Dear Andrew,
I think we would need to see the data to work out why this happens. Can you upload all the images, fields and matrices to our site and then email me the ref number you get?
Jesper
On 15 Mar 2012, at 23:25, Andrew Bock wrote:
> Hello,
>
> I am having trouble with convertwarp. I have a linear (FLIRT) and non-linear (FNIRT) warp that both work independently, but when I combine them with convertwarp the warp no longer works.
>
> Here is my code:
>
> convertwarp -o /home/andrew/mrtrix/subjects/eb$n/eb$n.fs2fa_warp.nii -r /home/andrew/mrtrix/subjects/eb$n/eb$n.FA.nii -m /home/andrew/mrtrix/subjects/eb$n/eb$n.fs2struct.mat -w /home/andrew/mrtrix/subjects/eb$n/eb$n.struct2fa_warp.nii
>
> when I run the following code, the image is quite distorted:
>
> applywarp -i /home/andrew/mrtrix/subjects/eb$n/eb$n.brain.nii -o /home/andrew/mrtrix/subjects/eb$n/eb$n.fs2faImg -r /home/andrew/mrtrix/subjects/eb$n/eb$n.FA.nii -w /home/andrew/mrtrix/subjects/eb$n/eb$n.fs2fa_warp.nii
>
> However, when I first run:
>
> #flirt -applyxfm -init /home/andrew/mrtrix/subjects/eb$n/eb$n.fs2struct.mat -in /home/andrew/mrtrix/subjects/eb$n/eb$n.brain.nii -ref /home/andrew/mrtrix/subjects/eb$n/eb$n.rawavg.nii -out /home/andrew/mrtrix/subjects/eb$n/eb$n.brain2raw.nii
>
> and then run:
>
> applywarp -i /home/andrew/mrtrix/subjects/eb$n/eb$n.brain2raw.nii -o /home/andrew/mrtrix/subjects/eb$n/eb$n.fs2faImg -r /home/andrew/mrtrix/subjects/eb$n/eb$n.FA.nii -w /home/andrew/mrtrix/subjects/eb$n/eb$n.struct2fa_warp.nii
>
> the transformation works.
>
> Any help would be appreciated.
>
> Andrew
>
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