volume size mismatching

Forums Forums Cortical Surface Extraction volume size mismatching

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    • #138
      abujamea
      Participant

      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]

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

    • #139
      David Shattuck
      Keymaster

      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

      • #142
        abujamea
        Participant

        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.

      • #143
        David Shattuck
        Keymaster

        Hi Abujamea –

        Great — happy to hear that solved the problem.

        thanks,
        David

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