full segmentation

Forums Forums Cortical Surface Extraction full segmentation

This topic contains 3 replies, has 3 voices, and was last updated by  Anand Joshi 2 years, 8 months ago.

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  • #801

    aliakbari
    Participant

    Dear all,
    in the sequence at the segmentation stage, we have 5 labels which refer to WM,GM,CSF and partial volumes.Are there any folders which you could see skull and scalp labels with above ? if not how can i have the 5 labels ( WM,GM,CSF,skull and scalp) together?
    looking forward to hearing from you
    thanks

  • #802

    sychoi
    Participant

    the subject.pvc.label.nii.gz will have GM/WM/CSF labels only.
    Then the subject.skull.label.nii.gz will have skull, scalp, space and brain labeled.

    detailed information can be found here: http://brainsuite.org/processing/surfaceextraction/skull-and-scalp/

  • #803

    aliakbari
    Participant

    well the subject.pvc.label.nii.gz have GM/WM/CSF and combinations of each(partial volume).I’d like to know if one can have the five tissues( GM,WM,CSF,skull and scalp) all together in a label without partial voolume being considered .

  • #814

    Anand Joshi
    Moderator

    To get WM GM CSF, you can use subject.pvc.frac.nii.gz. This file contains tissue fractions, i.e. amount of GM WM CSF at each voxel in the brain. Since at MR resolution, many voxels contain mixture of tissue, so this is a more realistic representation than the crisp segmentation.
    If you want information about WM GM CSF Skull and Scalp, you can use this file and subject.skull.label.nii.gz.

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