NiftyReg reg_resample results in strange artifacts when registering MNI-ICBM-152 atlas

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I'm using NiftyReg for image registration, and I have several artifacts when applying the warp from a non-linear registering of de facto standard MNI-ICBM-152 atlas.

Here are a few slices showing the artifacts:

I tested the registration to the the GG-366-0.7mm T1 atlas (after skull-stripping with BET from FSL) Here are the commands I ran:

reg_f3d -ref GG-366-T1-0.7mm.brain.nii.gz -flo MNI-ICBM-152-T1.brain.nii.gz -res MNI-ICBM-152-T1.nlin-GG.nii.gz -cpp MNI-ICBM-152-T1.nlin-GG.cpp.nii.gz reg_resample -ref GG-366-T1-0.7mm.brain.nii.gz -flo MNI-ICBM-152-WM.nii.gz -trans MNI-ICBM-152-WM.nlin-GG.cpp.nii.gz

This is using the latest git version of Nifty-Reg. Using the latest stable version (1.3.9) the result is the same, but the reg_resample program takes the -cpp parameter instead of -trans.

Any ideas if this is a bug in Nifty-Reg or can be worked-around?

Comments:

Moogugore
2022-04-02, 03:12:47

This topic is simply incomparable :), it is interesting to me)))
Goltizuru
2022-05-06, 02:56:19

Is grateful for the help in this matter, how can I thank you?
Ellison
2022-06-27, 18:49:20

nishtyag, everything is correctly written. Well done!