[David Shattuck]

Hi Abujamea –

It looks like a processing error happened earlier in the cortical surface extraction routine. Without seeing all of your output, my best guess is that the skull-stripping step didn’t remove a sufficient amount of the scalp/neck, which then resulted in a misclassification of GM during the tissue classification step.

Can you step through the processing steps for cortical extraction and see where if it failed there?

thanks,
David Shattuck

[abujamea]

Thank you David you are right, I did skull-stripping using FSL and then use Brainsuite for the rest of processing and it works perfect.

[David Shattuck]

Hi Abujamea –

Great — happy to hear that solved the problem.

thanks,
David

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