Hi Ajay-

As Rick mentioned, the use of 3dQwarp is unnecessary here, because there is a better way. That better way is using standard surfaces. Essentially you're identifying common nodes among all of your Freesurfer surfaces. See Page 55 of this document.

Quote
On such standard meshes, functional data mapped to node n on one subject can be directly compared to data mapped to node n on another subject’s surface.

Once you know the common nodes, you can do "vertex-wise" analyses across subjects because all of your data are "in alignment". You can then use any AFNI program (e.g. 3dttest++) to do group analyses and visualize the results on the standard mesh from the MNI template.

To get to this point, you only need to run your MNI template through freesurfer a single time. Then run freesurfer on all of your individual subjects. Following that step, run @SUMA_Make_Spec_FS on all of your subjects and on the MNI template. This will automatically create standard meshes (by calling MapIcosahedron for you) for each subject and the MNI template.

Once you have all of your single subject data on standard meshes (either by processing the data directly on standard surfaces or using SurfToSurf to map your data from subject original meshes to the standard mesh).

Hope this helps!