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) :
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!