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) | + | * 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: | + | |
| + | ** 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 | BrainStem.nrrd Cerabellum.nrrd RCaudate.nrrd LCaudate.nrrd RPutamen.nrrd LPutamen.nrrd | ||
RGlobusPallidus.nrrd LGlobusPallidus.nrrd RThalamus.nrrd LThalamus.nrrd RHippocampus.nrrd LHippocampus.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 | + | ./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 segmentationsInput: (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
