Hello Lingyan,

I think you have the gist of it. You shouldn't have to run @SUMA_Align_To_Experiment, although it shouldn't really hurt if the datasets are in the same space. My guess is that your datasets have some transformation in the header that is being applied on the transformation by the -sv volume or that the data is oblique. You can test for this by seeing how both volumes and surfaces look inside suma by adding a -vol mysvdset.nii.gz to the suma command line. You may want to show that command here too. To remove the obliquity considerations, make copies of all the datasets, maybe into a new directory. Then remove that information from the header (this is a destructive change, so do this only on copies) with "3drefit -deoblique mydsets". If you can't find a solution, you may send me the data, and I'll take a look. Let me know what you would like to do.

Daniel