Well, in the PACs looks fine. When converting to nii it is already wrapped.
I will go to the machine again and see. Thanks! 2012/10/30 Bruce Fischl <fis...@nmr.mgh.harvard.edu> > really? In what viewer? Does it happen in the rawavg.mgz? > > > On Tue, 30 Oct 2012, Daniel Ferreira wrote: > > Hi, >> I see. But why does it happen? If I look at the initial Dicom it is >> normal, >> no wrapped, as usually looks like. >> >> thanks >> >> 2012/10/23 Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> Hi Daniel >> >> it looks like you have too much wrap in your image, with a >> significant amount of brain wrapping to the top. Nothing will >> work on this >> >> sorry >> Bruce >> >> >> On Tue, 23 Oct 2012, Daniel Ferreira wrote: >> >> Hi Nick, >> Here comes attached the tkmedit orig.mgz >> >> thanks >> >> Daniel >> >> >> >> 2012/10/22 Nick Schmansky >> <ni...@nmr.mgh.harvard.edu> >> 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<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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