Hi Ajay,
Not sure about the best way to go about flipping a cortical surface. Since the process of converting surfaces to GIFTI and resampling to the fsaverage are all based on Freesurfer programs, I would suggest
asking the folks over at MGH/Martinos on the preferred way to do that. The
HCP group might also have thoughts on ways of handling this.
Once you get that L/R flip, then as long as you can get it into GIFTI and resampled to the fsaverage (using steps above), you should be all set to do analyses in AFNI.
-Peter
