thanks

2012/10/23 Bruce Fischl <fischl@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 <nicks@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 <fischl@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 <nicks@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
> >
> >
> >
> >
> > _______________________________________________
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> > Freesurfer@nmr.mgh.harvard.edu
> >
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>
>
>
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