Best regards,

--------------------------------
Xi Liang

梁茜
--------------------------------

> Date: Fri, 2 Oct 2009 09:59:47 +0100
> From: [log in to unmask]
> Subject: Re: [FSL] Cannot run IRTK after using FSL
> To: [log in to unmask]
>
> Hi,
>
> I'm afraid this is really an email that needs to go to the IRTK support.
> We can't really help here as it looks like an IRTK problem.
>
> Alternatively, you could try using fnirt instead and see if that works.
>
> All the best,
> Mark
>
>
> On 2 Oct 2009, at 09:40, Xi Liang wrote:
>
> > I am using IRTK to register two breast MRI image with contrast. I
> > first use
> > FLIRT to linear register two images, and then use IRTK to do the
> > norigid part. I
> > met two problems. The first one is I cannot transform the target
> > image to the
> > source image by .dof, which is converted from .mat (FSL). The second
> > issue is
> > nreg( in IRTK) terminates somehow. Could you see something i did
> > wrong?
> >
> > The follwoings are the scripts I used.
> >
> > # linear register the images by FLIRT and get output.mat
> > flirt -in target.nii.gz -ref source.nii.gz -out output.nii.gz -omat
> > output.mat
> >
> > # convert output.mat to output.dof
> > flirt2dof corratio.mat target.nii.gz source.nii.gz corratio.dof
> >
> > # transform target image (all intensity in corratio_dof.nii.gz is 0)
> > transformation target.nii.gz corratio_dof.nii.gz -dofin corratio.dof
> >
> > # Because the corratio.dof seems doesnt work, I use output.nii.gz to
> > register
> > to source.nii.gz directly. The parameters are download from Arno
> > Klein's mindlog
> > website.
> > nreg corratio.nii.gz source.nii.gz -parin Paper_parameters.txt -dofout
> > nonrigid.dof
> >
> > ## Then the following information is given, and the nreg program is
> > terminated
> > and no nonrigid.dof is produced.
> > Reading target ... done
> > Reading source ... done
> > Lambda 1 is ... 0
> > Lambda 2 is ... 0
> > Lambda 3 is ... 0
> > Control point spacing in X is ... 20
> > Control point spacing in Y is ... 20
> > Control point spacing in Z is ... 20
> > Can't read boolean value = True
> >