Image flip after registration

Hi everyone:

My Image flip after flirt registration. Could you help me figure out how to fix it? Thanks very much.

flirt -in freesurfer/mri/T1.nii.gz -ref b0.nii.gz -out test.nii.gz -omat test.omat -dof 6

T1 (input) :
b0 (reference):

output of registration:

Any help is greatly appreciated!

For FSL questions, you may want to ask on the FSL jiscmail forum. These are very different input images, so will want to give FLIRT a helping hand. My first thought would be that -usesqform would provide a better starting estimate. You could also restrict the search with searchx/searchy/searchz to constrain the search space.

These two images have very different scalp signal, which will likely hinder a good solution. You may want to use bet (I use it with the -R robust mode) for brain extraction.

You could even compute a shadow registration where you estimate flirt based on the brain extracted data and apply the transforms to the raw images. The FLIRT graphical user interface can illustrate this method.

@neurolabusc Thanks for your response, that was very clear and useful!