did you check the talairach.xfm too see if it is reasonable? Is that what you were looking at in tkregister2? Check that and the skull stripping. You can also look at the volumes to see which one is the last one that is ok (orig.mgz, nu.mgz, T1.mgz, brain.mgz, norm.mgz, ...)
On Fri, 9 Sep 2011, Sita Kakunoori wrote: > > Hi Christopher, > > If you want to upload the dataset, I can take a look. > > Sita. > > > On Fri, 9 Sep 2011, Christopher Luna wrote: > >> Hello, >> >> After running an *.img file through autorecon1. Freesurfer says it finishes >> with errors, but I cannot find any error messages in the command line >> output. Checking the tkregister2 of the output shows that the "Target" is >> just a white box, while the "Moveable" stills eems like a typical image that >> I would find in any other output. >> >> Are there some settings I need to alter for mri_convert? The IMG file looks >> fine before running autorecon1. >> >> Thanks, >> Christopher Luna >> MIT Brain and Cognitive Sciences, Class of 2012 >> Desimone Lab, McGovern Institute for Brain Research >> MIT Archery Club >> Alpha Kappa Psi Colony at MIT >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ 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.
