It is is really bright there, try putting a few control points in WM (make sure they are in WM)

On 3/3/20 12:30 PM, Laboratorio de Neurociencia Funcional wrote:

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Dear Freesurfeer experts, After running the recon-all in one of my subjets, part of the temporal lobe was partially excluded. Then, I tried to use the watershed algorithm to be less agressive in the skull stripping as follows:

recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -subjid sub_001

The problem was solved in the brainmask.mgz but not in the cortical surfaces. To handle this issue, I edited the white matter and run the recon-all -autorecon2-wm -autorecon3 without success. I also placed control points but the following error appeared after running the recon-all -autorecon2-cp -autorecon3:

recon-all -s sub_001 existed with errors

I noted that white matter of this part of the temporal lobe has high values (up to 132). What can I do to solve the problem with this subject?

Thank you in advance.

Best regards, Marina

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