Hi Peter,
Thanks for the speedy reply. I have run fsaverage through @SUMA_Make_Spec_FS. I have questions for each of the two options you gave me.

1) You said I can take the smoothed fsaverage warped thickness file ( Subject01.lh.thickness.fsaverage.gii) and do an analysis with 3dttest++. My question is do I have to first use MapIcosahedron on this file prior to the analysis? I would assume that the vertex of my thickness files have to match subject to subject somehow as well as matching fsaverage, or does this get taken care of by qcache warping them to fsaverage? I guess I am still a bit fuzzy on if MapIcosahedron is run on just the structrual brain or if we run on each of the measures as well (ie the smoothed thickness file), as well as why I would not need to run it in this case.

2) For the second option of using the subject specific std.141.?h.thickness.niml.dset and smoothing them with SurfSmooth and then doing a group analysis, I am not 100% clear. Does this mean that even though the std.141.?h.thickness.niml.dset file is in subject space, each vertex is mapped onto fsaverage somehow to do a group analysis. Or does this method bypass fsaverage altogether since it just a standard coordinate system, and we assume that the points will match up accurately when displayed with fsaverage?

3) For option 2, how would we run a group analysis. Would you still use 3dttest++ and if so, what would be the input?

4) For option1, do I have to run 3dttest++ separately on left and right hemisphere or is there a way to combine the data (ie 3dcalc) them? Would htis work for option 2 as well?

Thanks,
Ajay