There are two "popular" pipelines for using surfaces. The first, which is what I think you're talking about, is to process your data in the volume (afni_proc.py recommended) and then visualize the results on the surfaces. This makes use of traditional processing techniques like smoothing in the volume, and can use 3dQwarp for nonlinear registration.

The second approach is to process each participant's data on the surface early on. This requires that you run freesurfer on each individual subject in your study. If you are using afni_proc.py, you can add the "-surf" block to processing and it will take care of registering your EPI data with the surfaces.

It sounds like you want to use the first approach, or possibly a hybrid of the two. For the first, approach I would do the following:

1) Take your MNI template and process it through freesurfer (recon-all)
2) Run @SUMA_Make_Spec_FS on your output freesurfer directory (optional but recommended -GIFTI flag)
3) Process your data in the volume, registering the data to the Skull-stripped MNI template you supplied to Freesurfer (again I would suggest afni_proc.py)
4) Perform group analysis using one of the 3d programs (e.g. 3dttest++)
5) Display the results in both the volume and surface by doing the following:
A. Load MNI template underlay and statistics overlay in AFNI (start AFNI with -niml flag)
B. Load SUMA with -spec and -sv from the created "SUMA" folder made by @SUMA_Make_Spec_FS (usually inside subjects directory with freesurfer results)
C. In SUMA, press the "t" key to talk to AFNI
D. Changing the visualized sub-bricks and threshold in AFNI will update the SUMA display.

Let me know if that's what you were looking for. I have a bit more written in a blog post here. But happy to clarify. The main reason to run MapIcosahedron, which is run by @SUMA_Make_Spec_FS, is to make standard surfaces for the second pipeline. Though you could use them for a variety of purposes.



Edited 6 time(s). Last edit at 11/19/2015 02:17PM by Peter Molfese.