Hi Giacomo, all the freesurfer commands are stored in the subject's recon-all.log file. You should be able to find the mri_ca_label command in there and modify it.
cheers Bruce On Wed, 14 Oct 2009, Giacomo Mandruzzato wrote: > Thank you for the answer but sorry, I don't know how use mri_ca_label > function! > I have aparc+aseg.mgz volume segmentation and I would have a probabilistic > segmentation of gray matter cortical in ctx.mgz file. > How can I do? > I am a beginner freesurfer user! > > best > > Giacomo > > 2009/10/14 Bruce Fischl <fis...@nmr.mgh.harvard.edu> > >> Hi Giacomo, >> >> we don't write out the probabilities by default. To get them you would need >> to add -write_probs <prob volume name> to the mri_ca_label command line (you >> can find it in recon-all.log for each subject). >> >> cheers >> Bruce >> >> On Wed, 14 Oct 2009, Giacomo Mandruzzato wrote: >> >> ---------- Forwarded message ---------- >>> From: Giacomo Mandruzzato <giacomo.man...@gmail.com> >>> Date: 2009/10/14 >>> Subject: probabilistic segmentation of gray matter >>> To: freesurfer@nmr.mgh.harvard.edu >>> >>> >>> >>> Hi, >>> I have a question about a probabilistic segmentation of gray matter with >>> freesurfer. How can I do it? >>> if I binarize like this: >>> >>> mri_binarize --i aparc+aseg.mgz --min 999.5 --o ctx.mgz >>> >>> I obtain only a mask 0-1. Can I obtain a probablistic map like I obtained >>> with SPM and FSL of the gray matter? >>> thank you in advance >>> >>> Giacomo Mandruzzato >>> Student of Bioengineering >>> Universiti of Padova >>> >>> > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
