Dear mrtrix experts,

I want to achieve an affine (including rigid) and nonlinear transformation, but have some questions:

- What is the difference between
`rigid_affine_nonlinear`

and`affine_nonlinear`

in the`mrregister`

command?

Intuitively I would think the ‘affine’ part already covers rigid transformations. Is there a special reason why ‘rigid’ should be added explicitly besides affine, i.e. does it perform better?

Also, I’m confused about the output options:

- Suppose I choose the registration type
`-type rigid_affine_nonlinear`

, should I then define both rigid and affine outputs e.g.`-rigid rigid.txt -affine affine.txt`

, or is it sufficient to put`-affine rigid_affine.txt`

in the assumption that ‘rigid_affine.txt’ would then be the full affine transform (containing rigid transformation as well).

And if I would put`-rigid rigid.txt -affine affine.txt`

instead, would that mean that`affine.txt`

contains also the rigid transformations (i.e. equal to rigid_affine.txt in my previous example), or only the scaling and skewing, not covered by`rigid.txt`

?

Kind regards,

Thibo