Hi Again-

It's not clear entirely what's going on in your pipeline. My initial idea was simply to convert your MGZ files into GIFTI files doing something like what's described on my other blog:

mris_convert -c ./lh.thickness.fwhm10.fsaverage.mgh \
$SUBJECTS_DIR/fsaverage/surf/lh.white \
Subject01.lh.thickness.fsaverage.gii

No need to merge the hemispheres, just run two analyses. Or three if you want volume as well. I was assuming that your surfaces files were already aligned to some template. It sounds like you might be dealing with HCP data, in which case it would help to say what download you used.

Be careful that you're actually using NIFTI and GIFTI files, as in HCP-land, files like dscalar.nii file is likely a CIFTI file. While there's some (growing) support for CIFTI in AFNI, it would be better to split it into surfaces and volumes using the workbench tools (wb_command).

Hopefully that makes more sense.

-Peter