Topological correction

Forums Forums Cortical Surface Extraction Topological correction

This topic contains 4 replies, has 5 voices, and was last updated by  yeunkim 3 years, 12 months ago.

  • Author
    Posts
  • #194

    christ21
    Participant

    When I start the Cortical Surface Extraction Sequence using the GUI, the process always stops at topology correction during fixing topological defects of size 21, no matter which nii-file I use, and the Programme has to be closed. In the BrainSuite Log it only says ‘Too many edges in table’.
    I use BrainSuite 15c with Windows 7.
    Does anybody know what the reason for this is?
    Thank you very much for your help!

  • #195

    David Shattuck
    Keymaster

    What is the resolution of the images you are using?

    Usually when this happens it is because the image has not been segmented properly by the preceding steps.

    -David Shattuck

    • #244

      jthompson
      Participant

      Hello David,

      I am having the same issue. My image resolution is:
      Dimensions: 512x512x214
      Voxel: 0.5×0.5×1 (mm)

      Using T1.

      What parameters should I adjust (at which stage) to obtain better results?

      Thanks!!
      John

  • #228

    I have the same problem – running 15c in Windows 7.

  • #245

    yeunkim
    Participant

    Could you try loading up the *pvc.label.nii.gz (label volume of tissue types) file superimposed over your brain image? (Load either the unprocessed brain image or the bias field corrected (*bfc.nii.gz image) as Volume and load *pvc.label.nii.gz file as Label). From here, you can visually check the quality of the tissue segmentation. As you move your cursor around in the images, the bottom bar of your window will tell you which tissue type it has been labeled.

    If your image has been poorly segmented, you may want to try editing your brain mask (Skull Stripping) or bias field correction (Nonuniformity Correction) parameters. I hope this helps!

    Best,
    Yeun

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