View source for 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