Daniel, See this page which i just created which describes a workaround to a problem some people are having with the Talairach stage in the v5.1 release:
https://surfer.nmr.mgh.harvard.edu/fswiki/TalFailV5.1 Nick On Wed, 2012-10-17 at 08:24 +0200, Daniel Ferreira wrote: > Dear experts, > > Please, I'm getting the Talairach Failure Detection problem in one of > my subjects (message enclosed below). > > > I tried to follow the tutorial to fix a bad Talairach with: > > > 1) tkregister2 --mgz -s <id> --fstal --> not green lines appear, I > attach a screenshot. Both the standard and my MRI are slided down to > the bottom of the window. See also attached tkmedit file. > > > 2) Anyway, I tried also -notal-check to see if something changed in > spite Talairach failed, but it fails also (off course). > > > 3) I used -use-mritotal but I still get the same. However, this time > processing finishes without errors, but my MRI is still at the bottom > of the window and output cut all what is between middle temporal > regions and neck. > > > Please, any idea? > > > Thanks a lot > > > Daniel > > > > #@# Talairach Failure Detection Wed Oct 10 09:08:27 CEST 2012 > /home/daniel/FreeSurfer/subjects/N001511_d2/mri > > talairach_afd -T 0.005 -xfm transforms/talairach.xfm > > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm > ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) > Manual Talairach alignment may be necessary, or > include the -notal-check flag to skip this test, > making sure the -notal-check flag follows -all > or -autorecon1 in the command string. > See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach > Linux siv 2.6.32-33-generic #72-Ubuntu SMP Fri Jul 29 21:07:13 UTC > 2011 x86_64 GNU/Linux > > recon-all -s N001511_d2 exited with ERRORS at Wed Oct 10 09:08:27 CEST > 2012 > > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > _______________________________________________ > 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.
