Ok, so a successful work-around strategy currently would be a two command approach:
recon-all -s $subjid -i input.nii recon-all -s $subjid -all -expert expert.opts But it would be nice if recon-all -s $subjid -i input.nii -expert expert.opts worked as well :) cheers, -MH On Fri, 2011-11-11 at 14:52 -0600, Michael Harms wrote: > Hi guys, > There is an issue with recon-all abending if you use the -expert option > on the very first call to recon-all, because recon-all attempts to copy > to $subjid/scripts/expert-options before the scripts directory has been > created. > > As an attempted workaround I manually created an empty $subjid/scripts > directory so that the directory already existed. However, in > conjunction with the -i flag this then triggers the error of "existing > subject" and the -force option no longer exists to force the process to > proceed. > > cheers, > -MH > > _______________________________________________ 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.
