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Hi there,
I am attempting to fix pial boundary issues for a specific subject. I made edits to the brainmask volume as I noticed that the parts of the brain that need to be included were not considered brain. Then, I ran the command recommended when edits are made only to the brain mask to recreate pial surfaces.
After running the command, I noticed that the brainmask volume was updated. The parts excluded were now considered brain. However, the pial boundary still did not include them. The aseg volume also did not update to include the parts previously exluded from the brainmask. This is especially strange to me because other participants with similar errors did have successful changes to brainmask and aseg volumes as well as pial surfaces when performing the same edits and running the exact same command.
Freesurfer Version: freesurfer/6.0.0-ncf
Command Used: recon-all -autorecon-pial -subjid $SUBJ
Any troubleshooting suggestions? Not too sure what could be happening for this specific subject and its edits.
With Kindness,
Josie Ramirez
Research Coordinator - H. Kosakowski Lab
USC Dana and David Dornsife
University of Southern California