Dear Elin - eddy_correct works fine on this data for me. What operating
system are you running on?
Tim
On Mon, 4 Apr 2005, Elin Lundström wrote:
> Hi,
>
> now I have put a volume at
>
> http://www.smile.ki.se/testpatient2.nii.gz
>
> that produces three errors when I run eddy-correct.
>
> Thank you very much for your help.
>
> Regards,
> Elin
>
>
> --- Tim Behrens <[log in to unmask]> wrote:
> > Hi - the sform warning does not matter.
> >
> > See previous posts for a description of what the
> > sform matrix is:
> >
> > e.g.
> >
> http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind04&L=fsl&P=R140419&I=-1
> >
> > The second error is serious - it looks like flirt
> > has crashed on various
> > volume of your data - can you put some example data
> > on the web for us to
> > have a lok at?
> >
> > Thanks very much
> >
> > T
> >
> >
> >
> > On Fri, 1 Apr 2005, Elin Lundström wrote:
> >
> > > Hi,
> > >
> > > I have some problems concerning eddy_correct. When
> > I
> > > run it I get the output:
> > >
> > > WARNING: Both reference and input images have an
> > sform
> > > matrix set
> > > The output image will use the sform from the
> > reference
> > > image
> > >
> > > As I understand from looking at earlier mails in
> > the
> > > mailing list this warning is not a big problem.
> > But I
> > > still
> > > wonder what is meant by the sform
> > > matrix. If I run eddy_correct on a patient with a
> > > number of directions and b0 as reference, could
> > the
> > > sform matrix differ between the volumes?
> > >
> > > For some of the directions I get following output
> > > while running eddy_correct:
> > >
> > > /opt/fsl/bin/eddy_correct: line 94: 8148
> > Segmentation
> > > fault (core dumped)
> > > ${FSLDIR}/bin/flirt -in $i -ref $output -nosearch
> > -o
> > > $i >>${output}.ecclog
> > >
> > > Does this mean that the eddy_correct didn't
> > succeed
> > > for this direction? Is it a major error that needs
> > to
> > > be avoided?
> > >
> > > I also wonder if there is a way to know if the
> > > eddy_correct has succeeded without looking at the
> > log
> > > files or the images? If I run it on some hundreds
> > of
> > > patients Iwould like to know if some didn't
> > succeed
> > > without going through all of the patients
> > manually.
> > >
> > > Thank you very much.
> > >
> > > Best regards,
> > > Elin
> > >
> >
> > --
> >
> -------------------------------------------------------------------------------
> > Tim Behrens
> > Centre for Functional MRI of the Brain
> > The John Radcliffe Hospital
> > Headley Way Oxford OX3 9DU
> > Oxford University
> > Work 01865 222782
> > Mobile 07980 884537
> >
> -------------------------------------------------------------------------------
> >
>
--
-------------------------------------------------------------------------------
Tim Behrens
Centre for Functional MRI of the Brain
The John Radcliffe Hospital
Headley Way Oxford OX3 9DU
Oxford University
Work 01865 222782
Mobile 07980 884537
-------------------------------------------------------------------------------
|