Modules:Modelmaker-Documentation - Revision history

Nicole at 18:02, 17 December 2008

2008-12-17T18:02:58Z

Marianna at 20:13, 31 July 2008

2008-07-31T20:13:20Z

Nicole at 20:24, 10 April 2008

2008-04-10T20:24:00Z

Nicole at 20:16, 10 April 2008

2008-04-10T20:16:53Z

Kikinis at 18:50, 10 April 2008

2008-04-10T18:50:50Z

Nicole at 14:02, 10 April 2008

2008-04-10T14:02:02Z

Kikinis at 13:04, 9 April 2008

2008-04-09T13:04:39Z

Kikinis at 13:03, 9 April 2008

2008-04-09T13:03:07Z

Kikinis at 12:01, 9 April 2008

2008-04-09T12:01:00Z

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[[Documentation|Return to Slicer Documentation]]

← Older revision		Revision as of 18:02, 17 December 2008
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	*You can choose to not generate models from labels that do not have names.		*You can choose to not generate models from labels that do not have names.
		+
		+
		+	== Trouble shooting ==
		+
		+
		+	The two main reasons that the Model Maker may fail are:
		+	# the models were not created (see the error log; are you setting the Model Hierarchy drop down to create a new one?)
		+	# the models don't load/display.
		+
		+	If you run the Model Maker and "nothing happens" here are some ways to track down the problem.
		+
		+	* Check the Window->Error Log to see if there was a problem recorded after the Model Maker returned
		+	* Check in your temporary directory (View->Application Settings->Module Settings) to see if the .vtk files were created. If the files are there, try loading them manually via the Add Data panel.
		+	* There should also be a mrml file in the Temporary Directory that points to the models files and also defines the model colours, try loading that manually, using File->Load Scene.
		+	* There may be a bug in the rendering pipeline, check the Data module to see if the models are listed there. If so, try rotating the scene or adding a fiducial point to trigger a render.

@@ Line 11: / Line 11: @@
 * Input/Output:
 **The Input Volume drop down menu is populated with the label map volumes that are present in the scene
-**Models are imported into Slicer under a model hierarchy node, and their colors are set by the color table associated with the input label map volume. The model hierarchy node must be created before running the model maker, by selecting ''Create New ModelHierarchy'' from the Models drop down menu.
+**Models are imported into Slicer under a model hierarchy node, and their colors are set by the color table associated with the input label map volume. The model hierarchy node '''must be created''' before running the model maker, by selecting ''Create New ModelHierarchy'' from the Models drop down menu.
 *Create Multiple:
 **Any text entered in the ''Model Prefix'' box will be the starting string for the created model's file names. The label number and the color name will also be part of the file name.
 **If you want to create all models that correspond to all values in a labelmap volume, click the ''Generate All Models'' and ''Joint Smoothing'' boxes
 **''Joint Smoothing'' will ensure that all resulting models fit together smoothly, like jigsaw puzzle pieces. Otherwise the models will be smoothed independently and may overlap.
-**If you specify a list of Labels, it will override any start/end label settings.  If you click ''Generate All Models'' it will over ride the list of labels and any start/end label settings.
+**If you specify a list of Labels, it will override any start/end label settings.  If you click ''Generate All Models'' it will override the list of labels and any start/end label settings.
 *Model Maker Parameters:
 **You can set the number of smoothing iterations, target reduction in number of polygons (decimal percentage). Use 0 and 1 if you wish no smoothing nor decimation.
@@ Line 27: / Line 27: @@
 *Anatomical Information:
 **Here you can specify an external file linking label values with anatomical names.
-This was the original method of linking label map values to resultant model colors and names, but it has been superceded by an internal linkage between the input label map volume and it's color node. If you wish to specify a file for a volume node that does not have a color node associated with it. It must be a comma separated file, extension .csv, in the format:
+This was the original method of linking label map values to resultant model colors and names, but it has been superseded by an internal linkage between the input label map volume and it's color node. If you wish to specify a file for a volume node that does not have a color node associated with it. It must be a comma separated file, extension .csv, in the format:
    anatomyName1,label1
    anatomyName2,label2
 where anatomyName is a string, and label is an integer. If the volume node has a color node associated with it, that will override the anatomy label file.
-**You can choose to not generate models from labels that do not have names.

@@ Line 4: / Line 4: @@
 The Modelmaker is used to create 3D surface models from segmented image data, called label maps. Label maps can be the result of automated segmentation or interactive editing.
 The model maker is a pipeline of algorithms that start from the input label map, creates a binary label map with just the label(s) of interest set to 1, everything else to 0, generates a marching cubes model, runs triangle reduction and triangle smoothing algorithms. The pipeline was optimized for 1mm brain MRI data. For other geometries, adjustments of the parameters might be necessary.
 The model maker is compiled as both a command line executable passed arguments via the command line, and as a binary plug in that communicates through shared memory with Slicer3. The automatically created GUI, found by clickign on the Modules menu, Model Generation category, has the following elements:
@@ Line 11: / Line 13: @@
 **Models are imported into Slicer under a model hierarchy node, and their colors are set by the color table associated with the input label map volume. The model hierarchy node must be created before running the model maker, by selecting ''Create New ModelHierarchy'' from the Models drop down menu.
 *Create Multiple:
-** If you specify a list of Labels, it will override any start/end label settings.  If you click Generate All it will over ride the list of lables and any start/end label settings.
+**Any text entered in the ''Model Prefix'' box will be the starting string for the created model's file names. The label number and the color name will also be part of the file name.
-** If you want to create all models that correspond to all values in a labelmap volume, click the Generate All Models and Joint Smoothing boxes
+**If you want to create all models that correspond to all values in a labelmap volume, click the ''Generate All Models'' and ''Joint Smoothing'' boxes
 *Model Maker Parameters:
 **You can set the number of smoothing iterations, target reduction in number of polygons (decimal percentage). Use 0 and 1 if you wish no smoothing nor decimation.
 **You can set the flags to split normals or generate point normals in this pane as well.
-**You can save a copy of the models after intermediate steps (marching cubes, smoothing, and decimation if not joint smoothing, otherwise just after decimation); these models are not saved in the mrml file, turn off deleting temporary files first in the tcl window: [$::slicer3::CommandLineModuleGUI_Model_Maker GetLogic] DeleteTemporaryFilesOff
+***''Split Normals'' is useful for visualizing sharp features. However it creates holes in surfaces which affects measurements.
 *Anatomical Information:
 **Here you can specify an external file linking label values with anatomical names.
-This was the original method of linking label map values to resultant model colors and names, but it has been superceded by an internal linkage between the input label map volume and it's color node. If you wish to specify a file for a volume node that does not have a color node associated with it, a sample can be found in . It must be a comma separated file, extension .csv, in the format
+This was the original method of linking label map values to resultant model colors and names, but it has been superceded by an internal linkage between the input label map volume and it's color node. If you wish to specify a file for a volume node that does not have a color node associated with it. It must be a comma separated file, extension .csv, in the format:
    anatomyName1,label1
    anatomyName2,label2
 where anatomyName is a string, and label is an integer. If the volume node has a color node associated with it, that will override the anatomy label file.

@@ Line 2: / Line 2: @@
 [[Image:ModelMakerModule.png|thumb|350px|right|The Model Maker Module]]
-*The Modelmaker is used to create 3D surface models from segmented data. Label maps are the result of automated segmentation or interactive editing.
-**Model maker is a pipeline of algorithms that will take a binary label, generate a marching cubes model, run triangel reduction and triangle smoothing algorithms. The pipeline was optimized for 1mm brain MRI data. For other geometries, adjustments of the parameters might be necessary.
+The Modelmaker is used to create 3D surface models from segmented image data, called label maps. Label maps can be the result of automated segmentation or interactive editing.
-*Models are imported into Slicer under a model hierarchy node, and their colors are set by the color table associated with the input volume.
+The model maker is a pipeline of algorithms that start from the input label map, creates a binary label map with just the label(s) of interest set to 1, everything else to 0, generates a marching cubes model, runs triangle reduction and triangle smoothing algorithms. The pipeline was optimized for 1mm brain MRI data. For other geometries, adjustments of the parameters might be necessary.
-*Create Multiple:  If you specify a list of Labels, it will override any start/end label settings.  If you click Generate All it will over ride the list of lables and any start/end label settings.
+The model maker is compiled as both a command line executable passed arguments via the command line, and as a binary plug in that communicates through shared memory with Slicer3. The automatically created GUI, found by clickign on the Modules menu, Model Generation category, has the following elements:
 ** If you want to create all models that correspond to a labelmap, click the Generate All Models and Joint Smoothing boxes
 *Model Maker Parameters:
 **You can set the number of smoothing iterations, target reduction in number of polygons (decimal percentage). Use 0 and 1 if you wish no smoothing nor decimation.
 **You can set the flags to split normals or generate point normals in this pane as well.
 **You can save a copy of the models after intermediate steps (marching cubes, smoothing, and decimation if not joint smoothing, otherwise just after decimation); these models are not saved in the mrml file, turn off deleting temporary files first in the tcl window: [$::slicer3::CommandLineModuleGUI_Model_Maker GetLogic] DeleteTemporaryFilesOff
-*Anatomical Information: Here you can specify an external file linking label values with anatomical names.
+*Anatomical Information:
 This was the original method of linking label map values to resultant model colors and names, but it has been superceded by an internal linkage between the input label map volume and it's color node. If you wish to specify a file for a volume node that does not have a color node associated with it, a sample can be found in . It must be a comma separated file, extension .csv, in the format
    anatomyName1,label1
    anatomyName2,label2
 where anatomyName is a string, and label is an integer. If the volume node has a color node associated with it, that will override the anatomy label file.

@@ Line 1: / Line 1: @@
   [[Documentation|Return to Slicer Documentation]]
-[[Image:ModelMakerModule.png|thumb|right|The Model Maker Module]]
+[[Image:ModelMakerModule.png|thumb|350px|right|The Model Maker Module]]
 *The Modelmaker is used to create 3D surface models from segmented data. Label maps are the result of automated segmentation or interactive editing.
 **Model maker is a pipeline of algorithms that will take a binary label, generate a marching cubes model, run triangel reduction and triangle smoothing algorithms. The pipeline was optimized for 1mm brain MRI data. For other geometries, adjustments of the parameters might be necessary.

← Older revision		Revision as of 14:02, 10 April 2008
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	**You can save a copy of the models after intermediate steps (marching cubes, smoothing, and decimation if not joint smoothing, otherwise just after decimation); these models are not saved in the mrml file, turn off deleting temporary files first in the tcl window: [$::slicer3::CommandLineModuleGUI_Model_Maker GetLogic] DeleteTemporaryFilesOff		**You can save a copy of the models after intermediate steps (marching cubes, smoothing, and decimation if not joint smoothing, otherwise just after decimation); these models are not saved in the mrml file, turn off deleting temporary files first in the tcl window: [$::slicer3::CommandLineModuleGUI_Model_Maker GetLogic] DeleteTemporaryFilesOff
	*Anatomical Information: Here you can specify an external file linking label values with anatomical names.		*Anatomical Information: Here you can specify an external file linking label values with anatomical names.
		+	This was the original method of linking label map values to resultant model colors and names, but it has been superceded by an internal linkage between the input label map volume and it's color node. If you wish to specify a file for a volume node that does not have a color node associated with it, a sample can be found in . It must be a comma separated file, extension .csv, in the format
		+	anatomyName1,label1
		+	anatomyName2,label2
		+	where anatomyName is a string, and label is an integer. If the volume node has a color node associated with it, that will override the anatomy label file.

← Older revision		Revision as of 13:03, 9 April 2008
Line 1:		Line 1:
	[[Documentation\|Return to Slicer Documentation]]		[[Documentation\|Return to Slicer Documentation]]
		+
		+	[[Image:ModelMakerModule.png\|thumb\|right\|The Model Maker Module]]
		+	*The Modelmaker is used to create 3D surface models from segmented data. Label maps are the result of automated segmentation or interactive editing.
		+	**Model maker is a pipeline of algorithms that will take a binary label, generate a marching cubes model, run triangel reduction and triangle smoothing algorithms. The pipeline was optimized for 1mm brain MRI data. For other geometries, adjustments of the parameters might be necessary.
		+	*Models are imported into Slicer under a model hierarchy node, and their colors are set by the color table associated with the input volume.
		+	*Create Multiple: If you specify a list of Labels, it will override any start/end label settings. If you click Generate All it will over ride the list of lables and any start/end label settings.
		+	** If you want to create all models that correspond to a labelmap, click the Generate All Models and Joint Smoothing boxes
		+	*Model Maker Parameters: You can set the number of smoothing iterations, target reduction in number of polygons (decimal percentage). Use 0 and 1 if you wish no smoothing nor decimation. You can set the flags to split normals or generate point normals in this pane as well. You can save a copy of the models after intermediate steps (marching cubes, smoothing, and decimation if not joint smoothing, otherwise just after decimation); these models are not saved in the mrml file, turn off deleting temporary files first in the tcl window: [$::slicer3::CommandLineModuleGUI_Model_Maker GetLogic] DeleteTemporaryFilesOff Anatomical Information: Here you can specify an external file linking label values with anatomical names.