Hello Yang,
1- There is no script to align MEG data to Anatomical MRI. I don't have much experience with MEG software, but some MEG software (like CTF's) allow you to align the MEG data with high resolution MRI and write the results to disk. AFNI does read CTF's volumes directly, so if that is the software you are using then you're in luck. Otherwise, you'll need to understand the file format of your volumes and use AFNI's to3d to read the data and write it in AFNI's format.
2- It is best that you check out the documentation here:
[
afni.nimh.nih.gov]
In particular, search for "Figure 1" and "Figure 2" and read the documentation referring to them.
3- You can use the program 3dTagalign to manually set corresponding landmarks in two volumes and align them together. Documentation for doing this operation is also available here:
[
afni.nimh.nih.gov]
Search for "Aligning SurfVol to ExpVol using 3dTagalign"
-z
