Du,

Converting your dcm to nii with dcm2niix, I agree that the L/R A/P S/I labels are correct. The image origin (0,0,0 point), however, is ~5 slices down from the top of the image. Most brain imaging templates, like we're using internally, expect the image origin to be near the center of the brain. 

The image FOV is much larger than what our program was designed for, and cropping the .nii, as you've suggested, is a good idea. However, I can't confirm whether or not your cropping program has distorted the .nii header geometry, based on this original DICOM. If you want to upload a copy of your cropped .nii, I can take a look at that. You would want to crop the .nii as closely around the head as you can, and also ensure that your program has maintained the correct .nii sform and qform in the new cropped .nii  (so L/R A/P S/I are correct), and the origin ((0,0,0) coordinate) of the new .nii is also vaguely near the center of the brain. When the image origin is outside the image or near the edge of the FOV, image registration is unlikely to work properly because rotations are around a suboptimal axis. We use all internal tools for this sort of thing, so I don't have software to recommend, but I can look at your cropped image and see if it looks correct, if you want to send it to me.

Chris Schwarz

Originally posted by Du Wang:

Thank you, Chris, for explaining those details.

In my initial run, I used raw DICOM data, and most of the cases failed. Specifically, in example case 4, the face and ear mask showed very high intensity, and in case 5, the template face was applied to the wrong area. I've since converted the DICOM to NIfTI and cropped the image to focus only on the head.

I've uploaded the original DICOM for one sample case where the defacing result has a similar issue to example case 4.

Please let me know if you have any suggestions for the above two issues. 

Best,
Du