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)
• Individual label maps:
  • ICC: threshold Label.nrrd at all non-zero places, use default parameters in SLM to smooth the result, get binary label map

 ICC.nrrd

• • Smooth label 5,6,11-20, use SLM, take Label.nrrd as input, choose corresponding label to be smoothed, one at a time. All use default parameters. 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

• • Smooth WM: choose label 3, take Label.nrrd as input, default parameters in SLM, get

  WM_smooth.nrrd

• • Smooth CSF: choose label 1, take Label.nrrd as input, change sigma = 0 in SLM, get binary label map CSF_ori.nrrd for CSF same as in Label.nrrd. Go to editor, do a closing operation on CSF_ori.nrrd (a 4-neighbor dilation --an optional smoothing using SLM --followed by a 4-neighbor erosion) to get

   CSF_smooth.nrrd

• • GM: choose label 2, take Label.nrrd as input, change sigma = 0 in SLM, get binary label map GM_ori.nrrd for GM same as in Label.nrrd. Go to editor, do a 4-neighbor dilation to get

   GM_Dia.nrrd
  

Re-combine smoothed label maps

• Use the application Combine-sub-structures to generate the resulting smoothed label maps.

./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_Dia.nrrd outputAllLabel.nrrd