Dear Freesurfer experts,

I am needing to manually re-set T1.mgz intensity ranges in recon-all, because, currently, only voxels under 80 are getting segmented as gray matter, which is generally outside of the brain. Additionally, all voxels with an intensity of 80 or more are segmented as wm. I have attached an image of what this looks like.

I looked through this page ( http://ftp.nmr.mgh.harvard.edu/fswiki/recon-all#Arguments) but did not recognize a command that corresponds to what I need.

Could any of you tell me how to use expert options to set intensity ranges for wm or gm? I need to re-set both, I think.

Thank you so much!

Victor