Hi, yes, rerunning with force in this case is correct.
If you made edits to cross and want to rerun base, I would recommend to delete the base first and recreate it from scratch. Any edits in the base will not be meaningful anyway as the images (and maybe even the space) will change underneath. Best, Martin On Thu, 2011-07-21 at 07:19 -0400, Khoa Nguyen wrote: > Hi Jeff, > > I think you'll have to run with -force. In the newer version 5.1, this is > updated so that you don't have to anymore. And you might be right > that deleting the folder is not a good idea since the edits were made in > there. If you made edits in the cross and want to rerun the base, then you > can either do -force or delete the folder or delete whichever file you > made edits on (if made edits on wm.mgz in cross, delete wm.mgz in base). > > Martin, is that correct? > > -Khoa > > On Wed, 20 Jul 2011, Jeff Sadino wrote: > > > Hello, > > > > I have a subject with three timepoints I am putting through the longitudinal > > stream in fs 5.0.0. After the base template was created, I edited some of > > the pial surfaces on the base. Now when I run the command: > > "recon-all -base subject -autorecon2-pial -autorecon3", it says: > > "ERROR: /mnt/fs5/050079 exists, delete or re-run with -force" > > This is confusing to me because if I delete the folder, then wont my edits > > also be deleted? I ran it using the force flag, and it seems to be going > > ok. I just want to ask if this is the best way to do this. > > > > Thank you, > > Jeff Sadino > > > > _______________________________________________ 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.
