Hi all, I'm trying to transform T1 image in ACPC space to MNI space. I used the fnirt registration for this purpose but the registration for some of my subjects didn't work well. The transformed T1 look like to be shrinking in the frontal part compare to the MNI template. For a few subjects, the transformed T1 went beyond the MNI template a bit. What could be causing this misalignment and how should I fix this ? Thank you so much in advance! The script I used for registration is shown here:
flirt -inT1.nii.gz -ref MNI152_T1_2mm_brain -out T1_2mm.nii.gz -omat T1_2mm.mat -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12 -interp trilinear
fnirt --in=T1.nii.gz --aff=T1_2mm.mat --cout=my_nonlinear_transf --config=T1_2_MNI152_2mm
applywarp --ref=MNI152_T1_1mm --in=T1.nii.gz --warp=my_nonlinear_transf --out=brain_mni
Best,
Luie
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