11 Feb
2016
11 Feb
'16
10:36 a.m.
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