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 fischl@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.mandru@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