Hi Judith,

You have two transformations applied to SurfVol but only one is getting applied. To get the method you are using to work you will need to combine the 3dvolreg transform with the 3dnudge transform then apply the combination to SurfVol.

Here is a schematic of what needs to be done (This should work but there is a slight chance that it won't, verify results at each step):

3dvolreg -base Str_alnd_Func -prefix Strl_trans SurfVol --> a VOLREG_MATVEC_000000 is stored in Strl_trans+orig.HEAD

3drotate NUDGE_OPTIONS -prefix Strl_trans_nudge Strl_trans --> a ROTATE_MATVEC_000000 is stored in Strl_trans_nudge+orig.HEAD

cat_matvec 'Strl_trans+orig::VOLREG_MATVEC_000000' 'Strl_trans_nudge+orig::ROTATE_MATVEC_000000' > Combined_Trans.1D

3drotate -prefix Strl_trans_Combined -matvec Combined_Trans.1D SurfVol

The dataset Strl_trans_Combined+orig should be almost identical to Strl_trans_nudge except it was obtained with one transform from SurfVol.
Use Strl_trans_Combined as your -sv for suma, 3dVol2Surf and all other SUMA commands for these functionals.

In response to the other question. The misalignment you see in AFNI with a particular -sv will be present when you are mapping data. Whatever alignment you see in AFNI is the alignment you get with the other programs.

Lastly, I don't understand why you need to run 3dvolreg, followed by nudging. Assuming Str_alnd_Func is in good alignment with your function you should be able to get to it in one pass from SurfVol, unless the Str_alnd_Func (created using FS' inverse alignment transform) is of a different type (T2 Weighted MRI) than SurfVol (T1 Weighted MRI). If the two volumes are of the same MR contrast, try using @SUMA_AlignToExperiment -exp_anat Str_alnd_Func+orig -surf_anat SurfVol+orig
You can also add the -wd option (newish for @SUMA_AlignToExperiment) which will use a 12 parameter transform that might improve the alignment, in case the alignment by FS was a non-rigid transform.

cheers,
Zodot