[abujamea]

Hi everybody I am having a problem with size of the cortical surface results that it show smaller size than background MRI images. I tried to use different dicom to nifti converter but the result is the same. I dont know if any body had similar problem before, I appreciate your help and support.

It look like this [/url]

http://postimg.org/image/mlgfz9ak3/

[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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