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
> >
>
> --
>
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> 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
>
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