I used the following command to register CT and MR, but the result is completely incorrect. Did I use the wrong command or parameter?

[goodsave]

I used the following command to register CT and MR, but the result is completely incorrect. Did I use the wrong command or parameter?

reg_aladin -ref CT.nii -flo MR.nii -res MR_aligned.nii -aff MR_to_CT_affine.txt
reg_f3d -ref CT.nii -flo MR_aligned.nii -aff MR_to_CT_affine.txt -cpp MR_to_CT_cpp.nii -res MR_to_CT_registered.nii

May I ask how to use it?

[goodsave]

The left side is CT, and the right side is the registered MR

[goodsave]

https://cloud.ruicare.com/#s/_GB0YWWg
this is test data. You can try it, if you have time, thank you very much.

[koegl]

The link to the test data doesn't work for me, so I couldn't try it out

Maybe try different similarity metrics. Due to the differing contrasts between CTs and MRIs the registration might not find a good minimum for all metrics.
They are described in the section

Measure of similarity options

here