Thanks so much.As as clarification: should I make edits to the brainmask.mgz

or norm.mgz file. 
Likewise, is this the correct command to run to fix edits to the subcortical
segmentation:
 
normalization -maskbfs -segmentation -autorecon2-wm -autorecon3.

Thank you again for all of your help
Liane 



On Tue, Jul 16, 2013 at 11:40 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>
wrote:
      Hi Liane
      the brainmask is not for subcortical segmentation - use the
      norm.mgz if you want to visualize subcortical structures

      cheers
      Bruce
      On Tue, 16 Jul 2013, Liane Hunter wrote:


      Hello, 
      I noticed that when I am checking the subcortical
      segmentation the brainmask does not accurately display the
      subcortical structures 
      ( ie. the putamen is too small). The segmentation appears
      to be correct when I compare it to the original
      file. Does anyone know why this is the case?
      Also, if I make changes to the subcortical segmentation
      based on the original file will this change accurately
      edit the brainmask?

      Thank you.
      Sincerely, 
      Liane 

Liane HunterMD/Ph.D Candidate
Albert Einstein College of Medicine




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Liane HunterMD/Ph.D Candidate
Albert Einstein College of Medicine