“So far the best result comes from registering FLAIR to Magnitude (cost norm mut info, 6 DOF) and then multiplying the result by SWI.”
flirt -in FLAIR/FLAIR_bet.nii.gz -ref magnitude_bet.nii.gz -out FLAIR/FLAIR_to_MAG.nii.gz -omat FLAIR/FLAIR_to_MAG.mat -dof 6 -cost normmi
fslmaths SWI_bet.nii.gz -mul ../FLAIR/FLAIR_to_mag.nii.gz ../FLAIR/FLAIR_star.nii.gz;
lesion filled T1w (robustfov, invert matrix, transform lesion mask, lesion fill) question - submilimeter pipeline
use of FLAIR - -FLAIR, —plial