joshua, try adding -use-mritotal to the end of your recon-all command. it will use an alternate way to compute the talairach.xfm which works better on some data.
the change from v5.0 to v5.1 in the talairach stage was that in v5.1, the talairach.xfm is needed to compute nu.mgz, so the talairach stage needs to precede the nu_correct stage. this means the talairach stage can no longer use nu.mgz as input, which seems to work better than orig.mgz for some data (and is the case for your data). in the next release of freesurfer, recon-all will automatically try the alternate method (mritotal) if the default talairach_avi method fails the tal-check. n. On Wed, 2011-11-02 at 08:45 -0400, Bruce Fischl wrote: > can you send us an example that works in 5.0 and fails in 5.1? > > thanks > Bruce > On Wed, 2 Nov > 2011, Joshua Lee wrote: > > > Small Update: Error Disappears if Using Freesurfer version 5.0 instead of > > 5.1. However, since I am keenly interested in the hippocampal-subfield > > segmentation capabilities of the most recent version, I am loathe to regress > > to an earlier version of FreeSurfer > > - > > Joshua Lee > > Graduate Student > > Center for Mind and Brain & > > Department of Psychology > > University of California, Davis > > 530.747.3805 > > > > > > On Wed, Nov 2, 2011 at 2:29 AM, Joshua Lee <jki...@ucdavis.edu> wrote: > > #@# Talairach Failure Detection Wed Nov 2 02:03:32 EDT 2011 > > /home/virtualuser/freesurfer/subjects/test005/mri > > > > talairach_afd -T 0.005 -xfm transforms/talairach.xfm > > > > I am receiving the error (pasted below) on about half of my > > scans, despite all cans using same protocol. I detect no obvious > > issue with the quality of the images. I have original dicoms, > > and am using mri_convert to save into a single .mgz (or .nii, > > doesn't neem to make a difference), and the unpredictability of > > the error makes diagnosis problematic. TKMedit2 reveals > > absolutely wacky registrations. I am processing on Freesurfer > > 5.1, and have replicated issue on two different installations. I > > am designing a new longitudinal study inheriting the same > > imaging protocol and I do not want to get in a situation > > demanding manual editing of the talairach. Can anyone help me > > out? Thanks, Joshua > > > > ERROR: talairach_afd: Talairach Transform: > > transforms/talairach.xfm ***FAILED*** (p=0.0030, 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 FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 > > 01:57:59 UTC 2009 i686 GNU/Linux > > > > recon-all -s test005 exited with ERRORS at Wed Nov 2 02:03:32 > > EDT 2011 > > > > For more details, see the log file > > /home/virtualuser/freesurfer/subjects/test005/scripts/recon-all.log > > To report a problem, see > > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > - > > Joshua Lee > > Graduate Student > > Center for Mind and Brain & > > Department of Psychology > > University of California, Davis > > 530.747.3805 > > > > > > > > > _______________________________________________ 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.
