Well, a transformation is between spaces. An FA image obtained from diffusion data is in the same space as the data. So if you obtain a transformation to MNI using the FA, you can apply this transformation to images in the same space. Have a look at applywarp.
Stam
On 9 Oct 2013, at 11:10, Stefano Delli Pizzi wrote:
> Thank you. But is possible to perform non linear registration on data.nii.gz (I look in the guide only FA).
>
>
> Stefano
>
>
> ----Messaggio originale----
> Da: [log in to unmask]
> Data: 9-ott-2013 11.42
> A: <[log in to unmask]>
> Ogg: Re: [FSL] bedpostX directly in MNI space
>
> Hi Stefano,
>
> You can run tractography with masks in MNI space, as long as you provide the diffusion-> MNI transformations, there is no need to transform the data.
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> If you feel that these transformations are not good enough you should try to improve them rather than applying them to the data (as they will result to imperfectly co-registered data).
>
> Do you use a structural image as an intermediate step in the registration, i.e. diffusion->structural->MNI? Have you tried nonlinear registration with FNIRT? Finally, have you corrected for distortions the diffusion images? Large residual distortions can result to misalignments.
>
> Cheers
> Stam
>
>
>
> On 9 Oct 2013, at 10:23, Stefano wrote:
>
> > Hi list,
> >
> > I'm running probtrackX for hard segmentation of subcortical structure.
> >
> > I'd like to run this command with seed and target masks in MNI space.
> >
> > I'm noting some errors in co-registration, and I can not solve them.
> >
> > For this reason, I'd like to trasform the data.nii.gz. form diffusion to MNI space.
> >
> > After I'd like to run bedpostX directly in MNI space.
> >
> > Is it possible? When I run FLIRT I obtained nodif with 1 volume? Where is the other 15? In this way the bedpostX produces empty files.
> >
> > Please, give me a responce.
> >
> > Thank you very much.
> >
> >
> > Stefano
> >
>
>
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