Difference between revisions of "Smoothing multi-label brain segmentations"

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== Prepare smoothed label maps for separated labels ==
 
== Prepare smoothed label maps for separated labels ==
  
−
* Tool: smoothing label map slicer3 module (SLM), all use default parameters
+
* Tool: smoothing label map slicer3 module (SLM)
 
* Individual label maps:
 
* Individual label maps:
−
** ICC: threshold Label.nrrd at all non-zero places, use SLM to smooth the result, get binary label map
+
 
 +
** ICC: threshold Label.nrrd at all non-zero places, use default parameters in SLM to smooth the result, get binary label map
 +
 
 
   ICC.nrrd
 
   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  
+
** 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:  
−
   RGlobusPallidus.nrrd LGlobusPallidus.nrrd RThalamus.nrrd LThalamus.nrrd RHippocampus.nrrd LHippocampus.nrrd
+
 
 +
   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_smooth_Dia.nrrd outputAllLabel.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_Dia.nrrd outputAllLabel.nrrd

Latest revision as of 23:12, 27 January 2010

Home < 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
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