Thanks for providing so much information.
I’m trying to reproduce Kerstins above mentioned protocol for image registration.
Unfortunately I get an error message after the 2nd command:
Could not open matrix file tmp.nii.gz
I can run the command without the -init part and continue, but after mrtransform, I receive a non-registered and quite distorted t1 (see image at the end). Flirt registration from within the fsl gui works fine, but there I end up with such a low quality t1 image which is not useful at all
I tried it with skull stripped images as well - also not successful.
Does anyone have suggestions for a better registration?
I appreciate any help and I am sorry for my naive question.
Best regards, Lucius
