[Freesurfer] Using Freesurfer with post contrast MRI

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Hello Freesurfer users,

I have a general question regarding using freesurfer to process postcontrast MRI scans. I have tried to run recon-all with a few subject’s scans and there has been issues with the skullstripping as well as labeling high intensity areas like the venous sinuses as white matter. The runs don’t even finish usually. I was wondering if there is a method to run recon-all that helps take into account contrast. If that’s not possible, I am mainly focused on the cortical thickness of the occipital cortex. If I do a good job doing quality control around the occipital lobe, but a less robust job elsewhere, will it affect the cortical thickness measurements of the occipital cortex?

Best, Ricky