Re: [Freesurfer] mri_normalize, 110 is too dark

ld fail > > cheers > Bruce > > > > On Fri, 29 Jul 2016, tvg[fs] wrote: > >> Dear community and developers, >> >> I am experiencing issues during the normalization step, converting >> NU.mgz to T1.mgz. Gray matter is falsely recognized as white matte

[Freesurfer] mri_normalize, 110 is too dark

Dear community and developers, I am experiencing issues during the normalization step, converting NU.mgz to T1.mgz. Gray matter is falsely recognized as white matter and high intensity WM is ignored. The resulting T1.mgz collapses the wrong voxels into the 110 bin. It seems that what mri_normaliz

[Freesurfer] mri_watershed -brain_atlas undocumented?

- This is a repost. It seems it did not come trough yesterday. Apologies if this becomes a double post - Hi all, I noticed that during skull stripping the standard recon-all pipeline uses option "-brain_atlas" in the routine "mri_watershed". However documentation of this argument cannot be foun

[Freesurfer] mri_watershed -brain_atlas undocumented?

Hi all, I noticed that during skull stripping the standard recon-all pipeline uses option "-brain_atlas" in the routine "mri_watershed". However documentation of this argument cannot be found in the help section or on the website. mri_watershed --help | less -p atlas https://surfer.nmr.mgh.harvar