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

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== smoothing workflow ==
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== Input: (Label.nrrd) a multi-label map to be smoothed ==
  
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# input: a multi-label map to be smoothed. With structures:
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* WM label 3
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* CSF label 1
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* GM(without the following specified sub-cortical structures) label 2,
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* GM sub-cortical structures
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** RCaudate              label 13
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** LCaudate              label 14
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** RPutamen              label 15
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** LPutamen              label 16
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** RGlobusPallidus        label 17
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** LGlobusPallidus        label 18
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** RThalamus              label 11
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** LThalamus              label 12
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** RHippocampus          label 19
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** LHippocampus          label 20
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* Other
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** Cerebellum          Label 6
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** BrainStem          Label 5 
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== Prepare smoothed label maps for separated labels ==
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* Tool: smoothing label map slicer3 module (SLM)
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* Individual label maps:
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** ICC: threshold Label.nrrd at all non-zero places, use default parameters in SLM to smooth the result, get binary label map
  
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   * WM label 3
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   ICC.nrrd
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  * CSF label 1
 
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  * GM(without the following specified sub-cortical structures) label 2,
 
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  * GM sub-cortical structures
 
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    ** RCaudate      label 13
 
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    ** LCaudate      label 14
 
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    ** RPutamen      label 15
 
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    ** LPutamen      label 16
 
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    ** RCaudate      label 17
 
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    ** RCaudate      label 18
 
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    ** RCaudate      label 11
 
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    ** RCaudate      label 12
 
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    ** RCaudate      label 19
 
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    ** RCaudate      label 20
 
  
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** 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:
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# Segmentation using one of the approaches below
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# Up to Affine registration of the subject to bias-corrected, skull-stripped Baseline scan
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  BrainStem.nrrd  Cerabellum.nrrd  RCaudate.nrrd  LCaudate.nrrd  RPutamen.nrrd  LPutamen.nrrd
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# Map the Baseline ICC mask to the State 1 space
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# Skull stripping State 1 scan
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  RGlobusPallidus.nrrd  LGlobusPallidus.nrrd  RThalamus.nrrd  LThalamus.nrrd  RHippocampus.nrrd  LHippocampus.nrrd
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# Bias-correction of State 1 scan
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# Repeat up to affine registration of skull-stripped, bias-corrected State 1 scan to Baseline
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** Smooth WM: choose label 3, take Label.nrrd as input, default parameters in SLM, get
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  WM_smooth.nrrd
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** 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
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    CSF_smooth.nrrd
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** 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
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    GM_Dia.nrrd
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== Re-combine smoothed label maps ==
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* Use the application ''Combine-sub-structures'' to generate the resulting smoothed label maps.
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./Combine-sub-structures ICC.nrrd Cerabellum.nrrd RCaudate.nrrd LCaudate.nrrd RPutamen.nrrd LPutamen.nrrd RGlobusPallidus.nrrd LGlobusPallidus.nrrd
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  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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