Hello FreeSurfer Developers,

I have been using FreeSurfer for segmenting T1-weighted images, and I have
a question related to using the two outputs norm.mgz and brain.mgz.

It is my understanding that, by default, FreeSurfer uses the norm.mgz
volume to do partial volume weighting when outputting segmentation volumes
to aseg.stats based on aseg.mgz [^1]. Further, I understand that brain.mgz
is output from a second normalization step in the recon-all processing
stream, having taken norm.mgz as an input [^2].  The wiki says "*Intensity
normalization works better when the skull has been removed. Creates a new
brain.mgz volume*".

My question is: if brain.mgz is meant to be an improved version of
norm.mgz, why not use brain.mgz for partial volume weighting?  What
advantages does norm.mgz provide?

Thanks much,
Andrew Davis

[^1]: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
[^2]: https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all

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