Smoothing multi-label brain segmentations

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