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%2013.16.52.png > > 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 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
