Hi Maheen

you can look at the aseg.mgz or use the surfaces to create various compartments with mris_fill, but sulcal CSF is pretty hard to accurately detect with only a T1

cheers Bruce On Thu, 11 Feb 2016, Maheen Siddiqui wrote:

Dear FreeSurfer Users,  I have a T1 weighted MRI scan and have run the recon-all command on it. For my steps moving forward I need to have 4 layers of tissue i.e. 4 segmentation files - GM, WM, CSF and extra cerebral tissue. Which of the outputs from recon-all will give me the segmentation? I thought at first that brain.mgz was what I needed but having viewed brain.mgz in Freeview, it is just the skull stripped version of the T1 scan.

Is there any document that details all the outputs of recon-all?

Many thanks for any advice I can get!

Maheen