Hi, What was the reason for this switch? Intuitively it seems that a bias-corrected image is likely to get a better registration (since I assume the target has essentially uniform intensities).
Michael On Wed, Nov 2, 2011 at 1:15 PM, Nick Schmansky <ni...@nmr.mgh.harvard.edu>wrote: > no, v5.0 uses nu.mgz as input to the talairach_avi routine, whereas v5.1 > uses orig.mgz. > > its hard to say why it would fail for some subjects but not others, > other than head positioning and to some degree ventricle size makes a > difference. > > n. > > On Wed, 2011-11-02 at 16:10 -0400, Joshua Lee wrote: > > 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. > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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