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/][img]http://s21.postimg.org/mlgfz9ak3/Screen_Shot_2015_12_17_at_8_53_51_AM.jpg[/img][/url]
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?