what does orig.mgz look like in tkmedit? n.
On Thu, 2012-10-18 at 18:44 +0200, Daniel Ferreira wrote: > 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 > > 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 > > > > > 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
