Just out of curiosity, digging through recon-all finds this section quoted below, however I thought -cp and -wm started at different spots?:

case "-autorecon2-cp":
    case "-autorecon2-noaseg":
    case "-autorecon2-wm":
      set DoNormalization2 = 1;
      set DoSegmentation   = 1;
      set DoFill           = 1;
      set DoTessellate     = 1;
      set DoSmooth1        = 1;
      set DoInflate1       = 1;
      set DoQSphere        = 1;
      set DoFix            = 1;
      set DoMaskBFS        = 1;
      set DoWhiteSurfs     = 1;
      set DoSmooth2        = 1;
      set DoInflate2       = 1;
      set DoSegStats       = 0;
      set DoCurvHK         = 1;
      set DoCurvStats      = 1;
      breaksw

echo " -autorecon2-cp : process stages 12-23 (uses -f w/ mri_normalize, -keep w/ mri_seg)"
echo " -autorecon2-wm : process stages 15-23"
echo " -autorecon2-inflate1 : 6-18"
echo " -autorecon2-perhemi : tess, sm1, inf1, q, fix, sm2, inf2, finalsurf, ribbon"
echo " -autorecon3 : process stages 24-34"
echo " if edits made to correct pial, then run -autorecon-pial"

-Alex

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Alexander Li Cohen, M.D., Ph.D.
E-mail: Alexander.Cohen2@childrens.harvard.edu (Medical/Science Email)
E-mail: alexcohen@gmail.com (Lifetime Email)

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