Dear freesurfer experts, I need your help on recon. I tried to perform recon-all on my anonymized control subjects (chunk of face/eyes removed on T1.mgz) and run autorecon1. It ran smoothly till the end of workflow of autorecon1 and came up with the following: mri_watershed Error: GLOBAL region of the brain empty!
It then exited without compiling brainmask.mgz file.
What should i try from here!
Thanks for your help! Toh Wong Sydney, Australia
Hi Toh,
did you check the talairach transform? If it's ok, try either running the watershed skull stripping with a different preflooding height or without the atlas.
cheers Bruce
On Sat, 17 Jul 2010, Toh Hock Wong wrote:
Dear freesurfer experts, I need your help on recon. I tried to perform recon-all on my anonymized control subjects (chunk of face/eyes removed on T1.mgz) and run autorecon1. It ran smoothly till the end of workflow of autorecon1 and came up with the following: mri_watershed Error: GLOBAL region of the brain empty!
It then exited without compiling brainmask.mgz file.
What should i try from here!
Thanks for your help! Toh Wong Sydney, Australia
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Bruce Fischl -
Toh Hock Wong