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