Hi,
If your non-linear registration works well with the 2mm template then that's fine for what you need.
You can use the same warps and matrices to get a transformation to the 1mm template without having to re-run any registrations. All you need to do is replace the 2mm template with the 1mm template as the --ref in the applywarp call. This will then transform the input into the 1mm reference space.
All the best,
Mark
On 20 Nov 2012, at 20:46, Verena Rozanski <[log in to unmask]> wrote:
> Dear FSL-experts,
>
> I was trying to coregister a postoperative CT scan to MNI template via preoperative T1 scan using the following protocol:
>
> flirt –ref=T1 preop –in=CT postop –dof 6 –omat= CT2T1.mat
> flirt –ref=MNI152 template_brain –in=T1_brain –omat=T1flirt2template.mat
> fnirt –ref=MNI 152 template –in=T1 –aff=T1flirt2template.mat –cout=T1fnirt2template
> --config=T1_2_MNI152_2mm
> applywarp –ref=MNI152 template –in=CT –warp=T1fnirt2template –premat=CT2T1.mat –out=warped CT
>
>
> It worked all right for MNI152_T1_2mm, but not for 1mm, which I need for further tracking with MRIB58 template. I omitted the config-file and used default settings, but the result looks rather blurred (see screenshots). Then, I tried to change lambda and the regmode in fnirt, but without success.
>
> Any ideas on how to approve this are highly appreciated.
> Thank you very much!
>
> Best regards,
> Verena Rozanski
>
> <Screenshot 1.jpg><Screenshot 2.jpg>
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