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

[Ed Gronenschild]

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