I am running flirt to try and align an anatomical T1w image to a bo image so that I can overlay FA and RGB scans on top to check them.
However when I apply flirt with .....
fslreorient2std /Volumes/DANIEL/${subj}/${subj}.${cond}/b0_brain_0.4
flirt -dof 6 -in /Volumes/DANIEL/${subj}/${subj}.${cond}/anat_3d_final_al.nii -ref /Volumes/DANIEL/${subj}/${subj}.${cond}/b0_brain_0.4 -out /Volumes/DANIEL/${subj}/${subj}.${cond}/anat_registered_bo.nii
my anat_registered_bo.nii file is not at all aligned with the b0_brain_0.4 image. In fact, it seems to have made the image blurrier, flipped it, and shifted it even further from the bo image in an affine manner. The flirt seems to have made the anatomical image. I don't know if screen shots are ever submitted or if they are how one would go about doing so, so I did not include any.
Thank you for any help you might be able to provide in trouble shooting what I might be doing wrong.
Best,
Daniel Callow
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