Mrregister affine how to write 4x3 matrix

1

Hi,
I am trying to perform an affine (i.e. linear but not rigid) alignment.
I want to write the matrix for the transformation into a txt file.
Very similar to the example from the wiki - but not with nl_warp but just a simple matrix (4x3 or 4x4).
In the wiki the example is:
mrregister s.mif t.mif -type affine_nonlinear -nl_warp W_s2t.mif W_t2s.mif

So I am trying the same with affine, something like:

mrregister s.mif t.mif -type affine -whatever A_s2t.txt A_t2s.txt

I am trolling through the mrregister doc, but I find that specific documentation rather unclear.
mrtrix
Cheers
M.

2

Ah, I just got it.
It’s a little confusing though. One has to use ‘affine’ twice. Once without a dash and once with.

mrregister s.mif t.mif -type affine -affine s2t.mif

3

And the transform command doesn’t like affine but only linear…

mrtransform s.mif s_at_t.mif -linear s2t.txt -template t.mif -interp sinc