Fetal movement and nonrigid deformation of uterine organs are severe artifacts deteriorating in utero magnetic resonance imaging (MRI) of the moving fetus. Many image registration tools have been developed to correct motion artifacts in brain MRI, such as FSL, AFNI, ANTs, IRTK, Elastix, and so forth. Most of them are similar each other since they are based on common theories of image registration. Moreover, advances have been made to cope with the severe motion artifacts in MRI of the moving fetus during decades. I already have used some of existing tools for image registration in functional MRI of the fetus. But, has anyone quantitatively compared those tools for in utero functional MRI (for example, of the placenta and fetal brain)? Which image registration tool would you recommend for in vivo functional MRI of the fetal brain?
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Hi,
For cardiac imaging, we have used elastix for tracking but corrected only for translation & rotation and not deformation at this point. For different applications, we have also tinkered with the patch-to-volume tools provided from ICL/KCL: https://github.com/bkainz/fetalReconstruction
We have not done a quantitative comparison of different tools, but would be interested to hear your experience.
Hello Christopher,
Thank you for your comments. I have known that PVR works well for super-resolution reconstruction of T2-weighted images. I tried PVR for functional MRI of the fetus, but it does not work well because it did not have multiple images necessary for reconstruction while T2-weighted images consist of coronal, axial, and sagittal directions.
Elastix seems to be superior to others for non-rigid body registration. However, it took too much computation time, and sometimes intensities were seriously distorted like fluid with salt and pepper noise. It might be attributed to my fault in configuration. In the end, I moved to IRTK. If you want to do just rigid-body registration, ANTs might be a good choice.
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