afni.nimh.nih.gov

Hi all,

I am working on prepping images for preprocessing and running my MPRAGE files through 3dUnifize prior to using 3dSkullStrip.

I can definitely see that intensities have been normalized after 3dUnifize, but I am concerned about some peripheral areas of the white matter that still appear brighter than the rest, specifically areas close to the cortex. I tried adding the -gm option and the difference in those areas of the white matter still existed.

Is this something I should be concerned about? If so, how could I go about improving the images? I will attach photos of the before and after to give you all an idea of what I mean. In this example, the original is on the left and the unifized image is on the right.

I am using Version AFNI_17.2.09 (Aug 22 2017) and this is the line of code I ran: 3dUnifize -prefix 206_MPRAGE_unifize -input 206_anat_+orig.BRIK

Thanks in advance for your help!

Best,
Samantha