Hi all,
We're trying to use FLAIR images in our recon-all pipeline. For half of the participants there are no problems using: recon-all -subjid SUBJECT -i T1.nii -all -FLAIR FLAIR.nii -FLAIRpial
However for the other half the FLAIR registrations are either a bit off or completely flipped, including swapping axes. This then affects the generate surfaces.
The problem line seems to be: bbregister --s <subjid> --mov mri/orig/FLAIRraw.mgz --lta mri/transforms/FLAIRraw.lta --init-fsl --T2
as the output registration of these files is incorrect.
We've tried using mri_convert instead of dcm2nii. This does not solve the problem. Loading the FLAIR.nii in fslview, the image is upside down, but the letters indicating orientation are correct.
Do you have any suggestions about how to solve this problem?
Thanks, Konrad