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

From NAMIC Wiki
Jump to: navigation, search
 
(14 intermediate revisions by the same user not shown)
Line 1: Line 1:
−
== smoothing workflow ==
+
== Input: (Label.nrrd) a multi-label map to be smoothed ==
−
 
 
−
# input: a multi-label map to be smoothed. With structures:
 
  
 
* WM label 3
 
* WM label 3
Line 7: Line 5:
 
* GM(without the following specified sub-cortical structures) label 2,
 
* GM(without the following specified sub-cortical structures) label 2,
 
* GM sub-cortical structures
 
* GM sub-cortical structures
−
** RCaudate       label 13
+
** RCaudate               label 13
−
** LCaudate       label 14
+
** LCaudate               label 14
−
    ** RPutamen       label 15
+
** RPutamen               label 15
−
    ** LPutamen       label 16
+
** LPutamen               label 16
−
    ** RCaudate      label 17
+
** RGlobusPallidus        label 17
−
    ** RCaudate      label 18
+
** LGlobusPallidus        label 18
−
    ** RCaudate      label 11
+
** RThalamus              label 11
−
    ** RCaudate      label 12
+
** LThalamus              label 12
−
    ** RCaudate      label 19
+
** RHippocampus          label 19
−
    ** RCaudate      label 20
+
** 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
−
# Segmentation using one of the approaches below
+
 
−
# Up to Affine registration of the subject to bias-corrected, skull-stripped Baseline scan
+
  WM_smooth.nrrd
−
# Map the Baseline ICC mask to the State 1 space
+
 
−
# Skull stripping State 1 scan
+
** 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
−
# Bias-correction of State 1 scan
+
 
−
# Repeat up to affine registration of skull-stripped, bias-corrected State 1 scan to Baseline
+
    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

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
Retrieved from "https://www.na-mic.org/w/index.php?title=Smoothing_multi-label_brain_segmentations&oldid=48129"