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
>
> 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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> >
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> >
>
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>
>
>
>
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