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

[Claude LEPAGE]

Hi,

The way it is done in the cortical surface extraction pipeline is to
first correct t1 and t2 for non-uniformities using N3 in native space, 
then to use mritoself like this:

mritoself -nothreshold -mi -lsq6 t2.mnc t1.mnc t2_to_t1.xfm

No brain mask is used. I have yet to see a failed case with this
approach, but I'm sure it can fail. Easy to try.

Claude


> 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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