Dear Freesurfer expert,

I ran recon-all on one subject and part of the cortex was excluded.

I followed the FS tutorial to change the watershed preflooding height percentage by using the command below:

         recon-all -skullstrip -wsthresh 30 -clean-bm -subjid <subject name>

The new brainmask file did include all cortex but contain some non-brain tissue (tissue around spinal cord) as well.

Then I want to regenerate the aseg.mgz file. So I redo the recon-all command like below:

         recon-all -all -subjid <subject name>

The brainmask output was still like the old one, excluding part of cortex. The new reconstruction seems not use my edited brainmask.mgz. My question is:
  Do I need to add some flag in recon-all to make sure it use new watershed value/ edited brainmask.mgz?
  And how I can exclude the non-brain part in the brain mask while keeping all brain part? Simply changing the watershed value didn't do the work well.  

Thank you so much for your help!