[MINC-users] How to register T1 onto T2/PD?

[Soren Christensen]

hi ed,
 Did you try nothreshold and/or far options?

On 10/17/08, Ed Gronenschild <ed.gronenschild at mi.unimaas.nl> wrote:
> Hi,
>
> I need to register a coronal T1 stack onto an axial T2 stack
> of the same subject. Details of the stacks are:
> T1:
> 176 slices of 384 * 384 pixels, pixel size = 0.67 mm * 0.67 mm,
> slice thickness = 1.34 mm.
>
> T2:
> 50 slices of 256 * 256 pixels, pixel size = 1.0 mm * 1.0 mm,
> slice thickness = 2.00 mm
>
> The T2 slices are positioned such that they cover only the brain
> tissue (in the Z direction), whereas the T1 slices cover a much
> larger area, fully including the head and part of the neck.
>
> I tried the following two commands:
>
> mritoself T1.mnc T2.mnc T1_to_T2.xfm
> mincresample -transformation T1_to_T2.xfm -like T2.mnc \
> 	T1.mnc T1_to_T2.mnc
>
> That produced a stack that is incorrect in that it is shifted
> along the Z-axis.
>
> The same is true if I use a PD stack with the same size and
> orientation as T2.
>
> It looks as if the problem is mainly caused by the difference
> in extent of both stacks (mainly in the Z-direction).
> Is there another command to register a T1 onto a T2 or PD?
>
> Ed
>
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