Is that the command line you used? I don't think there is an -autorecon option.
doug
Teddy Youn wrote:
Hi again,
I had a quick question about generating wmparc.stats. I have tried to run recon3 with the -wmparc flag and have encountered an error where ?h.smoothwm is not being read even though my /surf folder has the files. Below is the output of what occurs in my xterm. We have v4.0.2 of FS on Leopard 10.5.2.
Thanks in advance,
-t
============================================================================== recon-all -autorecon -wmparc -no-isrunning -subjid St14-Initial INFO: SUBJECTS_DIR is /Volumes/ZetaData/Teddysfolder/CorrectedBrainsSiemens/TBISt14 Actual FREESURFER_HOME /Applications/freesurfer -rwxrwxrwx 1 teresa teresa 2712975 Mar 3 17:41 /Volumes/ZetaData/Teddysfolder/CorrectedBrainsSiemens/TBI/St14/St14-Initial/scripts/recon-all.log Darwin 0-1d-4f-48-96-f4.dyn.utdallas.edu 9.2.0 Darwin Kernel Version 9.2.0: Tue Feb 5 16:13:22 PST 2008; root:xnu-1228.3.13~1/RELEASE_I386 i386 #-------------------------------------------- #@# Sphere lh Mon Mar 3 17:43:27 CST 2008 /Volumes/ZetaData/Teddysfolder/CorrectedBrainsSiemens/TBI/St14/St14-Initial/scripts \n mris_sphere ../surf/lh.inflated ../surf/lh.sphere \n $Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $ $Id: mrisurf.c,v 1.557.2.5 2007/12/10 20:20:29 nicks Exp $ reading original vertex positions... MRISreadVertexPositions(../surf/lh.smoothwm): surfaces differ. Main: 194252 ver s 390408 faces, smoothwm: 188404 verts 378044 faces
No such file or directory MRISreadOriginalProperties: could not read surface file smoothwm No such file or directory Darwin 0-1d-4f-48-96-f4.dyn.utdallas.edu 9.2.0 Darwin Kernel Version 9.2.0: Tue Feb 5 16:13:22 PST 2008; root:xnu-1228.3.13~1/RELEASE_I386 i386
recon-all exited with ERRORS at Mon Mar 3 17:43:30 CST 2008
Doris Duke Clinical Research Fellow '07-'08 North Texas TBI Research Center UT Southwestern Medical Center at Dallas Warren Alpert School of Medicine at Brown University, MD '09 Teddy.Youn@utsouthwestern.edu (401)-714-2847
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