Modules:EMSegment-Command-Line3.6 - Revision history

Belhachemi at 05:01, 30 November 2010

2010-11-30T05:01:37Z

Belhachemi: /* Quick Tour of Features and Use */

2010-11-30T04:51:39Z

Quick Tour of Features and Use

Belhachemi: /* Use Cases, Examples, Tutorials */

2010-11-30T04:43:22Z

Use Cases, Examples, Tutorials

Belhachemi: /* Quick Tour of Features and Use */

2010-11-30T04:31:38Z

Quick Tour of Features and Use

Belhachemi: /* Module Name */

2010-11-30T04:30:25Z

Module Name

Belhachemi: /* Quick Tour of Features and Use */

2010-11-29T17:18:40Z

Quick Tour of Features and Use

Belhachemi: /* Development */

2010-11-08T22:07:12Z

Development

Belhachemi: /* More Information */

2010-11-08T22:03:28Z

More Information

Belhachemi: /* Usage */

2010-11-08T21:55:29Z

Usage

Belhachemi at 15:38, 19 August 2010

2010-08-19T15:38:14Z

@@ Line 43: / Line 43: @@
 [[Media:EMSegTutorial-AHM2008.ppt | Slides]] - [[Media:EMSegTutorial-AHM2008.zip | Data]]
- export EMSEG_TUTORIAL_DIR=/tmp/EMSegmentTutorial-Jan2008/
+* Export EMSEG_TUTORIAL_DIR environment variable ( e.g. <PATH TO TUTORIAL> = /tmp/EMSegmentTutorial-Jan2008/ )
 ===Quick Tour of Features and Use===
@@ Line 57: / Line 58: @@
 Here are some basic examples to run this module from command line directly
-* Export the Slicer3_HOME environmnt variable ( e.g. <PATH_TO_SLICER> = /tmp/3DSlicer/Slicer3-build/ )
+* Export the Slicer3_HOME environment variable ( e.g. <PATH_TO_SLICER> = /tmp/3DSlicer/Slicer3-build/ )
   export Slicer3_HOME=<PATH_TO_SLICER>
@@ Line 122: / Line 123: @@
 * [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/EMSegment/Testing/vtkEMSegmentBlackBoxSegmentationTest.cxx vtkEMSegmentBlackBoxSegmentationTest ]
 * [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/EMSegment/Testing/vtkEMSegmentMRMLManagerTest.cxx vtkEMSegmentMRMLManagerTest ]
-*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/EMSegment/Testing/vtkEMSegmentPreprocessingManagerTest.cxx vtkEMSegmentPreprocessingManagerTest  ]
+* [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/EMSegment/Testing/vtkEMSegmentPreprocessingManagerTest.cxx vtkEMSegmentPreprocessingManagerTest  ]
-*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/EMSegment/Testing/vtkEMSegmentReadWriteMRMLTest.cxx vtkEMSegmentReadWriteMRMLTest  ]
+* [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/EMSegment/Testing/vtkEMSegmentReadWriteMRMLTest.cxx vtkEMSegmentReadWriteMRMLTest  ]
-*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/EMSegment/Testing/vtkEMSegmentTestUtilities.cxx  vtkEMSegmentTestUtilities ]
+* [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/EMSegment/Testing/vtkEMSegmentTestUtilities.cxx  vtkEMSegmentTestUtilities ]
 ===Known bugs===

@@ Line 68: / Line 68: @@
   source ${Slicer3_HOME}/bin/Slicer3SetupPaths.sh
   RUN_NAME=BrainTutorial-Defaults
-  ${Slicer3_HOME}/Slicer3 --launch $Slicer3_HOME/lib/Slicer3/Plugins/EMSegmentCommandLine\
+ mkdir -p $EMSEG_TUTORIAL_DIR/Working/$RUN_NAME
-  --verbose\
+  ${Slicer3_HOME}/Slicer3 --launch $Slicer3_HOME/lib/Slicer3/Plugins/EMSegmentCommandLine \
-  --mrmlSceneFileName $EMSEG_TUTORIAL_DIR/EMSeg-Brain-MRT1T2.mrml\
+  --verbose \
-  --intermediateResultsDirectory $EMSEG_TUTORIAL_DIR/Working/$RUN_NAME\
+  --mrmlSceneFileName $EMSEG_TUTORIAL_DIR/EMSeg-Brain-MRT1T2.mrml \
-  --resultVolumeFileName VolumeData_Output/Segmentation-$RUN_NAME.nhdr\
+  --intermediateResultsDirectory $EMSEG_TUTORIAL_DIR/Working/$RUN_NAME \
 * Run the segmentation algorithm with new data
@@ Line 80: / Line 81: @@
   source ${Slicer3_HOME}/bin/Slicer3SetupPaths.sh
   RUN_NAME=BrainTutorial-SetTarget
-  ${Slicer3_HOME}/Slicer3 --launch $Slicer3_HOME/lib/Slicer3/Plugins/EMSegmentCommandLine\
+ mkdir -p $EMSEG_TUTORIAL_DIR/Working/$RUN_NAME
-  --verbose\
+  ${Slicer3_HOME}/Slicer3 --launch $Slicer3_HOME/lib/Slicer3/Plugins/EMSegmentCommandLine \
-  --mrmlSceneFileName $EMSEG_TUTORIAL_DIR/EMSeg-Brain-MRT1T2.mrml\
+  --verbose \
-  --targetVolumeFileNames\
+  --mrmlSceneFileName $EMSEG_TUTORIAL_DIR/EMSeg-Brain-MRT1T2.mrml \
-      $EMSEG_TUTORIAL_DIR/VolumeData_Input/Target/t1.nhdr,$EMSEG_TUTORIAL_DIR/VolumeData_Input/Target/t2.nhdr\
+  --targetVolumeFileNames \
-  --resultVolumeFileName\
+      $EMSEG_TUTORIAL_DIR/VolumeData_Input/Target/t1.nhdr,$EMSEG_TUTORIAL_DIR/VolumeData_Input/Target/t2.nhdr \
-      VolumeData_Output/Segmentation-$RUN_NAME.nhdr\
+  --resultVolumeFileName \
-  --intermediateResultsDirectory\
+      VolumeData_Output/Segmentation-$RUN_NAME.nhdr \
-      $EMSEG_TUTORIAL_DIR/Working/$RUN_NAME\
+  --intermediateResultsDirectory \
 * Run the MRI-Human-Brain task

← Older revision		Revision as of 04:43, 30 November 2010
Line 42:		Line 42:

	[[Media:EMSegTutorial-AHM2008.ppt \| Slides]] - [[Media:EMSegTutorial-AHM2008.zip \| Data]]		[[Media:EMSegTutorial-AHM2008.ppt \| Slides]] - [[Media:EMSegTutorial-AHM2008.zip \| Data]]
		+
		+	export EMSEG_TUTORIAL_DIR=/tmp/EMSegmentTutorial-Jan2008/

	===Quick Tour of Features and Use===		===Quick Tour of Features and Use===

@@ Line 47: / Line 47: @@
 The above EMSegment tutorial data set demonstrates the use of the command line interface.
-If the command-line module is invoked from Slicer3 GUI, there will be a '''Parameters panel:''' [[Image:EMSegment-CL-Panel.png|300px|thumb|EMSegment Simple Parameters Panel]]
+If the command-line module is invoked from Slicer3 GUI, there will be a '''Parameters panel:''' [[Image:EMSegment-CL-Panel.png|400px|thumb|EMSegment Simple Parameters Panel]]
 # MRML Scene: Select the mrml scene  for the tutorial parameter set
 # Result Labelmap: Select a new image filename for output labelmap

@@ Line 9: / Line 9: @@
 EM Segment Command-Line Executable
 {|
-|[[Image:EMSegment-CL-Panel.png|thumb|200px|Interface]]
+|[[Image:EMSegment-CL-Panel.png|thumb|400px|Interface]]
 |}

@@ Line 54: / Line 54: @@
 Here are some basic examples to run this module from command line directly
 * Run the executable to see the documentation
-  $SLICER_BUILD_DIR/lib/Slicer3/Plugins/EMSegmentCommandLine --help
+  ${Slicer3_HOME}/Slicer3 --launch $Slicer3_HOME/lib/Slicer3/Plugins/EMSegmentCommandLine --help
-*Run the segmentation algorithm with tutorial data
+* Run the segmentation algorithm with tutorial data
 The script "Run-BrainTutorial-Defaults.sh" demonstrates how to run the EMSegmenter on the tutorial data. The resulting labelmap is written into the VolumeData_Output directory.  Try adding the "--intermediateResultsDirectory myDirectoryName" flag to write out intermediate data.  Intermediate data is saved in the "myDirectoryName" directory: you can load this scene to visualize the intermediate data (e.g. intensity normalized and registered images) and segmentation results.
-  source SetupPaths.sh
+  source ${Slicer3_HOME}/bin/Slicer3SetupPaths.sh
   RUN_NAME=BrainTutorial-Defaults
-  $SLICER_BUILD_DIR/lib/Slicer3/Plugins/EMSegmentCommandLine\
+  ${Slicer3_HOME}/Slicer3 --launch $Slicer3_HOME/lib/Slicer3/Plugins/EMSegmentCommandLine\
   --verbose\
   --mrmlSceneFileName $EMSEG_TUTORIAL_DIR/EMSeg-Brain-MRT1T2.mrml\
@@ Line 70: / Line 73: @@
 * Run the segmentation algorithm with new data
-The other scripts, "BrainTutorial-SetTarget1.sh" and "BrainTutorial-SetTargetAndAtlas.sh", demonstrate how to run the EMSegmenter on new
+The other script, "BrainTutorial-SetTarget1.sh" demonstrate how to run the EMSegmenter on new
-data.  Because the tutorial EMSegment parameters are designed to  accept one T1 and one T2 input image, each script supplies one new T1 and one T2 to be segmented (NB: order is important).  The "BrainTutorial-SetTargetAndAtlas.sh" script shows how to specify atlas images on the command line.
+data. Because the tutorial EMSegment parameters are designed to  accept one T1 and one T2 input image, each script supplies one new T1 and one T2 to be segmented (NB: order is important).
-  source SetupPaths.sh
+ source ${Slicer3_HOME}/bin/Slicer3SetupPaths.sh
-  RUN_NAME=BrainTutorial-SetTargetAndAtlas
+ RUN_NAME=BrainTutorial-SetTarget
-  $SLICER_BUILD_DIR/lib/Slicer3/Plugins/EMSegmentCommandLine\
+ ${Slicer3_HOME}/Slicer3 --launch $Slicer3_HOME/lib/Slicer3/Plugins/EMSegmentCommandLine\
   --verbose\
   --mrmlSceneFileName $EMSEG_TUTORIAL_DIR/EMSeg-Brain-MRT1T2.mrml\
   --targetVolumeFileNames\
-   $EMSEG_TUTORIAL_DIR/VolumeData_Input/Target/t1.nhdr,$EMSEG_TUTORIAL_DIR/VolumeData_Input/Target/t2.nhdr\
+     $EMSEG_TUTORIAL_DIR/VolumeData_Input/Target/t1.nhdr,$EMSEG_TUTORIAL_DIR/VolumeData_Input/Target/t2.nhdr\
 == Development ==

@@ Line 84: / Line 84: @@
 == Development ==
+The EMSegment Command-line module is automatic generated from the EMSegmentCommandLine executable using the --xml option.
-The module is implemented as a command-line Slicer3 module to provide a command line interface to the EMSegment algorithm for script/batch processing of large collection of data with predefined parameters set.
+The EMSegmentCommandLine provides a command line interface to the EMSegment algorithm for script/batch processing of large collection of data with predefined parameters set.
 ===Notes from the Developer(s)===
-Algorithms used, library classes depended upon, use cases, etc.
+N/A
 ===Dependencies===

@@ Line 122: / Line 122: @@
 *API: [http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkEMSegmentMRMLManager.html MRML Manager] | [http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkEMSegmentLogic.html Module Logic] | [http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkEMSegmentGUI.html Module GUI]
 == More Information ==
-For more information about the EM Segmenter project in Slicer3 [[Slicer3:EM|see the old EMSegment Wiki page here]].
+*For more information about the EM Segmenter project see the [[EMSegmenter-Overview| EMSegmenter Wiki page here]]
 ===Acknowledgment===

@@ Line 31: / Line 31: @@
 == Usage ==
-The primary function of the '''EMSegment Template Builder''' module is to step the user through the process of calibrating, via algorithm parameters, the segmentation algorithm to a particular set of input data.  However, once a successful collection of parameters is established, the user will commonly want to bypass this detailed calibration process when segmenting new images by using those parameters collected from the calibration process in '''EMSegment Template Builder''' module.  The command-line executable provides this batch processing capability.
+The primary function of the <B>EMSegmenter</B> module is to step the user through the process of calibrating, via algorithm parameters, the segmentation algorithm to a particular set of input data.  However, once a successful collection of parameters is established, the user will commonly want to bypass this detailed calibration process when segmenting new images by using those parameters collected from the calibration process in <B>EMSegmenter</B> module. The <B>EMSegment Command-line module</B> which wraps the <B>EMSegmentCommandLine executable</B> provides this batch processing capability. The <B>EMSegment Command-line module</B> is automatic generated from the <B>EMSegmentCommandLine executable</B> using the --xml option.
 ===Use Cases, Examples, Tutorials===
@@ Line 51: / Line 51: @@
 # Result Labelmap: Select a new image filename for output labelmap
 # Target Volumes: Select input target volumes (Multiple files can be selected at one time)
 # Click `Apply’
@@ Line 83: / Line 82: @@
   --targetVolumeFileNames\
     $EMSEG_TUTORIAL_DIR/VolumeData_Input/Target/t1.nhdr,$EMSEG_TUTORIAL_DIR/VolumeData_Input/Target/t2.nhdr\
 == Development ==

← Older revision		Revision as of 15:38, 19 August 2010
Line 1:		Line 1:
	[[Documentation-3.6\|Return to Slicer 3.6 Documentation]]		[[Documentation-3.6\|Return to Slicer 3.6 Documentation]]
		+
		+	[[EMSegmenter-Overview\|Return to EMSegmenter Overview Page]]

	[[Announcements:Slicer3.6#Highlights\|Gallery of New Features]]		[[Announcements:Slicer3.6#Highlights\|Gallery of New Features]]