Hi Hae-Jeong,
most of the details of mri_normalize are given in the recon1 paper in NeuroImage, 1999 (Dale et al). It shifts the wm intensity, and the gray comes along with it, so it won't change the g/w contrast.
cheers, Bruce
On Thu, 20 Sep 2007, Hae-Jeong Park wrote:
Dear Freesurfer Helpers,
I think 'mri_normalize' might play an important step for the cortical thickness measurement. However, I could not find much information regarding 'mri_normalize' except for a brief description as below: "mri_normalize converts orig or nu volume from cortical reconstruction as input into a new volume where white matter image values all range around 110"
It only explains the level of white matter but not the intensity level of the gray matter which is also important to segment them. Is the intensity normalized proportionally or just shifted to make white matter level 110?
By looking at argument lists for mri_normalize, I could guess the process but I need some confirmation about how it works. Any reference or detailed explanation on procedures for mri_normalize would be greatly appreciated.
Hae-Jeong MoNET Yonsei University