOLCEKQ/SUMA/FIOLCEKQ_SurfVol+orig. -prefix ortho+suma

However, the output is nowhere even the log says:

++ Wrote dataset to disk in /home/wang/subjects/FIOLCEKQ/SUMA/ortho+suma+orig.BRIK


The whole log:
-----------------------------
[wang@wang analysis]$ @SUMA_AlignToExperiment -exp_anat ortho+orig. -surf_anat ~/subjects/FIOLCEKQ/SUMA/FIOLCEKQ_SurfVol+orig. -prefix ortho+suma
++ 3dinfo: AFNI version=AFNI_2007_05_29_1644 (Aug 17 2007) [64-bit]
++ 3dinfo: AFNI version=AFNI_2007_05_29_1644 (Aug 17 2007) [64-bit]
Center distance of 52.000000 mm

resampling ortho+orig to match /home/wang/subjects/FIOLCEKQ/SUMA/FIOLCEKQ_SurfVol+orig
3dresample -master /home/wang/subjects/FIOLCEKQ/SUMA/FIOLCEKQ_SurfVol+orig -prefix ortho_resamp_ -rmode Cu -inset ortho+orig


Registering /home/wang/subjects/FIOLCEKQ/SUMA/FIOLCEKQ_SurfVol+orig to ortho_resamp_+orig
3dvolreg -wtrim -clipit -twopass -twodup -zpad 8 -rotcom -verbose -base ortho_resamp_+orig -prefix ortho+suma /home/wang/subjects/FIOLCEKQ/SUMA/FIOLCEKQ_SurfVol+orig

++ 3dvolreg: AFNI version=AFNI_2007_05_29_1644 (Aug 17 2007) [64-bit]
++ Authored by: RW Cox
++ Notice: -wtrim is now always enabled
++ Notice: -clipit is now the default
++ Reading in base dataset ./ortho_resamp_+orig.BRIK
++ Reading input dataset /home/wang/subjects/FIOLCEKQ/SUMA/FIOLCEKQ_SurfVol+orig.BRIK
++ Edging: x=13 y=13 z=13
++ Creating mask for -maxdisp
+ Automask has 3862997 voxels
+ 123381 voxels left in -maxdisp mask after erosion
++ Start of first pass alignment on all sub-bricks
++ Computing first pass weight as sum of base and brick
++ Getting best coarse rot+shift [0]:xw[24.4%]**.*.***...........**.*..............*....... 9 -0 0 : 0 -20 0
++ Scale init = 0.0784255
++ Blurring first pass weight
++ CPU time for first pass=37.5 s
++ Initializing alignment base
++ Starting final pass on 1 sub-bricks: 0..
++ CPU time for realignment=73.1 s
++ Min : roll=+5.425 pitch=+1.739 yaw=+0.729 dS=+37.178 dL=-1.346 dP=-4.833
++ Mean: roll=+5.425 pitch=+1.739 yaw=+0.729 dS=+37.178 dL=-1.346 dP=-4.833
++ Max : roll=+5.425 pitch=+1.739 yaw=+0.729 dS=+37.178 dL=-1.346 dP=-4.833
++ Max displacements (mm) for each sub-brick:
++ Max displacements (mm) for each sub-brick:
43.36
++ Max displacement in automask = 43.36 (mm) at sub-brick 0
++ Wrote dataset to disk in /home/wang/subjects/FIOLCEKQ/SUMA/ortho+suma+orig.BRIK

3drotate fragment:

3drotate -Fourier -clipit -zpad 8 -rotate 5.4252I 1.7395R 0.7288A -ashift 37.1784S -1.3459L -4.8335P

removing temporary bricks ...
Done.