Hi Alex

that's pretty bad! You could start by specifying some expert options about the ranges of gray and white matter intensities to mri_segment and mris_make_surfaces. Hopefully someone will chime in with the syntax, as I don't remember it. You can also check the recon-all.log to see what ranges were automatically detected (which were clearly wrong in this case).

chers Bruce

p.s. actually recon-all --help is pretty detailed about this (search for "expert")

On Wed, 28 Aug 2013, Alexandre Gramfort wrote:

Hi,

after running recon-all on many datasets without any manual intervention, it looks like I finally have to.

As you can see in :

https://dl.dropboxusercontent.com/u/2140486/Screen%20Shot%202013-08-28%20at%...

the CSF is segmented as gray matter while white+gray matters are merged.

what's my best option to fix this?

thanks Alex _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer