Smoothing multi-label brain segmentations

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Input: (Label.nrrd) a multi-label map to be smoothed

  • 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
  • Other
    • Cerebellum Label 6
    • BrainStem Label 5

Prepare smoothed label maps for separated labels

  • Tool: smoothing label map slicer3 module (SLM), all use default parameters
  • Individual label maps:
    • ICC: threshold Label.nrrd at all non-zero places, use SLM to smooth the result, get binary label map
 ICC.nrrd
    • Smooth label 5,6,11-20, use SLM, choose corresponding label to be smoothed, one at a time. Result in label maps:
  BrainStem.nrrd   Cerabellum.nrrd   RCaudate.nrrd   LCaudate.nrrd   RPutamen.nrrd   LPutamen.nrrd 

  RGlobusPallidus.nrrd   LGlobusPallidus.nrrd   RThalamus.nrrd   LThalamus.nrrd   RHippocampus.nrrd   LHippocampus.nrrd
  

./Combine-sub-structures ICC.nrrd Cerabellum.nrrd RCaudate.nrrd LCaudate.nrrd RPutamen.nrrd LPutamen.nrrd RGlobusPallidus.nrrd LGlobusPallidus.nrrd RThalamus.nrrd LThalamus.nrrd RHippocampus.nrrd LHippocampus.nrrd CSF_smooth.nrrd WM_smooth.nrrd BrainStem.nrrd GM_smooth_Dia.nrrd outputAllLabel.nrrd
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