2010 Winter Project Week ProstateSeg - Revision history

Lasso: /* Key Investigators */

2010-01-08T16:41:29Z

Key Investigators

2010-01-08T16:36:02Z

To do

2010-01-08T16:34:57Z

To do

2010-01-07T18:37:19Z

To do

2010-01-07T13:49:26Z

To do

2010-01-07T00:57:04Z

Training

2010-01-07T00:30:33Z

Training

2010-01-07T00:20:16Z

2010-01-07T00:16:58Z

To do

2010-01-07T00:13:39Z

Segmentation

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 <h3>Progress</h3>
-The algorithm can be compiled using CMake on both linux and windows, test data are available.
+*The segmentation Slicer module has been created (available at http://svn.na-mic.org/NAMICSandBox/trunk/Queens/ProstateSeg/ShapeBased)
+*Tested segmentation on 3 images, execution time is 10-20 minutes
 </div>
 </div>

← Older revision		Revision as of 16:36, 8 January 2010
Line 82:		Line 82:
	**Filter for .sm file extension		**Filter for .sm file extension
	**Add model files to the package (or upload the model to the project wiki)		**Add model files to the package (or upload the model to the project wiki)
		+	*Add a quick test

@@ Line 78: / Line 78: @@
 ===To do===
 *Send intermediate training data (to test the training steps) => Yi
 *Slicer module for segmentation:
-**what is the min/max value for segmentation threshold? (0..2)? => Yi
+**Add/use the boost library in an extension module
 **Filter for .sm file extension

@@ Line 79: / Line 79: @@
 *Send intermediate training data (to test the training steps) => Yi
 *What does "douher" mean? =? Yi
-*Test Linux compilation => Andriy
+*Test Linux compilation => Andriy => DONE
 *Test Windows compilation => Andras
@@ Line 85: / Line 85: @@
 **what is the min/max value for segmentation threshold? (0..2)? => Yi
 **How to add model files to the extension package? => ask Katie
-**How to use the boost library? (if cannot be used, then just add the used boost files to the package) => ask Katie
+**How to use the boost library in an extension module? (if cannot be used, then just add the used boost files to the package) => ask Katie
-**Fix output image spacing, origin, orientation
+**Filter for .sm file extension

@@ Line 84: / Line 84: @@
 *Slicer module for segmentation:
 **what is the min/max value for segmentation threshold? (0..2)? => Yi
-**How to add model files to the extension package? => Katie
+**How to add model files to the extension package? => ask Katie
-**How to use the boost library? => Katie
+**How to use the boost library? (if cannot be used, then just add the used boost files to the package) => ask Katie

@@ Line 47: / Line 47: @@
 ===Training ===
 *Registration
-**alignTrainingShapes.bash (execution time is about 30min)
+**alignTrainingShapes.bash (execution time is about 30min) (AF: with the default value of 50000 points, execution time is few (>3?) hours)
 ***make isotropic (z direction)
 ***register

@@ Line 59: / Line 59: @@
 **alignTrainingShapesNonIso.bash: faster but not that accurate
 *Convert from binary to level set
-**ShapeBased\_reg\alignTrainingShapes\toSFLS\ => 1 executable
+**ShapeBased\_reg\alignTrainingShapes\toSFLS\ => 1 executable + 1 script (toSFLS.bash)
 ***Input: nrrd binary image
 ***Output: level set description

@@ Line 3: / Line 3: @@
 Image:PW-SLC2010.png|[[2010_Winter_Project_Week#Projects|Projects List]]
 Image:ProstateSegResults.png|Prostate segmentation result with the old (RandomWalk) algorithm - already integrated into Slicer
 </gallery>

← Older revision		Revision as of 00:16, 7 January 2010
Line 83:		Line 83:
	**what is the min/max value for segmentation threshold? (0..2)? => Yi		**what is the min/max value for segmentation threshold? (0..2)? => Yi
	**How to add model files to the extension package? => Katie		**How to add model files to the extension package? => Katie
		+	**How to use the boost library? => Katie

@@ Line 70: / Line 70: @@
 ===Segmentation===
-*ProstateSeg\ShapeBased\version20091203 => 1 executable (wholeseg)
+*ProstateSeg\ShapeBased\bin\wholeSeg => 1 executable (wholeseg)
 **Input: image to be segmented, and two points (at the left and right side of the prostate, on a center axial slice in IJK space)
 **Output: ?