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.coh...@childrens.harvard.edu (Medical/Science Email)
E-mail: alexco...@gmail.com (Lifetime Email)
----------------------------------------------------------------
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
