Originally posted by Mingrui Xia:
Thanks for your quick reply. Attached are both pial surfaces (lh.pial and rh.pial) as provided by FreeSurfer, the merged surface (merged.nv) with the BrainNet tool, and the aparc+aseg.nii VOI map, obtained with FreeSurfer after converting it to .nii with FreeSurfer's mri_convert. I also attached a picture of the result of plotting a couple of VOIs and the surface. As can be seen, they are not aligned at all.

According to FreeSurfer documentation, pial surfaces and VOI maps are in the same space, .i.e., the so-called "Anatomical Space" of FreeSurfer. Thus, the problem might be the way that BrainNet handles the .pial files...