Dear experts,
I'm applying the same code to different patients and for some the registration with fnirt fails.
I'm running these lines:
flirt -noresample -searchrx -120 120 -searchry -120 120 -searchrz -120 120 -in brain_lin_ASL.nii.gz -ref "$mniref"/MNI152_T1_2mm_brain.nii.gz -out brain_lin_ASL_lin_MNI.nii.gz -omat brain_lin_ASL_lin_MNI.mat -dof 12
fnirt --ref="$mniref"/MNI152_T1_2mm_brain.nii.gz --in=T1_lin_ASL.nii.gz --aff=brain_lin_ASL_lin_MNI.mat --config=T1_2_MNI152_2mm.cnf --fout=T1_lin_ASL_nl_MNI.mat --iout=T1_lin_ASL_nl_MNI.nii.gz
during the fnirt running there are warning/warnings like this:
Warning, Jacobian not within prescribed range. Prescription is 0.01 -- 100 and obtained range is -12.5089 -- 85.4155
in the end the image obtained from the registration is totally unrecognizable, while there gistration with flirt seems to be successful.
I hope you can solve my problem,
Thank you in advance.
Stefano
|