Dear all,
I am trying to register the b0 map to the T1 (or T2) image of a subject with BBR but I get weird results (out of plane).
I am using the following commands, is it correct?
flirt -ref $subj-T1.nii.gz -in $subj-b0.nii.gz -omat $subj-init.mat
flirt -ref $subj-T1.nii.gz -in $subj-b0.nii.gz -omat $subj-bbr.mat -out $subj-bbr.nii.gz -init $subj-init.mat -wmseg $subj-wm.nii.gz -cost bbr
Also could you provide me with some information on the usage of bbrtype and bbrslope?
I suppose that according to "Accurate and robust brain image alignment using boundary-based registration" the bbrslope is set positive for gray matter brighter than white and the inverse. What would be the values that I should use according to your experience?
Thank you very much,
Antonis
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