There is a little bit of intensity normalization in the orig.mgz. You can convert the 001.mgz to anatomical space with mri_vol2vol, something like

mri_vol2vol --mov orig/001.mgz --targ orig.mgz --regheader --o 001.anat.mgz

Jared Price wrote:

I guess I am not entirely sure what the contrast properties of orig.mgz are. After looking at the recon-all DevTable I don't see anything that explicitly mentions any intensity normalization occurring before this point so I imagine it would work. I guess I will just ask you for your suggestion. For this particular task I would like the grayscale image to be as close to the original dicom images as possible with perhaps the one exception of reslicing. Jared

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