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
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