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

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==  Input: a multi-label map to be smoothed ==
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==  Input: (Label.nrrd) a multi-label map to be smoothed ==
  
 
* WM label 3
 
* WM label 3
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** BrainStem          Label 5   
 
** BrainStem          Label 5   
 
   
 
   
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# Segmentation using one of the approaches below
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== Prepare smoothed label maps for separated labels ==
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# Up to Affine registration of the subject to bias-corrected, skull-stripped Baseline scan
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# Map the Baseline ICC mask to the State 1 space
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* Tool: smoothing label map slicer3 module (SLM), all use default parameters
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# Skull stripping State 1 scan
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* Individual label maps:
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# Bias-correction of State 1 scan
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** ICC: threshold Label.nrrd at all non-zero places, use SLM to smooth the result, get binary label map
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# Repeat up to affine registration of skull-stripped, bias-corrected State 1 scan to Baseline
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  ICC.nrrd
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** Smooth label 5,6,11-20, use SLM, choose corresponding label to be smoothed, one at a time. Result in label maps:
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  BrainStem.nrrd Cerabellum.nrrd RCaudate.nrrd LCaudate.nrrd RPutamen.nrrd LPutamen.nrrd RGlobusPallidus.nrrd LGlobusPallidus.nrrd RThalamus.nrrd LThalamus.nrrd RHippocampus.nrrd LHippocampus.nrrd
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./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

Revision as of 22:45, 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), 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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