Hello Taosheng,

Sorry for the delay, but it is Gang Chen's fault! You can certainly do all of 1. and all of 2.
The manual/documentation is mostly in suma.pdf . The outline goes something like this:
1- Create the surfaces, with FreeSurfer say.

2- Run AFNI's: @SUMA_Make_Spec_FS -sid Festus -GIFTI
That would import FreeSurfer's surfaces, parcellations (volume and surface) into SUMA land

3- Map your subject data onto the 'standard mesh surfaces' (see suma.pdf for a start, I can point you to other refs if you need them later). By using standard meshes you can readily go into group analysis whenever you choose to do so with minimal effort. Standard meshes are created automatically by @SUMA_Make_Spec_FS . Setup can be done for you with afni_proc.py

4- Drawing ROI is quite simple with SUMA's Draw ROI (also in the PDF), selecting ROIs from FreeSurfer's parcellation is also quite simple (see run_* scripts under the afni/ and SUMA/ directories in suma_demo.tgz which is used at the bootcamp for various examples)

5- There is a retinotopy pipeline (@RetinoProc) along with downloadable demo data and scripts (just run @RetinoProc -fetch_demo) courtesy of Peter J. Kohler and Sergey V. Fogelson.

6- Note that AFNI can automatically process single subject data either in the volume or on the surface with afni_proc.py. All you need is two extra options to go from full analysis in the volume to analysis on the surface.

7- All of AFNI's group analysis programs including the advanced ones (3dMEMA, 3dLME, 3dMVM will work on surface data just fine).

I wish you could have attended the bootcamp a couple of weeks ago, we covered most of that stuff in detail! I am sure you'll run into some bumps, but I will try to respond faster.

cheers,
z