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Hi Yoonho,
I'm not an expert but since your inquiry doesn't yet have a reply I thought I'd try to answer it as much as I can.
1. -whitesurf process is preceded over smooth2 and inflated2 in recon-all file, really it is not. why? It seems the second smooth -> inflate -> sphere process is run just to help with the spherical registration and thus the parcellation.
I think -whitesurf must be run after that second smooth2 and inflate2 process because it depends on the parcellation result for some anatomical information to make sure the surface geometry is correct, but it still uses the original tessellation result as its basis as the second smoothing might hurt the resulting surface quality.
2. This error first started during -cortribbon process, also occurs in other processes such as -cortparc2, -cortparc3, -hyporelabel, -aparc2aseg, and -wmparc. But these process does not ask for a file called aseg as input if you check it on the homepage. Can you tell me how to fix it? In not just those places but many other places, FS uses some hard-coded input files to read in the segmentation results, transformation matrix, annotation info, etc. I think you just need to provide it with the required segmentation file.
Best, Horsng