EMSegmenter-CreateTask - Revision history

Pohl: /* Step 1: Create Template without Preprocessing */

2012-08-02T21:46:42Z

Step 1: Create Template without Preprocessing

Pohl: /* Step 1: Create Template without Preprocessing */

2012-08-02T21:45:57Z

Step 1: Create Template without Preprocessing

Pohl: /* Task creation process - for developer */

2012-08-02T21:44:42Z

Task creation process - for developer

Pohl: /* Task creation process - for developer */

2012-08-02T21:29:42Z

Task creation process - for developer

Pohl: /* Task creation process - for developer */

2012-08-02T21:24:20Z

Task creation process - for developer

Pohl: /* Task creation process - for developer */

2012-08-02T21:21:00Z

Task creation process - for developer

Pohl: /* Task creation process - for developer */

2012-08-02T21:18:09Z

Task creation process - for developer

Belhachemi: /* Task creation process - for developer */

2010-12-08T21:32:20Z

Task creation process - for developer

Belhachemi at 21:35, 1 December 2010

2010-12-01T21:35:32Z

Belhachemi: Created page with '=Task creation process - for developer= The goal is to create a task with the name 'Hello World' After following the instructions below the new task will consist of following fi…'

2010-12-01T21:34:08Z

Created page with '=Task creation process - for developer= The goal is to create a task with the name 'Hello World' After following the instructions below the new task will consist of following fi…'

New page

=Task creation process - for developer=
The goal is to create a task with the name 'Hello World'

After following the instructions below the new task will consist of following files:
./Slicer3/Modules/EMSegment/Tasks/Hello-World.mrml
./Slicer3/Modules/EMSegment/Tasks/Hello-World.tcl
./Slicer3/Modules/EMSegment/Tasks/Hello-World/<atlas_file_1>
./Slicer3/Modules/EMSegment/Tasks/Hello-World/<atlas_file_2>
[...]
./Slicer3/Modules/EMSegment/Tasks/Hello-World/<atlas_file_i>
[...]
./Slicer3/Modules/EMSegment/Tasks/Hello-World/<atlas_file_N>

* Create a new directory ./Slicer3/Modules/EMSegment/Tasks/Hello-World

* Copy the atlas files for air, GM, T1 into this directory.

* Start Slicer
* Switch to the EMSegmenter module
* Create new task
** Name: Hello World
** Pre-processing: None
* Basically follow our EMSegmenter advanced tutorial, but create a simple tree
** load ./Slicer3/Modules/EMSegment/Testing/TestData/MiscVolumeData/MRIHumanBrain_T1_aligned.nrrd
** Add a channel, call it T1, assign MRIHumanBrain_T1_aligned
** Create a simple anatomical tree (air and GM)
** Load atlas files only from ./Slicer3/Modules/EMSegment/Tasks/Hello-World/
** generate mean and covariance values
** specify node weights
* At step 9/9. click on 'Create Template File'
** Save the file under ./Slicer3/Modules/EMSegment/Tasks/Hello-World.mrml
** The target node and some other unneeded nodes will be removed from the mrml scene and written to disk.
* Close Slicer
* Copy our standard tcl file ./Slicer3/Modules/EMSegment/Tasks/Template.tcl to ./Slicer3/Modules/EMSegment/Tasks/Hello-World.tcl
* Adjust this tcl file to include your pre-processing pipeline.
* edit ./Slicer3/Modules/EMSegment/Tasks/Hello-World.tcl to specify your own pre-processing
* edit ./Slicer3/Modules/EMSegment/Tasks/Hello-World.mrml to use your own pre-processing
** - <EMS TclTaskFilename="GenericTask.tcl" ></EMS>
** + <EMS TclTaskFilename="Hello-World.tcl" ></EMS>
* touch ../Slicer3/Modules/EMSegment/CMakeLists.txt and do a 'make' to copy the new files into the binary directory

The result of the process above can also be downloaded here:
After Installing both files this 'Hello World' task will appear in the task list under the name 'Hello World'.

@@ Line 26: / Line 26: @@
 **  Name:           Hello World
 **  Pre-processing: None
-* Now follow up to Step 9 our [[Media:EMSegmenterTutorialAdvancedMode-Slicer-3.6.3-1.pdf | EMSegmenter advanced tutorial ]] with the following modifcations:
+* Now follow up the [[Media:EMSegmenterTutorialAdvancedMode-Slicer-3.6.3-1.pdf | EMSegmenter advanced tutorial ]] up to Step 9 with the following modifcations:
 ** load <DIR>/../Testing/TestData/MiscVolumeData/MRIHumanBrain_T1_aligned.nrrd
 ** Add a channel, call it T1, assign MRIHumanBrain_T1_aligned
 **  Load atlas files only from <DIR>/Hello-World/
 **  for Slicer 3 only: generate mean and covariance values

@@ Line 26: / Line 26: @@
 **  Name:           Hello World
 **  Pre-processing: None
-* Now follow up to Step 9 our [EMSegmenter advanced tutorial EMSegmenterTutorialAdvancedMode-Slicer-3.6.3-1.pdf ] with the following modifcations:
+* Now follow up to Step 9 our [[Media:EMSegmenterTutorialAdvancedMode-Slicer-3.6.3-1.pdf | EMSegmenter advanced tutorial ]] with the following modifcations:
 ** load <DIR>/../Testing/TestData/MiscVolumeData/MRIHumanBrain_T1_aligned.nrrd
 ** Add a channel, call it T1, assign MRIHumanBrain_T1_aligned

@@ Line 6: / Line 6: @@
   <DIR> = for Slicer 3 as Slicer3/Modules/EMSegment/Tasks/ (source directory) and
           for Slicer 4 as Slicer-build/share/Slicer-4.*/qt-loadable-modules/EMSegment/Tasks (build directory)
 After following the instructions below the new task will consist of following files:
@@ Line 15: / Line 14: @@
   <DIR>/Hello-World/<atlas_file_N>
+== Step 1: Create Template without Preprocessing ==
 * Create a new directory <DIR>/Hello-World
@@ Line 27: / Line 26: @@
 **  Name:           Hello World
 **  Pre-processing: None
-* Basically follow our EMSegmenter advanced tutorial, but create a simple tree
+* Now follow up to Step 9 our [EMSegmenter advanced tutorial EMSegmenterTutorialAdvancedMode-Slicer-3.6.3-1.pdf ] with the following modifcations:
 ** load <DIR>/../Testing/TestData/MiscVolumeData/MRIHumanBrain_T1_aligned.nrrd
 ** Add a channel, call it T1, assign MRIHumanBrain_T1_aligned
-**  Create a simple anatomical tree (air and GM)
+**  Create a simple anatomical tree (air, GM, ... )
 **  Load atlas files only from <DIR>/Hello-World/
-**  generate mean and covariance values
+**  for Slicer 3 only: generate mean and covariance values
-**  specify node weights
+* At step 9/9. click on 'Create Template File' and save the file under <DIR>/Hello-World.mrml. Hello-World.mrml now only consists of nodes needed to parameterize the EMSegmenter.
 * Close Slicer
 * Copy our standard tcl file <DIR>/Template.tcl to <DIR>/Hello-World.tcl
-* Adjust this tcl file to include your pre-processing pipeline.
+* Edit <DIR>/Hello-World.tcl to customize/modify the pre-processing pipeline
-* edit <DIR>/Hello-World.tcl to specify your own pre-processing
+* Edit <DIR>/Hello-World.mrml to use your own pre-processing by replacing  <EMSGlobalParameters ... TclTaskFilename="GenericTask.tcl" ... > with  <EMSGlobalParameters ... TclTaskFilename="Hello-World.tcl" ...>
-The result of the process above can also be downloaded here:
+When you start Slicer again 'Hello World' should appear in the task list of the EMSegmenter.
 =EMSegmenter-Task Template=
 Please use this [[EMSegmenter-Tasks:Template| wiki page]] as a template for you task specific Wiki page.

@@ Line 12: / Line 12: @@
   <DIR>/Hello-World.tcl
   <DIR>/Hello-World/<atlas_file_1>
   [...]
   <DIR>/Hello-World/<atlas_file_N>
@@ Line 21: / Line 18: @@
 * Create a new directory <DIR>/Hello-World
-* Copy the atlas files for air, GM, T1 into this directory.
+* Copy the atlas files for air, CSF, greymatter, whitematter, and T1 from <DIR>/MRI-Human-Brain into this directory.
 * Start Slicer
 * Switch to the EMSegmenter module
 * Create new task

@@ Line 4: / Line 4: @@
 =Task creation process - for developer=
 The goal is to create a task with the name 'Hello World' in Slicer 3 and Slicer 4. Before doing so, we define
+ <dir> = for Slicer 3 as Slicer3/Modules/EMSegment/Tasks/ (source directory) and
-<dir> = for Slicer3 as Slicer3/Modules/EMSegment/Tasks/ (source directory) and Slicer 4 as Slicer-build/share/Slicer-4.*/qt-loadable-modules/EMSegment/Tasks (build directory)
+         for Slicer 4 as Slicer-build/share/Slicer-4.*/qt-loadable-modules/EMSegment/Tasks (build directory)
 After following the instructions below the new task will consist of following files:

@@ Line 3: / Line 3: @@
 =Task creation process - for developer=
-The goal is to create a task with the name 'Hello World'
+The goal is to create a task with the name 'Hello World' in Slicer 3 and Slicer 4. Before doing so, we define
 After following the instructions below the new task will consist of following files:
-  ./Slicer3/Modules/EMSegment/Tasks/Hello-World.mrml
+  <dir>/Hello-World.mrml
   ./Slicer3/Modules/EMSegment/Tasks/Hello-World.tcl
   ./Slicer3/Modules/EMSegment/Tasks/Hello-World/<atlas_file_1>

← Older revision		Revision as of 21:32, 8 December 2010
Line 47:		Line 47:
	The result of the process above can also be downloaded here:		The result of the process above can also be downloaded here:
	After Installing both files this 'Hello World' task will appear in the task list under the name 'Hello World'.		After Installing both files this 'Hello World' task will appear in the task list under the name 'Hello World'.
		+
		+	=EMSegmenter-Task Template=
		+	Please use this [[EMSegmenter-Tasks:Template\| wiki page]] as a template for you task specific Wiki page.

← Older revision		Revision as of 21:35, 1 December 2010
Line 1:		Line 1:
		+	[[EMSegmenter-Tasks\|Return to EMSegmenter Task Overview Page]]
		+
		+
	=Task creation process - for developer=		=Task creation process - for developer=
	The goal is to create a task with the name 'Hello World'		The goal is to create a task with the name 'Hello World'