Hi,
There seem to be a couple small bugs in recon-all (FS 5.3) regarding the interface of trying to do a "clean" run on top of processing that used an expert-options file:
1) The "-xopts-clean" flag doesn't work. It sets XOptsClean = 1, but doesn't set XOptsUse = 0. Consequently, because the default value of XOptsUse = 1, the error condition gets triggered in the "check_params" section in which both XOptsUse and XOptsClean
= 1
2) If you run with the "-clean" flag (recon-all -s $subj -all -clean) on a run that previously involved an expert-options file, it errors out on the first attempt:
--
talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm ERROR: cannot find /BlueArc-scratch/mharms/PDS_v1/D110609_L538_5.3_clean/FreesurferOutput/110609_L538/scripts/expert-options
ERROR: flag ERROR: not recognized
Linux node166 2.6.18-164.el5 #1 SMP Tue Aug 18 15:51:48 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 110609_L538 exited with ERRORS at Wed Jul 10 17:37:37 CDT 2013
--
i.e., the $XOptsFile is set to non-null, despite DoCleanXopts = 1, which causes a problem.
After the first attempt, scripts/expert-options gets moved to the trash folder, and it therefore works on the second attempt.
3) I don't know if this is intentional, but there are separate "-clean-xopts" and "-xopts-clean" flags which set distinct variables.
cheers,
-MH
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Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.
Tel: 314-747-6173
St. Louis, MO 63110
Email: mharms@wustl.edu