Smoothing multi-label brain segmentations

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Home < Smoothing multi-label brain segmentations

smoothing workflow

  1. input: a multi-label map to be smoothed. With structures:
  • WM label 3
  • CSF label 1
  • GM(without the following specified sub-cortical structures) label 2,
  • GM sub-cortical structures
    • RCaudate label 13
    • LCaudate label 14
    • RPutamen label 15
    • LPutamen label 16
    • RGlobusPallidus label 17
    • LGlobusPallidus label 18
    • RThalamus label 11
    • LThalamus label 12
    • RHippocampus label 19
    • LHippocampus label 20


  1. Segmentation using one of the approaches below
  2. Up to Affine registration of the subject to bias-corrected, skull-stripped Baseline scan
  3. Map the Baseline ICC mask to the State 1 space
  4. Skull stripping State 1 scan
  5. Bias-correction of State 1 scan
  6. Repeat up to affine registration of skull-stripped, bias-corrected State 1 scan to Baseline