Pial surface

Forums Forums Cortical Surface Extraction Pial surface

This topic contains 6 replies, has 3 voices, and was last updated by  f.ramezani 1 week, 4 days ago.

  • Author
    Posts
  • #804

    f.ramezani
    Participant

    Dear Brainsuite team,
    How do you expand inner cortex (after doing topology correction)to outer boundary for making pial surface? I mean what’s the algorithm?

  • #811

    yeunkim
    Participant

    Hi,

    The method for pial surface generation is described here:

    http://brainsuite.org/processing/surfaceextraction/pial/

    Please let us know if you have more questions.

    Best,
    Yeun

  • #815

    f.ramezani
    Participant

    Hi,
    I would appreciate your help with a question; how can i obtain the volume after Pial surface stage or indeed obtaining the GM,CSF and WM labels after the topology correction and wisp removal stages? I’ve seen a contour view showing the inner and OUTER boundaries of the cortex in BrainSuite_Workshop_2017 file ( Pial surface title) but i can’t find if there are any features or output files in the app which contains the labels or volumes after Pial surface stage.
    Looking forward to hearing from you.
    Thank you

  • #816

    Anand Joshi
    Moderator

    The white matter mask after topology correction is stored in subject.dewisp.mask.nii.gz files.
    The WM GM and CSF tissue types are stored in subject.pvc.label.nii.gz. Since at MR resolution, most voxels contains a mixture of tissues. The partial tissue fractrions are stored in subject.pvc.frac.nii.gz. These are before topology correction, but depending on your application, these might serve the purpose. Please refer to the following link for more information.
    http://brainsuite.org/processing/surfaceextraction/pvc/

  • #819

    f.ramezani
    Participant

    Yes i know these outputs, but they don’t contain the outer cortex; which is obtained by expanding the inner cortex( inner cortex is obtained by applying the topology correction ad wisp removal) in pial surface stage.

  • #820

    Anand Joshi
    Moderator

    Hi BrainSuite does not currently store a mask corresponding to the pial surface, since at voxel resolution, such a mask does not retain sulcal depths in the pial surface. Can you please explain a bit more on what you are trying to do, so that we can see if there an output that will serve the purpose? thanks,

  • #821

    f.ramezani
    Participant

    Well i’m looking for the outer boundary of the cortex label which is obtained by expanding the inner cortex in pial surface stage.( In BrainSuite topology correction stage affects the inner boundary not the outer; so the outer boundary is defined in making the pial surface). Can you please have a look at BrainSuite_Workshop_2017_GUI_David_Shattuck file; pial surface part ? Am wondering how the volume is shown there after the pial surface.

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