Thanks Nick, Is use-mritotal equivalent to what version 5.0 does by default?
Also, any suggestions on why this talairach error would occur only on a portion of my data, despite all being collected with the same imaging protocol, same conversions from dicom, etc? - 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 4:02 PM, Nick Schmansky <ni...@nmr.mgh.harvard.edu>wrote: > 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 > > > > 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. > >
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