Hi, I did recon-all -i <dicoms> -s <id>
and then what Nick posted. 2012/10/18 Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Hi Daniel > > what was your original data format? Did you start with dicoms? > Bruce > > On Thu, 18 Oct 2012, Daniel Ferreira wrote: > > Thanks Nick very much for your suggestion. >> Unfortunately it did not fix the error. >> >> I run the mri_nu_correct command trying several -n values (1, 5, 20), >> then I >> -talairach, but the output is always the same. Talairach finish but when I >> check it the brain and standars are slided down to the bottom of the >> window. >> See a new output attached. >> >> What can be happening here? Any idea to fix it? >> >> thanks >> >> Daniel >> >> >> >> 2012/10/17 Nick Schmansky <ni...@nmr.mgh.harvard.edu> >> 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<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<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<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<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<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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