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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! Vicky