No problem!
Just noticed one typo: the option to output flirt
matrix is "-omat" of course...
Gwenaelle
--- "Wang, Ling" <[log in to unmask]> a écrit :
> Hi Gwenaelle,
>
> thank you very much for your help! I will try the
> method you mentioned.
> Thanks again!
>
> Best wishes,
> Ling
>
>
> 2008/1/18, Gwenaëlle DOUAUD
> <[log in to unmask]>:
> >
> > Hi Ling,
> >
> > basically, your two images are far too different:
> your
> > T1w has a lot of neck in it compared with the bo
> etc.
> > You should bet both images first.
> > I've checked and it's working with your T1w image
> > being betted with -f 0.3, the b0 with -f 0.2. If
> you
> > want the whole b0 to be registered to the T1, then
> you
> > need to output the flirt matrix (-pmat) and to
> apply
> > it to your entire bo (-init
> b0_brain_t0_t1_brain.mat
> > -applyxfm).
> >
> > Hope this helps,
> > Gwenaelle
> >
> >
> > --- "Wang, Ling" <[log in to unmask]> a écrit
> :
> >
> > > Dear FSL Experts,
> > >
> > > I met a problem with flirt. When I used flirt to
> > > register the dti data (e.g.,
> > > the B0 image) to t1 image, I found the outputted
> > > image is not correct (its
> > > orientation is totally changed). The command
> > > outputted by flirt is :
> > > flirt -in /daten/Reg/B0_first.nii.gz -ref
> > > /daten/Reg/t1.nii.gz -out
> > > /daten/Reg/B0_first_t1.nii.gz -omat
> > > /daten/Reg/B0_first_t1.mat -bins 256
> > > -cost mutualinfo -searchrx -180 180 -searchry
> -180
> > > 180 -searchrz -180 180
> > > -dof 12 -interp trilinear
> > >
> > > However, I met this problem only for some
> subjects'
> > > data, other data are
> > > fine with flirt.
> > >
> > > I have uploaded the images I used to
> > > http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi,
> and
> > > the number of the upload
> > > session is 846956.
> > > Could please so kindly have a look on that?
> Thank
> > > you very much in advance!
> > >
> > > Best wishes,
> > > Ling Wang
> > >
> > > --
> > > Ling Wang
> > > Cognitive Neurology
> > > Institute of Neuroscience and Biophysics -
> Medicine
> > > Research Centre Juelich
> > > 52425 Juelich, Germany
> > > phone: +49-2461-618609
> > > Fax: +49-2461-612820
> > >
> >
> >
> >
> >
> >
>
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> >
>
>
>
> --
> Ling Wang
> Cognitive Neurology
> Institute of Neuroscience and Biophysics - Medicine
> Research Centre Juelich
> 52425 Juelich, Germany
> phone: +49-2461-618609
> Fax: +49-2461-612820
>
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