https://www.slicer.org/w/api.php?action=feedcontributions&user=Pohl&feedformat=atomSlicer Wiki - User contributions [en]2024-03-29T06:59:53ZUser contributionsMediaWiki 1.33.0https://www.slicer.org/w/index.php?title=EMSegmenter-Tasks:cineMRI&diff=28146EMSegmenter-Tasks:cineMRI2012-08-27T21:17:17Z<p>Pohl: moved EMSegmenter-Tasks:cineMARI to EMSegmenter-Tasks:cineMRI</p>
<hr />
<div>[[EMSegmenter-Tasks|Return to EMSegmenter Task Overview Page]]<br />
<br />
=Endiastole Cine MR Segmentation =<br />
<br />
=Description=<br />
<br />
=Anatomical Tree=<br />
* root<br />
** background <br />
** Myocardium <br />
** Right Ventricle <br />
** Left Ventricle<br />
<br />
=Atlas=<br />
<br />
=Result=<br />
[[Image:EMSegment-CardioA1-grey.jpg|630px]]<br><BR><br />
[[Image:EMSegment-CardioA1seg.jpg|630px]]<br />
<br />
=Collaborators=<br />
Benoit Desjardins (UPenn) <br><br />
Harold Litt (UPenn)<br />
<br />
=Acknowledgment=<br />
The construction of the pipeline was supported by funding from NIH NCRR 2P41RR013218 Supplement.<br />
<br />
=Citations=<br />
* Pohl K, Bouix S, Nakamura M, Rohlfing T, McCarley R, Kikinis R, Grimson W, Shenton M, Wells W. [http://www.slicer.org/pages/Special:PubDB_View?dspaceid=608 A Hierarchical Algorithm for MR Brain Image Parcellation.] IEEE Transactions on Medical Imaging. 2007 Sept;26(9):1201-1212.</div>Pohlhttps://www.slicer.org/w/index.php?title=EMSegmenter-Tasks:cineMARI&diff=28147EMSegmenter-Tasks:cineMARI2012-08-27T21:17:17Z<p>Pohl: moved EMSegmenter-Tasks:cineMARI to EMSegmenter-Tasks:cineMRI</p>
<hr />
<div>#REDIRECT [[EMSegmenter-Tasks:cineMRI]]</div>Pohlhttps://www.slicer.org/w/index.php?title=EMSegmenter-CreateTask&diff=27706EMSegmenter-CreateTask2012-08-02T21:46:42Z<p>Pohl: /* Step 1: Create Template without Preprocessing */</p>
<hr />
<div>[[EMSegmenter-Tasks|Return to EMSegmenter Task Overview Page]]<br />
<br />
<br />
=Task creation process - for developer=<br />
The goal is to create a task with the name 'Hello World' in Slicer 3 and Slicer 4. Before doing so, we define <br />
<DIR> = for Slicer 3 as Slicer3/Modules/EMSegment/Tasks/ (source directory) and <br />
for Slicer 4 as Slicer-build/share/Slicer-4.*/qt-loadable-modules/EMSegment/Tasks (build directory)<br />
<br />
After following the instructions below the new task will consist of following files:<br />
<DIR>/Hello-World.mrml<br />
<DIR>/Hello-World.tcl<br />
<DIR>/Hello-World/<atlas_file_1><br />
[...]<br />
<DIR>/Hello-World/<atlas_file_N><br />
<br />
== Step 1: Create Template without Preprocessing ==<br />
* Create a new directory <DIR>/Hello-World<br />
<br />
* Copy the atlas files for air, CSF, greymatter, whitematter, and T1 from <DIR>/MRI-Human-Brain into this directory.<br />
<br />
* Start Slicer<br />
* Set Scene of Slicer to <DIR> by saving scene in <DIR>. Afterwards remove resulting mrml file from <DIR> as it is not needed anymore<br />
<br />
* Switch to the EMSegmenter module<br />
* Create new task<br />
** Name: Hello World<br />
** Pre-processing: None<br />
* Now follow up the [[Media:EMSegmenterTutorialAdvancedMode-Slicer-3.6.3-1.pdf | EMSegmenter advanced tutorial ]] up to Step 9 with the following modifcations:<br />
** load <DIR>/../Testing/TestData/MiscVolumeData/MRIHumanBrain_T1_aligned.nrrd<br />
** Add a channel, call it T1, assign MRIHumanBrain_T1_aligned<br />
** Load atlas files only from <DIR>/Hello-World/ <br />
** for Slicer 3 only: generate mean and covariance values <br />
* 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. <br />
* Close Slicer<br />
<br />
== Step 2: Include Preprocessing (Optional) ==<br />
For templates that do not include atlas files the following instructions are optional <br />
* Copy our standard tcl file <DIR>/Template.tcl to <DIR>/Hello-World.tcl<br />
* Edit <DIR>/Hello-World.tcl to customize/modify the pre-processing pipeline<br />
* Edit <DIR>/Hello-World.mrml to use your own pre-processing by replacing <EMSGlobalParameters ... TclTaskFilename="GenericTask.tcl" ... > with <EMSGlobalParameters ... TclTaskFilename="Hello-World.tcl" ...><br />
<br />
== Step 3: Update Slicer Build (only for Slicer 3) ==<br />
touch <DIR>/../CMakeLists.txt and do a 'make' to copy the new files into the binary directory<br />
<br />
When you start Slicer again 'Hello World' should appear in the task list of the EMSegmenter.<br />
<br />
=EMSegmenter-Task Template=<br />
Please use this [[EMSegmenter-Tasks:Template| wiki page]] as a template for you task specific Wiki page.</div>Pohlhttps://www.slicer.org/w/index.php?title=EMSegmenter-CreateTask&diff=27705EMSegmenter-CreateTask2012-08-02T21:45:57Z<p>Pohl: /* Step 1: Create Template without Preprocessing */</p>
<hr />
<div>[[EMSegmenter-Tasks|Return to EMSegmenter Task Overview Page]]<br />
<br />
<br />
=Task creation process - for developer=<br />
The goal is to create a task with the name 'Hello World' in Slicer 3 and Slicer 4. Before doing so, we define <br />
<DIR> = for Slicer 3 as Slicer3/Modules/EMSegment/Tasks/ (source directory) and <br />
for Slicer 4 as Slicer-build/share/Slicer-4.*/qt-loadable-modules/EMSegment/Tasks (build directory)<br />
<br />
After following the instructions below the new task will consist of following files:<br />
<DIR>/Hello-World.mrml<br />
<DIR>/Hello-World.tcl<br />
<DIR>/Hello-World/<atlas_file_1><br />
[...]<br />
<DIR>/Hello-World/<atlas_file_N><br />
<br />
== Step 1: Create Template without Preprocessing ==<br />
* Create a new directory <DIR>/Hello-World<br />
<br />
* Copy the atlas files for air, CSF, greymatter, whitematter, and T1 from <DIR>/MRI-Human-Brain into this directory.<br />
<br />
* Start Slicer<br />
* Set Scene of Slicer to <DIR> by saving scene in <DIR>. Afterwards remove resulting mrml file from <DIR> as it is not needed anymore<br />
<br />
* Switch to the EMSegmenter module<br />
* Create new task<br />
** Name: Hello World<br />
** Pre-processing: None<br />
* Now follow up to Step 9 our [[Media:EMSegmenterTutorialAdvancedMode-Slicer-3.6.3-1.pdf | EMSegmenter advanced tutorial ]] with the following modifcations:<br />
** load <DIR>/../Testing/TestData/MiscVolumeData/MRIHumanBrain_T1_aligned.nrrd<br />
** Add a channel, call it T1, assign MRIHumanBrain_T1_aligned<br />
** Create a simple anatomical tree (air, GM, ... )<br />
** Load atlas files only from <DIR>/Hello-World/ <br />
** for Slicer 3 only: generate mean and covariance values <br />
* 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. <br />
* Close Slicer<br />
<br />
== Step 2: Include Preprocessing (Optional) ==<br />
For templates that do not include atlas files the following instructions are optional <br />
* Copy our standard tcl file <DIR>/Template.tcl to <DIR>/Hello-World.tcl<br />
* Edit <DIR>/Hello-World.tcl to customize/modify the pre-processing pipeline<br />
* Edit <DIR>/Hello-World.mrml to use your own pre-processing by replacing <EMSGlobalParameters ... TclTaskFilename="GenericTask.tcl" ... > with <EMSGlobalParameters ... TclTaskFilename="Hello-World.tcl" ...><br />
<br />
== Step 3: Update Slicer Build (only for Slicer 3) ==<br />
touch <DIR>/../CMakeLists.txt and do a 'make' to copy the new files into the binary directory<br />
<br />
When you start Slicer again 'Hello World' should appear in the task list of the EMSegmenter.<br />
<br />
=EMSegmenter-Task Template=<br />
Please use this [[EMSegmenter-Tasks:Template| wiki page]] as a template for you task specific Wiki page.</div>Pohlhttps://www.slicer.org/w/index.php?title=EMSegmenter-CreateTask&diff=27704EMSegmenter-CreateTask2012-08-02T21:44:42Z<p>Pohl: /* Task creation process - for developer */</p>
<hr />
<div>[[EMSegmenter-Tasks|Return to EMSegmenter Task Overview Page]]<br />
<br />
<br />
=Task creation process - for developer=<br />
The goal is to create a task with the name 'Hello World' in Slicer 3 and Slicer 4. Before doing so, we define <br />
<DIR> = for Slicer 3 as Slicer3/Modules/EMSegment/Tasks/ (source directory) and <br />
for Slicer 4 as Slicer-build/share/Slicer-4.*/qt-loadable-modules/EMSegment/Tasks (build directory)<br />
<br />
After following the instructions below the new task will consist of following files:<br />
<DIR>/Hello-World.mrml<br />
<DIR>/Hello-World.tcl<br />
<DIR>/Hello-World/<atlas_file_1><br />
[...]<br />
<DIR>/Hello-World/<atlas_file_N><br />
<br />
== Step 1: Create Template without Preprocessing ==<br />
* Create a new directory <DIR>/Hello-World<br />
<br />
* Copy the atlas files for air, CSF, greymatter, whitematter, and T1 from <DIR>/MRI-Human-Brain into this directory.<br />
<br />
* Start Slicer<br />
* Set Scene of Slicer to <DIR> by saving scene in <DIR>. Afterwards remove resulting mrml file from <DIR> as it is not needed anymore<br />
<br />
* Switch to the EMSegmenter module<br />
* Create new task<br />
** Name: Hello World<br />
** Pre-processing: None<br />
* Now follow up to Step 9 our [EMSegmenter advanced tutorial EMSegmenterTutorialAdvancedMode-Slicer-3.6.3-1.pdf ] with the following modifcations:<br />
** load <DIR>/../Testing/TestData/MiscVolumeData/MRIHumanBrain_T1_aligned.nrrd<br />
** Add a channel, call it T1, assign MRIHumanBrain_T1_aligned<br />
** Create a simple anatomical tree (air, GM, ... )<br />
** Load atlas files only from <DIR>/Hello-World/ <br />
** for Slicer 3 only: generate mean and covariance values <br />
* 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. <br />
* Close Slicer<br />
<br />
== Step 2: Include Preprocessing (Optional) ==<br />
For templates that do not include atlas files the following instructions are optional <br />
* Copy our standard tcl file <DIR>/Template.tcl to <DIR>/Hello-World.tcl<br />
* Edit <DIR>/Hello-World.tcl to customize/modify the pre-processing pipeline<br />
* Edit <DIR>/Hello-World.mrml to use your own pre-processing by replacing <EMSGlobalParameters ... TclTaskFilename="GenericTask.tcl" ... > with <EMSGlobalParameters ... TclTaskFilename="Hello-World.tcl" ...><br />
<br />
== Step 3: Update Slicer Build (only for Slicer 3) ==<br />
touch <DIR>/../CMakeLists.txt and do a 'make' to copy the new files into the binary directory<br />
<br />
When you start Slicer again 'Hello World' should appear in the task list of the EMSegmenter.<br />
<br />
=EMSegmenter-Task Template=<br />
Please use this [[EMSegmenter-Tasks:Template| wiki page]] as a template for you task specific Wiki page.</div>Pohlhttps://www.slicer.org/w/index.php?title=EMSegmenter-CreateTask&diff=27703EMSegmenter-CreateTask2012-08-02T21:29:42Z<p>Pohl: /* Task creation process - for developer */</p>
<hr />
<div>[[EMSegmenter-Tasks|Return to EMSegmenter Task Overview Page]]<br />
<br />
<br />
=Task creation process - for developer=<br />
The goal is to create a task with the name 'Hello World' in Slicer 3 and Slicer 4. Before doing so, we define <br />
<DIR> = for Slicer 3 as Slicer3/Modules/EMSegment/Tasks/ (source directory) and <br />
for Slicer 4 as Slicer-build/share/Slicer-4.*/qt-loadable-modules/EMSegment/Tasks (build directory)<br />
<br />
<br />
After following the instructions below the new task will consist of following files:<br />
<DIR>/Hello-World.mrml<br />
<DIR>/Hello-World.tcl<br />
<DIR>/Hello-World/<atlas_file_1><br />
[...]<br />
<DIR>/Hello-World/<atlas_file_N><br />
<br />
<br />
* Create a new directory <DIR>/Hello-World<br />
<br />
* Copy the atlas files for air, CSF, greymatter, whitematter, and T1 from <DIR>/MRI-Human-Brain into this directory.<br />
<br />
* Start Slicer<br />
* Set Scene of Slicer to <DIR> by saving scene in <DIR>. Afterwards remove resulting mrml file from <DIR> as it is not needed anymore<br />
<br />
* Switch to the EMSegmenter module<br />
* Create new task<br />
** Name: Hello World<br />
** Pre-processing: None<br />
* Basically follow our EMSegmenter advanced tutorial, but create a simple tree<br />
** load <DIR>/../Testing/TestData/MiscVolumeData/MRIHumanBrain_T1_aligned.nrrd<br />
** Add a channel, call it T1, assign MRIHumanBrain_T1_aligned<br />
** Create a simple anatomical tree (air and GM)<br />
** Load atlas files only from <DIR>/Hello-World/<br />
** generate mean and covariance values<br />
** specify node weights<br />
* At step 9/9. click on 'Create Template File'<br />
** Save the file under <DIR>/Hello-World.mrml<br />
** The target node and some other unneeded nodes will be removed from the mrml scene and written to disk.<br />
* Close Slicer<br />
* Copy our standard tcl file <DIR>/Template.tcl to <DIR>/Hello-World.tcl<br />
* Adjust this tcl file to include your pre-processing pipeline.<br />
* edit <DIR>/Hello-World.tcl to specify your own pre-processing<br />
* edit <DIR>/Hello-World.mrml to use your own pre-processing<br />
** - <EMS TclTaskFilename="GenericTask.tcl" ></EMS><br />
** + <EMS TclTaskFilename="Hello-World.tcl" ></EMS><br />
* For Slicer 3 only :<br />
touch ../Slicer3/Modules/EMSegment/CMakeLists.txt and do a 'make' to copy the new files into the binary directory<br />
<br />
<br />
The result of the process above can also be downloaded here:<br />
After Installing both files this 'Hello World' task will appear in the task list under the name 'Hello World'.<br />
<br />
=EMSegmenter-Task Template=<br />
Please use this [[EMSegmenter-Tasks:Template| wiki page]] as a template for you task specific Wiki page.</div>Pohlhttps://www.slicer.org/w/index.php?title=EMSegmenter-CreateTask&diff=27702EMSegmenter-CreateTask2012-08-02T21:24:20Z<p>Pohl: /* Task creation process - for developer */</p>
<hr />
<div>[[EMSegmenter-Tasks|Return to EMSegmenter Task Overview Page]]<br />
<br />
<br />
=Task creation process - for developer=<br />
The goal is to create a task with the name 'Hello World' in Slicer 3 and Slicer 4. Before doing so, we define <br />
<DIR> = for Slicer 3 as Slicer3/Modules/EMSegment/Tasks/ (source directory) and <br />
for Slicer 4 as Slicer-build/share/Slicer-4.*/qt-loadable-modules/EMSegment/Tasks (build directory)<br />
<br />
<br />
After following the instructions below the new task will consist of following files:<br />
<DIR>/Hello-World.mrml<br />
<DIR>/Hello-World.tcl<br />
<DIR>/Hello-World/<atlas_file_1><br />
<DIR>/Hello-World/<atlas_file_2><br />
[...]<br />
<DIR>/Hello-World/<atlas_file_i><br />
[...]<br />
<DIR>/Hello-World/<atlas_file_N><br />
<br />
<br />
* Create a new directory <DIR>/Hello-World<br />
<br />
* Copy the atlas files for air, GM, T1 into this directory.<br />
<br />
* Start Slicer<br />
* Switch to the EMSegmenter module<br />
* Create new task<br />
** Name: Hello World<br />
** Pre-processing: None<br />
* Basically follow our EMSegmenter advanced tutorial, but create a simple tree<br />
** load <DIR>/../Testing/TestData/MiscVolumeData/MRIHumanBrain_T1_aligned.nrrd<br />
** Add a channel, call it T1, assign MRIHumanBrain_T1_aligned<br />
** Create a simple anatomical tree (air and GM)<br />
** Load atlas files only from <DIR>/Hello-World/<br />
** generate mean and covariance values<br />
** specify node weights<br />
* At step 9/9. click on 'Create Template File'<br />
** Save the file under <DIR>/Hello-World.mrml<br />
** The target node and some other unneeded nodes will be removed from the mrml scene and written to disk.<br />
* Close Slicer<br />
* Copy our standard tcl file <DIR>/Template.tcl to <DIR>/Hello-World.tcl<br />
* Adjust this tcl file to include your pre-processing pipeline.<br />
* edit <DIR>/Hello-World.tcl to specify your own pre-processing<br />
* edit <DIR>/Hello-World.mrml to use your own pre-processing<br />
** - <EMS TclTaskFilename="GenericTask.tcl" ></EMS><br />
** + <EMS TclTaskFilename="Hello-World.tcl" ></EMS><br />
* For Slicer 3 only :<br />
touch ../Slicer3/Modules/EMSegment/CMakeLists.txt and do a 'make' to copy the new files into the binary directory<br />
<br />
<br />
The result of the process above can also be downloaded here:<br />
After Installing both files this 'Hello World' task will appear in the task list under the name 'Hello World'.<br />
<br />
=EMSegmenter-Task Template=<br />
Please use this [[EMSegmenter-Tasks:Template| wiki page]] as a template for you task specific Wiki page.</div>Pohlhttps://www.slicer.org/w/index.php?title=EMSegmenter-CreateTask&diff=27701EMSegmenter-CreateTask2012-08-02T21:21:00Z<p>Pohl: /* Task creation process - for developer */</p>
<hr />
<div>[[EMSegmenter-Tasks|Return to EMSegmenter Task Overview Page]]<br />
<br />
<br />
=Task creation process - for developer=<br />
The goal is to create a task with the name 'Hello World' in Slicer 3 and Slicer 4. Before doing so, we define <br />
<dir> = for Slicer 3 as Slicer3/Modules/EMSegment/Tasks/ (source directory) and <br />
for Slicer 4 as Slicer-build/share/Slicer-4.*/qt-loadable-modules/EMSegment/Tasks (build directory)<br />
<br />
After following the instructions below the new task will consist of following files:<br />
<dir>/Hello-World.mrml<br />
./Slicer3/Modules/EMSegment/Tasks/Hello-World.tcl<br />
./Slicer3/Modules/EMSegment/Tasks/Hello-World/<atlas_file_1><br />
./Slicer3/Modules/EMSegment/Tasks/Hello-World/<atlas_file_2><br />
[...]<br />
./Slicer3/Modules/EMSegment/Tasks/Hello-World/<atlas_file_i><br />
[...]<br />
./Slicer3/Modules/EMSegment/Tasks/Hello-World/<atlas_file_N><br />
<br />
<br />
* Create a new directory ./Slicer3/Modules/EMSegment/Tasks/Hello-World<br />
<br />
* Copy the atlas files for air, GM, T1 into this directory.<br />
<br />
* Start Slicer<br />
* Switch to the EMSegmenter module<br />
* Create new task<br />
** Name: Hello World<br />
** Pre-processing: None<br />
* Basically follow our EMSegmenter advanced tutorial, but create a simple tree<br />
** load ./Slicer3/Modules/EMSegment/Testing/TestData/MiscVolumeData/MRIHumanBrain_T1_aligned.nrrd<br />
** Add a channel, call it T1, assign MRIHumanBrain_T1_aligned<br />
** Create a simple anatomical tree (air and GM)<br />
** Load atlas files only from ./Slicer3/Modules/EMSegment/Tasks/Hello-World/<br />
** generate mean and covariance values<br />
** specify node weights<br />
* At step 9/9. click on 'Create Template File'<br />
** Save the file under ./Slicer3/Modules/EMSegment/Tasks/Hello-World.mrml<br />
** The target node and some other unneeded nodes will be removed from the mrml scene and written to disk.<br />
* Close Slicer<br />
* Copy our standard tcl file ./Slicer3/Modules/EMSegment/Tasks/Template.tcl to ./Slicer3/Modules/EMSegment/Tasks/Hello-World.tcl<br />
* Adjust this tcl file to include your pre-processing pipeline.<br />
* edit ./Slicer3/Modules/EMSegment/Tasks/Hello-World.tcl to specify your own pre-processing<br />
* edit ./Slicer3/Modules/EMSegment/Tasks/Hello-World.mrml to use your own pre-processing<br />
** - <EMS TclTaskFilename="GenericTask.tcl" ></EMS><br />
** + <EMS TclTaskFilename="Hello-World.tcl" ></EMS><br />
* touch ../Slicer3/Modules/EMSegment/CMakeLists.txt and do a 'make' to copy the new files into the binary directory<br />
<br />
<br />
The result of the process above can also be downloaded here:<br />
After Installing both files this 'Hello World' task will appear in the task list under the name 'Hello World'.<br />
<br />
=EMSegmenter-Task Template=<br />
Please use this [[EMSegmenter-Tasks:Template| wiki page]] as a template for you task specific Wiki page.</div>Pohlhttps://www.slicer.org/w/index.php?title=EMSegmenter-CreateTask&diff=27700EMSegmenter-CreateTask2012-08-02T21:18:09Z<p>Pohl: /* Task creation process - for developer */</p>
<hr />
<div>[[EMSegmenter-Tasks|Return to EMSegmenter Task Overview Page]]<br />
<br />
<br />
=Task creation process - for developer=<br />
The goal is to create a task with the name 'Hello World' in Slicer 3 and Slicer 4. Before doing so, we define <br />
<br />
<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)<br />
<br />
After following the instructions below the new task will consist of following files:<br />
<dir>/Hello-World.mrml<br />
./Slicer3/Modules/EMSegment/Tasks/Hello-World.tcl<br />
./Slicer3/Modules/EMSegment/Tasks/Hello-World/<atlas_file_1><br />
./Slicer3/Modules/EMSegment/Tasks/Hello-World/<atlas_file_2><br />
[...]<br />
./Slicer3/Modules/EMSegment/Tasks/Hello-World/<atlas_file_i><br />
[...]<br />
./Slicer3/Modules/EMSegment/Tasks/Hello-World/<atlas_file_N><br />
<br />
<br />
* Create a new directory ./Slicer3/Modules/EMSegment/Tasks/Hello-World<br />
<br />
* Copy the atlas files for air, GM, T1 into this directory.<br />
<br />
* Start Slicer<br />
* Switch to the EMSegmenter module<br />
* Create new task<br />
** Name: Hello World<br />
** Pre-processing: None<br />
* Basically follow our EMSegmenter advanced tutorial, but create a simple tree<br />
** load ./Slicer3/Modules/EMSegment/Testing/TestData/MiscVolumeData/MRIHumanBrain_T1_aligned.nrrd<br />
** Add a channel, call it T1, assign MRIHumanBrain_T1_aligned<br />
** Create a simple anatomical tree (air and GM)<br />
** Load atlas files only from ./Slicer3/Modules/EMSegment/Tasks/Hello-World/<br />
** generate mean and covariance values<br />
** specify node weights<br />
* At step 9/9. click on 'Create Template File'<br />
** Save the file under ./Slicer3/Modules/EMSegment/Tasks/Hello-World.mrml<br />
** The target node and some other unneeded nodes will be removed from the mrml scene and written to disk.<br />
* Close Slicer<br />
* Copy our standard tcl file ./Slicer3/Modules/EMSegment/Tasks/Template.tcl to ./Slicer3/Modules/EMSegment/Tasks/Hello-World.tcl<br />
* Adjust this tcl file to include your pre-processing pipeline.<br />
* edit ./Slicer3/Modules/EMSegment/Tasks/Hello-World.tcl to specify your own pre-processing<br />
* edit ./Slicer3/Modules/EMSegment/Tasks/Hello-World.mrml to use your own pre-processing<br />
** - <EMS TclTaskFilename="GenericTask.tcl" ></EMS><br />
** + <EMS TclTaskFilename="Hello-World.tcl" ></EMS><br />
* touch ../Slicer3/Modules/EMSegment/CMakeLists.txt and do a 'make' to copy the new files into the binary directory<br />
<br />
<br />
The result of the process above can also be downloaded here:<br />
After Installing both files this 'Hello World' task will appear in the task list under the name 'Hello World'.<br />
<br />
=EMSegmenter-Task Template=<br />
Please use this [[EMSegmenter-Tasks:Template| wiki page]] as a template for you task specific Wiki page.</div>Pohlhttps://www.slicer.org/w/index.php?title=Developer_Meetings/20120724&diff=27673Developer Meetings/201207242012-07-24T20:21:03Z<p>Pohl: /* To discuss */</p>
<hr />
<div>Attendees: <br />
<br />
== To discuss ==<br />
* Jc: Traveling for the coming 3 weeks<br />
* Is <code>vtkSlicerROILogic</code> still used ? See https://github.com/Slicer/Slicer/blob/master/Base/Logic/vtkSlicerROILogic.h<br />
* Python libraries for extension vtk logic (only on mac?)<br />
** extensions testing with python scripts See http://www.na-mic.org/Bug/view.php?id=2251<br />
* performance issues in the qMRMLModel<br />
* Are the nightly builds incremental or are they fresh rebuilds? We should trigger a fresh rebuild for the dcmtk change.<br />
* skullstripper installation<br />
*itkv4<br />
* http://www.na-mic.org/Bug/view.php?id=1537<br />
* libGL.so.1 error<br />
* Is the intermediate file problem with EMSegmenter test resolved ?<br />
<br />
== Conclusion ==</div>Pohlhttps://www.slicer.org/w/index.php?title=Developer_Meetings/20120724&diff=27672Developer Meetings/201207242012-07-24T20:19:43Z<p>Pohl: /* To discuss */</p>
<hr />
<div>Attendees: <br />
<br />
== To discuss ==<br />
* Jc: Traveling for the coming 3 weeks<br />
* Is <code>vtkSlicerROILogic</code> still used ? See https://github.com/Slicer/Slicer/blob/master/Base/Logic/vtkSlicerROILogic.h<br />
* Python libraries for extension vtk logic (only on mac?)<br />
** extensions testing with python scripts See http://www.na-mic.org/Bug/view.php?id=2251<br />
* performance issues in the qMRMLModel<br />
* Are the nightly builds incremental or are they fresh rebuilds? We should trigger a fresh rebuild for the dcmtk change.<br />
* skullstripper installation<br />
*itkv4<br />
* http://www.na-mic.org/Bug/view.php?id=1537<br />
<br />
== Conclusion ==</div>Pohlhttps://www.slicer.org/w/index.php?title=Documentation/4.0&diff=23719Documentation/4.02011-12-12T17:41:51Z<p>Pohl: /* Segmentation */</p>
<hr />
<div>__NOTOC__<br />
<br />
<!-- TODO: Create a template that will list all documentation links --><br />
<small><span class="versionlist">[[Documentation/4.0|4.0]] [[Documentation/3.6|3.6]] [[Documentation/3.5|3.5]] [[Documentation/3.4|3.4]] [[Documentation/3.2|3.2]] [[Documentation|ALL VERSIONS]]</span></small><br />
<br />
=Table of Content=<br />
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"<br />
|-<br />
! width="33%"|<br />
! |<br />
! width="33%"|<br />
! |<br />
! width="33%"|<br />
|- <br />
|valign="top"|<br />
<br />
===Slicer Application===<br />
----<br />
*[[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI| Main Application GUI]]<br />
<br />
*[[Documentation/{{documentation/version}}/SlicerApplication/KeyboardShortcuts | "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak)<br />
<br />
*[[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration | Computer configurations]]<br />
*[[Documentation/{{documentation/version}}/SlicerApplication/LoadingData | Loading]] or [[Documentation/{{documentation/version}}/SlicerApplication/SavingData | Saving]] data and listing of [[Documentation/{{documentation/version}}/SlicerApplication/SupportedDataFormat | supported data formats]]. (Julien Finet)<br />
<!-- : scenes, DICOM, volumes, models, fiducials, transforms, etc. --><br />
<br />
*[[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]]<br />
<br />
===Mailing Lists===<br />
----<br />
* [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users Mailing list for users]<br />
:[http://slicer-users.65878.n3.nabble.com/ Search] in archives on nabble.com<br />
* [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-devel Mailing list for developers]<br />
:[http://slicer-devel.65872.n3.nabble.com/ Search] in archives on nabble.com<br />
<br />
<!--<br />
*[[Modules:ExtensionsManagementWizard-Documentation-4.0| Extensions Management Wizard]] (xx)<br />
--><br />
<br />
|bgcolor="#CCCCCC"|<br />
|valign="top"|<br />
<br />
===Module Categories ===<br />
----<br />
* [[#Core Modules|Core Modules]]<br />
* [[#Wizards|Wizards]]<br />
* [[#Informatics|Informatics]]<br />
* [[#Registration|Registration]]<br />
* [[#Segmentation|Segmentation]]<br />
* [[#Quantification|Quantification]]<br />
* [[#Diffusion|Diffusion]]<br />
* [[#IGT|IGT]]<br />
* [[#Filtering|Filtering]]<br />
* [[#Surface Models|Surface Models]]<br />
* [[#Converters|Converters]]<br />
* [[#Endoscopy|Endoscopy]]<br />
* [[#Developer Tools|Developer Tools]]<br />
* [[#Legacy|Legacy]]<br />
|bgcolor="#CCCCCC"|<br />
|valign="top"|<br />
<br />
===Miscellaneous===<br />
----<br />
<!-- * [[Documentation/{{documentation/version}}/ImageGallery|Image gallery]] --><br />
<br />
* [[Slicer4:VisualBlog|Visual blog]]<br />
: Set of screenshots showing Slicer in action.<br />
<br />
<!--<br />
* [[Documents and links]]<br />
: Set of presentations made on Slicer and document talking about it.<br />
<br />
--><br />
* [[Documentation/4.0/Training|Training pages]]<br />
: Information on how to use Slicer {{documentation/version}}<br />
<br />
* [[Documentation/{{documentation/version}}/FAQ|FAQ]]<br />
: Set of common questions/answers<br />
<br />
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes]]<br />
: Platform specific issues and considerations<br />
<br />
===Developers Corner===<br />
----<br />
* [[Documentation/{{documentation/version}}/Developers | Developers Information]]<br />
: Handy Developer Info<br />
|}<br />
<br />
=General Information=<br />
{|width="100%"<br />
|rowspan="3"|<br />
{{Infobox<br />
|name = 3D Slicer {{documentation/version}}<br />
|above = 3D Slicer<br />
|abovestyle = <br />
<br />
|image = [[File:3DSlicer4Logo-H-218X144.png|218px|alt=3D Slicer {{documentation/version}}]]<br />
|imagestyle = <br />
|headerstyle = background:#E7DCC3;<br />
|labelstyle = <br />
|datastyle = <br />
<br />
|header1 = Description<br />
|label1 = <br />
|data1 =<br />
|header2 =<br />
|label2 = <br />
|data2 = Research platform for the analysis and visualization of medical images, including image guided therapy.<br />
|header3 =<br />
|label3 = <br />
|data3 = Free and extensible open source package.<br />
|header4 =<br />
|label4 = Multi-platform<br />
|data4 = Linux, MacOSX, Windows<br />
|header5 =<br />
|label5 = Version<br />
|data5 = {{documentation/version}}<br />
|header6 =<br />
|label6 = License<br />
|data6 = [http://www.slicer.org/pages/LicenseText Contribution and Software License Agreement]<br />
}}<br />
|align="center"|<br />
[[{{collaborator|logo|slicer4}}|x350px]] <br />
|-<br />
|<br />
{{ombox<br />
|type=content<br />
|text=The {{documentation/version}} release of 3D Slicer contains significant changes both to the organization of the software and to the functionality. Please check the [[Documentation/{{documentation/version}}/Announcements | Announcement]] page for more details. The community contributing to Slicer {{documentation/version}} is acknowledged [http://www.slicer.org/pages/Acknowledgments here].<br />
}}<br />
|-<br />
|<br />
{{ombox | text = For information on how to obtain Slicer {{documentation/version}} please go to the [[Snapshots|Download Pages]]. }}<br />
|}<br />
<br />
=Modules by Category=<br />
==Core Modules==<br />
*[[Documentation/{{documentation/version}}/Modules/Annotations|Annotations]] (Nicole Aucoin) <br />
*[[Documentation/{{documentation/version}}/Modules/Colors|Colors]] (Nicole Aucoin) <br />
*[[Documentation/{{documentation/version}}/Modules/Data|Data]] (Julien Finet)<br />
*[[Documentation/{{documentation/version}}/Modules/DICOM|DICOM]] (Steve Pieper)<br />
*[[Documentation/{{documentation/version}}/Modules/Editor|Editor]] (Steve Pieper)<br />
*[[Documentation/{{documentation/version}}/Modules/Models|Models]] (Nicole Aucoin)<br />
*[[Documentation/{{documentation/version}}/Modules/SceneViews|SceneViews]] (Nicole Aucoin) <br />
*[[Documentation/{{documentation/version}}/Modules/Transforms|Transforms]] (Alex Yarmarkovich) <br />
*[[Documentation/{{documentation/version}}/Modules/ViewControllers|View Controllers]] (Jim Miller) <br />
*[[Documentation/{{documentation/version}}/Modules/Volumes|Volumes]] (Steve Pieper)<br />
*[[Documentation/{{documentation/version}}/Modules/VolumeRendering|Volume Rendering]] (Julien Finet)<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerWelcome|Welcome to Slicer]] (Wendy Plesniak)<br />
<br />
==Wizards==<br />
*[[Documentation/{{documentation/version}}/Modules/ChangeTracker|ChangeTracker]] (Andrey Fedorov)<br />
<br />
==Informatics==<br />
*[[Documentation/{{documentation/version}}/Modules/SampleData|Sample Data]] (Steve Pieper)<br />
<br />
==Registration==<br />
*[[Documentation/4.0/Modules/BRAINSFit|General Brainsfit Registration]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/BRAINSResample|Resample Image (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]<br />
*Specialized<br />
**[[Documentation/4.0/Modules/ACPCTransform|ACPC Transform]] (Nicole Aucoin)<br />
**[[Documentation/4.0/Modules/BRAINSDemonWarp|Demon Registration (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/TransformFromFiducials|Fiducial Registration (BRAINS)]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]<br />
**Vector Demon Registration (Hans Johnson)<br />
<br />
==Segmentation==<br />
*[[Documentation/4.0/Modules/EMSegment Easy|EMSegment Easy (no atlas)]] (Kilian Pohl) <br />
*[[Documentation/4.0/Modules/EMSegmenter|EMSegment (with atlas)]] (Kilian Pohl) <br />
*[[Documentation/4.0/Modules/Simple Region Growing|Simple Region Growing]] (Jim Miller, Harini Veeraraghavan) <br />
*Specialized<br />
**[[Documentation/4.0/Modules/EMSegment Command-line | EMSegment Command-line]] (Kilian Pohl)<br />
**[[Documentation/4.0/Modules/ForegroundMasking|Foreground Masking (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/MeshContourSegmentation|Mesh Contour Segmentation]] (Allen Tannenbaum) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/RobustStatisticsSegmenter|Robust Statistics Segmentation]] (Yi Gao)<br />
<br />
==Quantification==<br />
*[[Documentation/{{documentation/version}}/Modules/DataProbe|Data Probe]] (Steve Pieper)<br />
*[[Documentation/4.0/Modules/LabelStatistics|Label Statistics]] (Steve Pieper)<br />
*[[Documentation/4.0/Modules/SUVComputation|SUV Computation]] (Nicole Aucoin)<br />
* Change quantification<br />
** [[Documentation/4.0/Modules/IntensityDifferenceMetric|Intensity Difference Metric]] (Andrey Fedorov)<br />
<br />
==Diffusion== <br />
*DWI to Full Brain Tractography (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
*Denoising<br />
**Joint Rician LMMSE Image Filter (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**Rician LMMSE Image Filter (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
*Tractography<br />
**[[Documentation/4.0/Modules/TractographyDisplay|Tractography Display]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/TractographyFiducialSeeding|Tractography Fiducial Seeding]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/Seeding|Tractography Labelmap Seeding]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
*Utilities<br />
**[[Documentation/4.0/Modules/DiffusionTensorEstimation|Diffusion Tensor Estimation]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/DiffusionTensorMathematics|Diffusion Tensor Scalar Measurements]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/DiffusionWeightedMasking|Mask from Diffusion Weighted Images]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/ResampleDTI|Resample DTI Volume]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
==IGT==<br />
<br />
==Filtering==<br />
*[[Documentation/4.0/Modules/N4ITKBiasFieldCorrection | N4ITK Bias Field Correction]] (Andrey Fedorov)<br />
*[[Documentation/4.0/Modules/CheckerBoard|CheckerBoard]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/ExtractSkeleton|Extract Skeleton]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/HistogramMatching|Histogram Matching]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/ImageLabelCombine|Image Label Combine]] (Alex Yarmarkovich) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/ResampleScalarVectorDWIVolume|Resample Scalar/Vector/DWI Volume]] (Francois Budin) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/Threshold|Threshold Image]] (Nicole Aucoin) <br />
*[[Documentation/4.0/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*Resample Tools<br />
**[[Documentation/4.0/Modules/ResampleVolume|Resample Volume]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*Arithmetic <br />
**[[Documentation/4.0/Modules/Add| Add Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/Cast| Cast Image]] (Nicole Aucoin) <br />
**[[Documentation/4.0/Modules/Mask| Mask Image]] (Nicole Aucoin) <br />
**[[Documentation/4.0/Modules/Multiply| Multiply Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/Subtract| Subtract Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*Denoising<br />
**[[Documentation/4.0/Modules/GradientAnisotropicDiffusion |Gradient Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]] <br />
**[[Documentation/4.0/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/GaussianBlurImageFilter|Gaussian Blur]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/MedianImageFilter|Median Image Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*Morphology<br />
**[[Documentation/4.0/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole]] (Jim Miller)<br />
**[[Documentation/4.0/Modules/GrayscaleGrindPeakImageFilter|Grayscale Grind Peak]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
==Surface Models==<br />
*[[Documentation/4.0/Modules/GrayscaleModelMaker| Grayscale Model Maker]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*Label Map Smoothing<br />
*[[Documentation/4.0/Modules/MergeModels| Merge Models]] (Nicole Aucoin) <br />
*[[Documentation/4.0/Modules/ModelMaker| Model Maker]] (Nicole Aucoin) <br />
*[[Documentation/4.0/Modules/PolyDataToLabelmap| PolyData To LabelMap]] (Nicole Aucoin) <br />
*[[Documentation/4.0/Modules/ProbeVolumeWithModel| Probe Volume with Model (Paint)]] (Lauren O'Donnell) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
==Converters==<br />
*[[Documentation/4.0/Modules/ImageReadDicomWrite|Create Dicom Series]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/Crop Volume|Crop Volume]] (Andrey Fedorov)<br />
*[[Documentation/4.0/Modules/DicomToNrrdConverter|Dicom to Nrrd Converter]] (Jim Miller) <br />
*[[Documentation/4.0/Modules/OrientImage| Orient Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
==Endoscopy==<br />
*[[Documentation/4.0/Modules/Endoscopy|Endoscopy]] (Steve Pieper)<br />
<br />
==Developer Tools==<br />
*[[Documentation/4.0/Modules/Cameras|Cameras]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/EventBroker|Event Broker]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/ExecutionModelTour |Execution Model Tour]] (JC Fillion-Robin) [[image:UnderConstruction.png|tumb|10px]]<br />
*Module Template<br />
*Multiple Models Example<br />
*Performance Tests<br />
*Tractography<br />
<br />
==Legacy==<br />
*Converters<br />
**BSpline to Deformation Field<br />
*Diffusion<br />
**Denoising<br />
***Unbiased Non Local Means Filter for DWI<br />
*Filtering<br />
**[[Documentation/4.0/Modules/MRIBiasFieldCorrection|MRI Bias Field Correction]] (Sylvain Jaume) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/OtsuThresholdImageFilter|Otsu Threshold]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]<br />
**Resample Scalar Volume<br />
*Registration<br />
**[[Documentation/4.0/Modules/RigidRegistration|Rigid Registration]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/AffineRegistration|Affine Registration]] (Daniel Blezek) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/BSplineDeformableRegistration|Nonrigid BSpline Registration]] [[image:UnderConstruction.png|tumb|10px]]<br />
**Nonrigid BSpline Registration<br />
**Expert Automated Registration<br />
**[[Documentation/4.0/Modules/LinearRegistration|Linear Registration]] [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/TestGridTransformRegistration|Test Grid Transform Registration]] [[image:UnderConstruction.png|tumb|10px]]<br />
**Robust Multiresolution Affine Registration<br />
*Segmentation<br />
**[[Documentation/4.0/Modules/OtsuThresholdSegmentation|Otsu Threshold Segmentation]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
=Extensions=<br />
<br />
'''Introduction'''<br />
<br />
* Slicer Extensions are the "on-ramp" to the Slicer "highway". slicer Extensions provide a voluntary mechanism for anybody, including third parties, to extend the functionality of 3d Slicer.<br />
* While the '''Slicer license''' is suggested for extensions, it is '''not required'''. Please review the documentation of the extension carefully as some extensions might have a "non-Slicer" license.<br />
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. <br />
* In case of problems with extensions, please talk directly to the developers of the extensions.<br />
* Information for developers can be found [[Slicer4:Extensions|here]]. See [[Module:EndUserDocumentationTemplate-4.0|here]] for the end-user documentation template.<br />
* In Slicer 4, all new modules will begin as "Immature Extensions". They will progress to the status of "Mature Extensions", when they meet all the criteria listed below. In order to become part of the main Slicer distribution a discussion with the Slicer core team will have to be initiated after reaching the mature extension status. While extensions can be made available under many licenses, the main Slicer distribution will contain ONLY code under the slicer license, with no known IP liabilities.<br />
<br />
==Collections==<br />
Collections are groups of extensions that can be downloaded in a single operation. You can think of them as the equivalent to a playlist.<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
! id<br />
! Thumbnail<br />
! Name<br />
! Short Description<br />
! Maturity<br />
! Slicer License<br />
! Search terms<br />
! Contact Information<br />
|-<br />
| 1<br />
| [[Image:Slicervmtk logo.png|60px|lleft|Replace the image with your image, replace the generic documentation link with a link to your documentation|link=Module:EndUserDocumentationTemplate-4.0]] <br />
| MyCollection<br />
| This is a collection of extensions that will do something miraculous with your images<br />
| [[File:StableExtensionIcon.png|80px]]<br />
| [[File:SlicerLicenseIcon.png|80px]]<br />
| segmentation, level set<br />
| my-email at mit.edu<br />
|-<br />
|}<br />
<br />
<br />
<br />
<br />
==Table Of Extensions==<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
! id<br />
! Thumbnail<br />
! Name<br />
! Short Description<br />
! Maturity<br />
! Slicer License<br />
! Search terms<br />
! Contact Information<br />
|-<br />
| 1<br />
| [[Image:SkullStripperSurface-3-6.png|60px|lleft|Replace the image with your image, replace the generic documentation linke with a link to your documentation|link=Module:EndUserDocumentationTemplate-4.0]] <br />
| MyExtension<br />
| This is an extension that will do something wonderful with your data<br />
| [[File:ExperimentalExtensionIcon.png|80px]]<br />
| [[File:NoSlicerLicenseIcon.png|80px]]<br />
| filter, anisotropic<br />
| my-email at gmail.com<br />
|-<br />
| 2<br />
| [[Image:Slicervmtk logo.png|60px|lleft|Replace the image with your image, replace the generic documentation linke with a link to your documentation|link=Module:EndUserDocumentationTemplate-4.0]] <br />
| MyExtension<br />
| This is an extension that will do something miraculous with your images<br />
| [[File:StableExtensionIcon.png|80px]]<br />
| [[File:SlicerLicenseIcon.png|80px]]<br />
| segmentation, level set<br />
| my-email at mit.edu<br />
|-<br />
|}<br />
<br />
<br />
<br />
'''Caption for the table of extensions'''<br />
<gallery heights="50px" perrow="4"><br />
Image:SlicerLicenseIcon.png| Distributed under the [http://www.slicer.org/pages/LicenseText Slicer License]<br />
Image:NoSlicerLicenseIcon.png| Distributed under a Non Slicer License<br />
Image:ExperimentalExtensionIcon.png|Work in progress (aka mess)<br>Use with care<br>Might not work all the time<br>Might not be available for all platforms<br />
Image:StableExtensionIcon.png|Stable <br>Full documentation <br>Works as advertised <br>Compiles on all supported platforms<br>Email support works<br />
</gallery></div>Pohlhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/EMSegment_Command-line&diff=23717Documentation/4.0/Modules/EMSegment Command-line2011-12-12T17:40:39Z<p>Pohl: moved Documentation/4.0/EMSegment Command-line to Documentation/4.0/Modules/EMSegment Command-line:&#32;otherwise automatic templates do not work</p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work was funded by the ARRA Supplement to the Neuroimage Analysis Center (NAC), funded by the National Institutes of Health. Information on NAC can be obtained from the [http://nac.spl.harvard.edu/pages/Overview NAC website].<br><br />
Author: Kilian Pohl, UPenn <br><br />
Contributor1: Daniel Haehn, UPENN<br><br />
Contact: Kilian Pohl, <email>pohl.kilian@gmail.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:UPenn-logo.png|University of Pennsylvania<br />
|Image:Logo-splnew.jpg|Surgical Planning Laboratory <br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
{{documentation/{{documentation/version}}/module-description|xmlurl=http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/EMSegment/CommandLineApplication/EMSegmentCommandLine.xml?revision=16924&view=co}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
<br />
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.<br />
<br />
This module is especially appropriate for segmenting large quantity of data by scripted/batch processing. It requires predefined parameter set, and new target/atlas images can be specified on command line. A list of predefined task is given [[ EMSegmenter-Tasks | here]]. <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
These slides and data describe the Slicer3 implementation of all three EMSegment modules and demonstrate their use.<br />
<br />
[[Media:EMSegTutorial-AHM2008.ppt | Slides]] - [[Media:EMSegTutorial-AHM2008.zip | Data]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
A list of all the panels in the interface, their features, what they mean, and how to use them. For instance:<br />
<br />
{{documentation/{{documentation/version}}/module-parametersdescription|xmlurl=http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/EMSegment/CommandLineApplication/EMSegmentCommandLine.xml?revision=16924&view=co}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
Pohl K, Bouix S, Nakamura M, Rohlfing T, McCarley R, Kikinis R, Grimson W, Shenton M, Wells W. [http://www.slicer.org/pages/Special:PubDB_View?dspaceid=608 A Hierarchical Algorithm for MR Brain Image Parcellation.] IEEE Transactions on Medical Imaging. 2007 Sept;26(9):1201-1212. <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|{{documentation/modulename}}|type=CLI|category=<br />
{{documentation/{{documentation/version}}/module-category| xmlurl=http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/EMSegment/CommandLineApplication/EMSegmentCommandLine.xml?revision=16924&view=co}}<br />
}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=<br />
{{documentation/{{documentation/version}}/module-category|<br />
xmlurl=http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/EMSegment/CommandLineApplication/EMSegmentCommandLine.xml?revision=16924&view=co}}<br />
}}<br />
<br />
<!-- ---------------------------- --></div>Pohlhttps://www.slicer.org/w/index.php?title=Documentation/4.0/EMSegment_Command-line&diff=23718Documentation/4.0/EMSegment Command-line2011-12-12T17:40:39Z<p>Pohl: moved Documentation/4.0/EMSegment Command-line to Documentation/4.0/Modules/EMSegment Command-line:&#32;otherwise automatic templates do not work</p>
<hr />
<div>#REDIRECT [[Documentation/4.0/Modules/EMSegment Command-line]]</div>Pohlhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/EMSegment_Command-line&diff=23693Documentation/4.0/Modules/EMSegment Command-line2011-12-11T20:19:11Z<p>Pohl: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work was funded by the ARRA Supplement to the Neuroimage Analysis Center (NAC), funded by the National Institutes of Health. Information on NAC can be obtained from the [http://nac.spl.harvard.edu/pages/Overview NAC website].<br><br />
Author: Kilian Pohl, UPenn <br><br />
Contributor1: Daniel Haehn, UPENN<br><br />
Contact: Kilian Pohl, <email>pohl.kilian@gmail.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:UPenn-logo.png|University of Pennsylvania<br />
|Image:Logo-splnew.jpg|Surgical Planning Laboratory <br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
{{documentation/{{documentation/version}}/module-description|xmlurl=http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/EMSegment/CommandLineApplication/EMSegmentCommandLine.xml?revision=16924&view=co}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
<br />
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.<br />
<br />
This module is especially appropriate for segmenting large quantity of data by scripted/batch processing. It requires predefined parameter set, and new target/atlas images can be specified on command line. A list of predefined task is given [[ EMSegmenter-Tasks | here]]. <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
These slides and data describe the Slicer3 implementation of all three EMSegment modules and demonstrate their use.<br />
<br />
[[Media:EMSegTutorial-AHM2008.ppt | Slides]] - [[Media:EMSegTutorial-AHM2008.zip | Data]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
A list of all the panels in the interface, their features, what they mean, and how to use them. For instance:<br />
<br />
{{documentation/{{documentation/version}}/module-parametersdescription|xmlurl=http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/EMSegment/CommandLineApplication/EMSegmentCommandLine.xml?revision=16924&view=co}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
Pohl K, Bouix S, Nakamura M, Rohlfing T, McCarley R, Kikinis R, Grimson W, Shenton M, Wells W. [http://www.slicer.org/pages/Special:PubDB_View?dspaceid=608 A Hierarchical Algorithm for MR Brain Image Parcellation.] IEEE Transactions on Medical Imaging. 2007 Sept;26(9):1201-1212. <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|{{documentation/modulename}}|type=CLI|category=<br />
{{documentation/{{documentation/version}}/module-category| xmlurl=http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/EMSegment/CommandLineApplication/EMSegmentCommandLine.xml?revision=16924&view=co}}<br />
}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=<br />
{{documentation/{{documentation/version}}/module-category|<br />
xmlurl=http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/EMSegment/CommandLineApplication/EMSegmentCommandLine.xml?revision=16924&view=co}}<br />
}}<br />
<br />
<!-- ---------------------------- --></div>Pohlhttps://www.slicer.org/w/index.php?title=Documentation/4.0&diff=23692Documentation/4.02011-12-11T20:14:11Z<p>Pohl: /* Segmentation */</p>
<hr />
<div>__NOTOC__<br />
<br />
<!-- TODO: Create a template that will list all documentation links --><br />
<small><span class="versionlist">[[Documentation/4.0|4.0]] [[Documentation/3.6|3.6]] [[Documentation/3.5|3.5]] [[Documentation/3.4|3.4]] [[Documentation/3.2|3.2]] [[Documentation|ALL VERSIONS]]</span></small><br />
<br />
=Table of Content=<br />
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"<br />
|-<br />
! width="33%"|<br />
! |<br />
! width="33%"|<br />
! |<br />
! width="33%"|<br />
|- <br />
|valign="top"|<br />
<br />
===Slicer Application===<br />
----<br />
*[[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI| Main Application GUI]]<br />
<br />
*[[Documentation/{{documentation/version}}/SlicerApplication/KeyboardShortcuts | "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak)<br />
<br />
*[[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration | Computer configurations]]<br />
*[[Documentation/{{documentation/version}}/SlicerApplication/LoadingData | Loading]] or [[Documentation/{{documentation/version}}/SlicerApplication/SavingData | Saving]] data and listing of [[Documentation/{{documentation/version}}/SlicerApplication/SupportedDataFormat | supported data formats]]. (Julien Finet)<br />
<!-- : scenes, DICOM, volumes, models, fiducials, transforms, etc. --><br />
<br />
*[[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]]<br />
<br />
===Mailing Lists===<br />
----<br />
* [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users Mailing list for users]<br />
:[http://slicer-users.65878.n3.nabble.com/ Search] in archives on nabble.com<br />
* [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-devel Mailing list for developers]<br />
:[http://slicer-devel.65872.n3.nabble.com/ Search] in archives on nabble.com<br />
<br />
<!--<br />
*[[Modules:ExtensionsManagementWizard-Documentation-4.0| Extensions Management Wizard]] (xx)<br />
--><br />
<br />
|bgcolor="#CCCCCC"|<br />
|valign="top"|<br />
<br />
===Module Categories ===<br />
----<br />
* [[#Core Modules|Core Modules]]<br />
* [[#Wizards|Wizards]]<br />
* [[#Informatics|Informatics]]<br />
* [[#Registration|Registration]]<br />
* [[#Segmentation|Segmentation]]<br />
* [[#Quantification|Quantification]]<br />
* [[#Diffusion|Diffusion]]<br />
* [[#IGT|IGT]]<br />
* [[#Filtering|Filtering]]<br />
* [[#Surface Models|Surface Models]]<br />
* [[#Converters|Converters]]<br />
* [[#Endoscopy|Endoscopy]]<br />
* [[#Developer Tools|Developer Tools]]<br />
* [[#Legacy|Legacy]]<br />
|bgcolor="#CCCCCC"|<br />
|valign="top"|<br />
<br />
===Miscellaneous===<br />
----<br />
<!-- * [[Documentation/{{documentation/version}}/ImageGallery|Image gallery]] --><br />
<br />
* [[Slicer4:VisualBlog|Visual blog]]<br />
: Set of screenshots showing Slicer in action.<br />
<br />
<!--<br />
* [[Documents and links]]<br />
: Set of presentations made on Slicer and document talking about it.<br />
<br />
--><br />
* [[Documentation/4.0/Training|Training pages]]<br />
: Information on how to use Slicer {{documentation/version}}<br />
<br />
* [[Documentation/{{documentation/version}}/FAQ|FAQ]]<br />
: Set of common questions/answers<br />
<br />
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes]]<br />
: Platform specific issues and considerations<br />
<br />
===Developers Corner===<br />
----<br />
* [[Documentation/{{documentation/version}}/Developers | Developers Information]]<br />
: Handy Developer Info<br />
|}<br />
<br />
=General Information=<br />
{|width="100%"<br />
|rowspan="3"|<br />
{{Infobox<br />
|name = 3D Slicer {{documentation/version}}<br />
|above = 3D Slicer<br />
|abovestyle = <br />
<br />
|image = [[File:3DSlicer4Logo-H-218X144.png|218px|alt=3D Slicer {{documentation/version}}]]<br />
|imagestyle = <br />
|headerstyle = background:#E7DCC3;<br />
|labelstyle = <br />
|datastyle = <br />
<br />
|header1 = Description<br />
|label1 = <br />
|data1 =<br />
|header2 =<br />
|label2 = <br />
|data2 = Research platform for the analysis and visualization of medical images, including image guided therapy.<br />
|header3 =<br />
|label3 = <br />
|data3 = Free and extensible open source package.<br />
|header4 =<br />
|label4 = Multi-platform<br />
|data4 = Linux, MacOSX, Windows<br />
|header5 =<br />
|label5 = Version<br />
|data5 = {{documentation/version}}<br />
|header6 =<br />
|label6 = License<br />
|data6 = [http://www.slicer.org/pages/LicenseText Contribution and Software License Agreement]<br />
}}<br />
|align="center"|<br />
[[{{collaborator|logo|slicer4}}|x350px]] <br />
|-<br />
|<br />
{{ombox<br />
|type=content<br />
|text=The {{documentation/version}} release of 3D Slicer contains significant changes both to the organization of the software and to the functionality. Please check the [[Documentation/{{documentation/version}}/Announcements | Announcement]] page for more details. The community contributing to Slicer {{documentation/version}} is acknowledged [http://www.slicer.org/pages/Acknowledgments here].<br />
}}<br />
|-<br />
|<br />
{{ombox | text = For information on how to obtain Slicer {{documentation/version}} please go to the [[Snapshots|Download Pages]]. }}<br />
|}<br />
<br />
=Modules by Category=<br />
==Core Modules==<br />
*[[Documentation/{{documentation/version}}/Modules/Annotations|Annotations]] (Nicole Aucoin) <br />
*[[Documentation/{{documentation/version}}/Modules/Colors|Colors]] (Nicole Aucoin) <br />
*[[Documentation/{{documentation/version}}/Modules/Data|Data]] (Julien Finet)<br />
*[[Documentation/{{documentation/version}}/Modules/DICOM|DICOM]] (Steve Pieper)<br />
*[[Documentation/{{documentation/version}}/Modules/Editor|Editor]] (Steve Pieper)<br />
*[[Documentation/{{documentation/version}}/Modules/Models|Models]] (Nicole Aucoin)<br />
*[[Documentation/{{documentation/version}}/Modules/SceneViews|SceneViews]] (Nicole Aucoin) <br />
*[[Documentation/{{documentation/version}}/Modules/Transforms|Transforms]] (Alex Yarmarkovich) <br />
*[[Documentation/{{documentation/version}}/Modules/ViewControllers|View Controllers]] (Jim Miller) <br />
*[[Documentation/{{documentation/version}}/Modules/Volumes|Volumes]] (Steve Pieper)<br />
*[[Documentation/{{documentation/version}}/Modules/VolumeRendering|Volume Rendering]] (Julien Finet)<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerWelcome|Welcome to Slicer]] (Wendy Plesniak)<br />
<br />
==Wizards==<br />
*[[Documentation/{{documentation/version}}/Modules/ChangeTracker|ChangeTracker]] (Andrey Fedorov)<br />
<br />
==Informatics==<br />
*[[Documentation/{{documentation/version}}/Modules/SampleData|Sample Data]] (Steve Pieper)<br />
<br />
==Registration==<br />
*[[Documentation/4.0/Modules/BRAINSFit|General Brainsfit Registration]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/BRAINSResample|Resample Image (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]<br />
*Specialized<br />
**[[Documentation/4.0/Modules/ACPCTransform|ACPC Transform]] (Nicole Aucoin)<br />
**[[Documentation/4.0/Modules/BRAINSDemonWarp|Demon Registration (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/TransformFromFiducials|Fiducial Registration (BRAINS)]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]<br />
**Vector Demon Registration (Hans Johnson)<br />
<br />
==Segmentation==<br />
*[[Documentation/4.0/Modules/EMSegment Easy|EMSegment Easy (no atlas)]] (Kilian Pohl) <br />
*[[Documentation/4.0/Modules/EMSegmenter|EMSegment (with atlas)]] (Kilian Pohl) <br />
*[[Documentation/4.0/Modules/Simple Region Growing|Simple Region Growing]] (Jim Miller, Harini Veeraraghavan) <br />
*Specialized<br />
**[[Documentation/4.0/EMSegment Command-line | EMSegment Command-line]] (Kilian Pohl)<br />
**[[Documentation/4.0/Modules/ForegroundMasking|Foreground Masking (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/MeshContourSegmentation|Mesh Contour Segmentation]] (Allen Tannenbaum) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/RobustStatisticsSegmenter|Robust Statistics Segmentation]] (Yi Gao)<br />
<br />
==Quantification==<br />
*[[Documentation/{{documentation/version}}/Modules/DataProbe|Data Probe]] (Steve Pieper)<br />
*[[Documentation/4.0/Modules/LabelStatistics|Label Statistics]] (Steve Pieper)<br />
*[[Documentation/4.0/Modules/SUVComputation|SUV Computation]] (Nicole Aucoin)<br />
* Change quantification<br />
** [[Documentation/4.0/Modules/IntensityDifferenceMetric|Intensity Difference Metric]] (Andrey Fedorov)<br />
<br />
==Diffusion== <br />
*DWI to Full Brain Tractography (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
*Denoising<br />
**Joint Rician LMMSE Image Filter (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**Rician LMMSE Image Filter (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
*Tractography<br />
**[[Documentation/4.0/Modules/TractographyDisplay|Tractography Display]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/TractographyFiducialSeeding|Tractography Fiducial Seeding]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/Seeding|Tractography Labelmap Seeding]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
*Utilities<br />
**[[Documentation/4.0/Modules/DiffusionTensorEstimation|Diffusion Tensor Estimation]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/DiffusionTensorMathematics|Diffusion Tensor Scalar Measurements]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/DiffusionWeightedMasking|Mask from Diffusion Weighted Images]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/ResampleDTI|Resample DTI Volume]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
==IGT==<br />
<br />
==Filtering==<br />
*[[Documentation/4.0/Modules/N4ITKBiasFieldCorrection | N4ITK Bias Field Correction]] (Andrey Fedorov)<br />
*[[Documentation/4.0/Modules/CheckerBoard|CheckerBoard]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/ExtractSkeleton|Extract Skeleton]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/HistogramMatching|Histogram Matching]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/ImageLabelCombine|Image Label Combine]] (Alex Yarmarkovich) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/ResampleScalarVectorDWIVolume|Resample Scalar/Vector/DWI Volume]] (Francois Budin) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/Threshold|Threshold Image]] (Nicole Aucoin) <br />
*[[Documentation/4.0/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*Resample Tools<br />
**[[Documentation/4.0/Modules/ResampleVolume|Resample Volume]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*Arithmetic <br />
**[[Documentation/4.0/Modules/Add| Add Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/Cast| Cast Image]] (Nicole Aucoin) <br />
**[[Documentation/4.0/Modules/Mask| Mask Image]] (Nicole Aucoin) <br />
**[[Documentation/4.0/Modules/Multiply| Multiply Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/Subtract| Subtract Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*Denoising<br />
**[[Documentation/4.0/Modules/GradientAnisotropicDiffusion |Gradient Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]] <br />
**[[Documentation/4.0/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/GaussianBlurImageFilter|Gaussian Blur]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/MedianImageFilter|Median Image Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*Morphology<br />
**[[Documentation/4.0/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole]] (Jim Miller)<br />
**[[Documentation/4.0/Modules/GrayscaleGrindPeakImageFilter|Grayscale Grind Peak]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
==Surface Models==<br />
*[[Documentation/4.0/Modules/GrayscaleModelMaker| Grayscale Model Maker]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*Label Map Smoothing<br />
*[[Documentation/4.0/Modules/MergeModels| Merge Models]] (Nicole Aucoin) <br />
*[[Documentation/4.0/Modules/ModelMaker| Model Maker]] (Nicole Aucoin) <br />
*[[Documentation/4.0/Modules/PolyDataToLabelmap| PolyData To LabelMap]] (Nicole Aucoin) <br />
*[[Documentation/4.0/Modules/ProbeVolumeWithModel| Probe Volume with Model (Paint)]] (Lauren O'Donnell) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
==Converters==<br />
*[[Documentation/4.0/Modules/ImageReadDicomWrite|Create Dicom Series]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/Crop Volume|Crop Volume]] (Andrey Fedorov)<br />
*[[Documentation/4.0/Modules/DicomToNrrdConverter|Dicom to Nrrd Converter]] (Jim Miller) <br />
*[[Documentation/4.0/Modules/OrientImage| Orient Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
==Endoscopy==<br />
*[[Documentation/4.0/Modules/Endoscopy|Endoscopy]] (Steve Pieper)<br />
<br />
==Developer Tools==<br />
*[[Documentation/4.0/Modules/Cameras|Cameras]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/EventBroker|Event Broker]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/ExecutionModelTour |Execution Model Tour]] (JC Fillion-Robin) [[image:UnderConstruction.png|tumb|10px]]<br />
*Module Template<br />
*Multiple Models Example<br />
*Performance Tests<br />
*Tractography<br />
<br />
==Legacy==<br />
*Converters<br />
**BSpline to Deformation Field<br />
*Diffusion<br />
**Denoising<br />
***Unbiased Non Local Means Filter for DWI<br />
*Filtering<br />
**[[Documentation/4.0/Modules/MRIBiasFieldCorrection|MRI Bias Field Correction]] (Sylvain Jaume) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/OtsuThresholdImageFilter|Otsu Threshold]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]<br />
**Resample Scalar Volume<br />
*Registration<br />
**[[Documentation/4.0/Modules/RigidRegistration|Rigid Registration]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/AffineRegistration|Affine Registration]] (Daniel Blezek) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/BSplineDeformableRegistration|Nonrigid BSpline Registration]] [[image:UnderConstruction.png|tumb|10px]]<br />
**Nonrigid BSpline Registration<br />
**Expert Automated Registration<br />
**[[Documentation/4.0/Modules/LinearRegistration|Linear Registration]] [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/TestGridTransformRegistration|Test Grid Transform Registration]] [[image:UnderConstruction.png|tumb|10px]]<br />
**Robust Multiresolution Affine Registration<br />
*Segmentation<br />
**[[Documentation/4.0/Modules/OtsuThresholdSegmentation|Otsu Threshold Segmentation]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
=Extensions=<br />
<br />
'''Introduction'''<br />
<br />
* Slicer Extensions are the "on-ramp" to the Slicer "highway". slicer Extensions provide a voluntary mechanism for anybody, including third parties, to extend the functionality of 3d Slicer.<br />
* While the '''Slicer license''' is suggested for extensions, it is '''not required'''. Please review the documentation of the extension carefully as some extensions might have a "non-Slicer" license.<br />
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. <br />
* In case of problems with extensions, please talk directly to the developers of the extensions.<br />
* Information for developers can be found [[Slicer4:Extensions|here]]. See [[Module:EndUserDocumentationTemplate-4.0|here]] for the end-user documentation template.<br />
* In Slicer 4, all new modules will begin as "Immature Extensions". They will progress to the status of "Mature Extensions", when they meet all the criteria listed below. In order to become part of the main Slicer distribution a discussion with the Slicer core team will have to be initiated after reaching the mature extension status. While extensions can be made available under many licenses, the main Slicer distribution will contain ONLY code under the slicer license, with no known IP liabilities.<br />
<br />
==Collections==<br />
Collections are groups of extensions that can be downloaded in a single operation. You can think of them as the equivalent to a playlist.<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
! id<br />
! Thumbnail<br />
! Name<br />
! Short Description<br />
! Maturity<br />
! Slicer License<br />
! Search terms<br />
! Contact Information<br />
|-<br />
| 1<br />
| [[Image:Slicervmtk logo.png|60px|lleft|Replace the image with your image, replace the generic documentation link with a link to your documentation|link=Module:EndUserDocumentationTemplate-4.0]] <br />
| MyCollection<br />
| This is a collection of extensions that will do something miraculous with your images<br />
| [[File:StableExtensionIcon.png|80px]]<br />
| [[File:SlicerLicenseIcon.png|80px]]<br />
| segmentation, level set<br />
| my-email at mit.edu<br />
|-<br />
|}<br />
<br />
<br />
<br />
<br />
==Table Of Extensions==<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
! id<br />
! Thumbnail<br />
! Name<br />
! Short Description<br />
! Maturity<br />
! Slicer License<br />
! Search terms<br />
! Contact Information<br />
|-<br />
| 1<br />
| [[Image:SkullStripperSurface-3-6.png|60px|lleft|Replace the image with your image, replace the generic documentation linke with a link to your documentation|link=Module:EndUserDocumentationTemplate-4.0]] <br />
| MyExtension<br />
| This is an extension that will do something wonderful with your data<br />
| [[File:ExperimentalExtensionIcon.png|80px]]<br />
| [[File:NoSlicerLicenseIcon.png|80px]]<br />
| filter, anisotropic<br />
| my-email at gmail.com<br />
|-<br />
| 2<br />
| [[Image:Slicervmtk logo.png|60px|lleft|Replace the image with your image, replace the generic documentation linke with a link to your documentation|link=Module:EndUserDocumentationTemplate-4.0]] <br />
| MyExtension<br />
| This is an extension that will do something miraculous with your images<br />
| [[File:StableExtensionIcon.png|80px]]<br />
| [[File:SlicerLicenseIcon.png|80px]]<br />
| segmentation, level set<br />
| my-email at mit.edu<br />
|-<br />
|}<br />
<br />
<br />
<br />
'''Caption for the table of extensions'''<br />
<gallery heights="50px" perrow="4"><br />
Image:SlicerLicenseIcon.png| Distributed under the [http://www.slicer.org/pages/LicenseText Slicer License]<br />
Image:NoSlicerLicenseIcon.png| Distributed under a Non Slicer License<br />
Image:ExperimentalExtensionIcon.png|Work in progress (aka mess)<br>Use with care<br>Might not work all the time<br>Might not be available for all platforms<br />
Image:StableExtensionIcon.png|Stable <br>Full documentation <br>Works as advertised <br>Compiles on all supported platforms<br>Email support works<br />
</gallery></div>Pohlhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/EMSegment_Command-line&diff=23691Documentation/4.0/Modules/EMSegment Command-line2011-12-11T20:13:00Z<p>Pohl: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work was funded by the ARRA Supplement to the Neuroimage Analysis Center (NAC), funded by the National Institutes of Health. Information on NAC can be obtained from the [http://nac.spl.harvard.edu/pages/Overview NAC website].<br><br />
Author: Kilian Pohl, UPenn <br><br />
Contributor1: Daniel Haehn, UPENN<br><br />
Contact: Kilian Pohl, <email>pohl.kilian@gmail.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:UPenn-logo.png|University of Pennsylvania<br />
|Image:Logo-splnew.jpg|Surgical Planning Laboratory <br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
{{documentation/{{documentation/version}}/module-description|xmlurl=http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/EMSegment/CommandLineApplication/EMSegmentCommandLine.xml?revision=16924&view=co}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
<br />
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.<br />
<br />
This module is especially appropriate for segmenting large quantity of data by scripted/batch processing. It requires predefined parameter set, and new target/atlas images can be specified on command line. A list of predefined task is given [[ EMSegmenter-Tasks | here]]. <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
These slides and data describe the Slicer3 implementation of all three EMSegment modules and demonstrate their use.<br />
<br />
[[Media:EMSegTutorial-AHM2008.ppt | Slides]] - [[Media:EMSegTutorial-AHM2008.zip | Data]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
A list of all the panels in the interface, their features, what they mean, and how to use them. For instance:<br />
<br />
{{documentation/{{documentation/version}}/module-parametersdescription|xmlurl=http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/EMSegment/CommandLineApplication/EMSegmentCommandLine.xml?revision=16924&view=co}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
Pohl K, Bouix S, Nakamura M, Rohlfing T, McCarley R, Kikinis R, Grimson W, Shenton M, Wells W. [http://www.slicer.org/pages/Special:PubDB_View?dspaceid=608 A Hierarchical Algorithm for MR Brain Image Parcellation.] IEEE Transactions on Medical Imaging. 2007 Sept;26(9):1201-1212. <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|{{documentation/modulename}}|type=CLI|category=<br />
{{documentation/{{documentation/version}}/module-category| xmlurl=http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/EMSegment/CommandLineApplication/EMSegmentCommandLine.xml?revision=16924&view=co}}<br />
}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=<br />
{{documentation/{{documentation/version}}/module-category|<br />
xmlurl=http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/EMSegment/CommandLineApplication/EMSegmentCommandLine.xml?revision=16924&view=co}}<br />
}}</div>Pohlhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/EMSegment_Command-line&diff=23689Documentation/4.0/Modules/EMSegment Command-line2011-12-11T19:59:39Z<p>Pohl: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work was funded by the ARRA Supplement to the Neuroimage Analysis Center (NAC), funded by the National Institutes of Health. Information on NAC can be obtained from the [http://nac.spl.harvard.edu/pages/Overview NAC website].<br><br />
Author: Kilian Pohl, UPenn <br><br />
Contributor1: Daniel Haehn, UPENN<br><br />
Contact: Kilian Pohl, <email>pohl.kilian@gmail.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:UPenn-logo.png|University of Pennsylvania<br />
|Image:Logo-splnew.jpg|Surgical Planning Laboratory <br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
{{documentation/{{documentation/version}}/module-description|xmlurl=http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/EMSegment/CommandLineApplication/EMSegmentCommandLine.xml?revision=16914&view=co}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
<br />
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.<br />
<br />
This module is especially appropriate for segmenting large quantity of data by scripted/batch processing. It requires predefined parameter set, and new target/atlas images can be specified on command line. A list of predefined task is given [[ EMSegmenter-Tasks | here]]. <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
These slides and data describe the Slicer3 implementation of all three EMSegment modules and demonstrate their use.<br />
<br />
[[Media:EMSegTutorial-AHM2008.ppt | Slides]] - [[Media:EMSegTutorial-AHM2008.zip | Data]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
A list of all the panels in the interface, their features, what they mean, and how to use them. For instance:<br />
<br />
{{documentation/{{documentation/version}}/module-parametersdescription|xmlurl=http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/EMSegment/CommandLineApplication/EMSegmentCommandLine.xml?revision=16914&view=co}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
Pohl K, Bouix S, Nakamura M, Rohlfing T, McCarley R, Kikinis R, Grimson W, Shenton M, Wells W. [http://www.slicer.org/pages/Special:PubDB_View?dspaceid=608 A Hierarchical Algorithm for MR Brain Image Parcellation.] IEEE Transactions on Medical Imaging. 2007 Sept;26(9):1201-1212. <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|{{documentation/modulename}}|type=CLI|category=<br />
{{documentation/{{documentation/version}}/module-category| xmlurl=http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/EMSegment/CommandLineApplication/EMSegmentCommandLine.xml?revision=16914&view=co}}<br />
}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=<br />
{{documentation/{{documentation/version}}/module-category|<br />
xmlurl=http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/EMSegment/CommandLineApplication/EMSegmentCommandLine.xml?revision=16914&view=co}}<br />
}}</div>Pohlhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/EMSegment_Command-line&diff=23688Documentation/4.0/Modules/EMSegment Command-line2011-12-11T19:42:05Z<p>Pohl: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work was funded by the ARRA Supplement to the Neuroimage Analysis Center (NAC), funded by the National Institutes of Health. Information on NAC can be obtained from the [http://nac.spl.harvard.edu/pages/Overview NAC website].<br><br />
Author: Kilian Pohl, UPenn <br><br />
Contributor1: Daniel Haehn, UPENN<br><br />
Contact: Kilian Pohl, <email>pohl.kilian@gmail.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:UPenn-logo.png|University of Pennsylvania<br />
|Image:Logo-splnew.jpg|Surgical Planning Laboratory <br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
{{documentation/{{documentation/version}}/module-description|xmlurl=http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/EMSegment/CommandLineApplication/EMSegmentCommandLine.xml?revision=16914&view=co}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
<br />
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.<br />
<br />
This module is especially appropriate for segmenting large quantity of data by scripted/batch processing. It requires predefined parameter set, and new target/atlas images can be specified on command line. A list of predefined task is given [[ EMSegmenter-Tasks | here]]. <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
These slides and data describe the Slicer3 implementation of all three EMSegment modules and demonstrate their use.<br />
<br />
[[Media:EMSegTutorial-AHM2008.ppt | Slides]] - [[Media:EMSegTutorial-AHM2008.zip | Data]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
A list of all the panels in the interface, their features, what they mean, and how to use them. For instance:<br />
<br />
{|style="width: 100%"<br />
|<br />
* Input panel1:<br />
** First input<br />
** Second input<br />
* Parameters panel:<br />
** First parameter<br />
** Second parameter<br />
* Output panel:<br />
** First output<br />
** Second output<br />
* Viewing panel:<br />
| align="right" |<br />
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 1]]<br />
|-<br />
|<br />
* Input panel2:<br />
** First input<br />
** Second input<br />
* Parameters panel:<br />
** First parameter<br />
** Second parameter<br />
* Output panel:<br />
** First output<br />
** Second output<br />
* Viewing panel:<br />
| align="right" |<br />
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 2]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
* Point to other modules that have similar functionality<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
Publications related to this module go here. Links to pdfs would be useful.<br />
For extensions: link to the source code repository and additional documentation<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
{{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
If you are documenting a CLI, the category should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-category|xmlurl=http://path/to/YOURMODULENAME.xml }}</pre><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Pohlhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/EMSegment_Command-line&diff=23687Documentation/4.0/Modules/EMSegment Command-line2011-12-11T19:39:28Z<p>Pohl: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work was funded by the ARRA Supplement to the Neuroimage Analysis Center (NAC), funded by the National Institutes of Health. Information on NAC can be obtained from the [http://nac.spl.harvard.edu/pages/Overview NAC website].<br><br />
Author: Kilian Pohl, UPenn <br><br />
Contributor1: Daniel Haehn, UPENN<br><br />
Contact: Kilian Pohl, <email>pohl.kilian@gmail.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:UPenn-logo.png|University of Pennsylvania<br />
|Image:Logo-splnew.jpg|Surgical Planning Laboratory <br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
{{documentation/{{documentation/version}}/module-description|xmlurl=http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/EMSegment/CommandLineApplication/EMSegmentCommandLine.xml?revision=16914&view=co}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
<br />
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.<br />
<br />
This module is especially appropriate for segmenting large quantity of data by scripted/batch processing. It requires predefined parameter set, and new target/atlas images can be specified on command line. A list of predefined task is given [ Modules:EMSegment-Command-Line3.6 here]. <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
These slides and data describe the Slicer3 implementation of all three EMSegment modules and demonstrate their use.<br />
<br />
[[Media:EMSegTutorial-AHM2008.ppt | Slides]] - [[Media:EMSegTutorial-AHM2008.zip | Data]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
A list of all the panels in the interface, their features, what they mean, and how to use them. For instance:<br />
<br />
{|style="width: 100%"<br />
|<br />
* Input panel1:<br />
** First input<br />
** Second input<br />
* Parameters panel:<br />
** First parameter<br />
** Second parameter<br />
* Output panel:<br />
** First output<br />
** Second output<br />
* Viewing panel:<br />
| align="right" |<br />
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 1]]<br />
|-<br />
|<br />
* Input panel2:<br />
** First input<br />
** Second input<br />
* Parameters panel:<br />
** First parameter<br />
** Second parameter<br />
* Output panel:<br />
** First output<br />
** Second output<br />
* Viewing panel:<br />
| align="right" |<br />
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 2]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
* Point to other modules that have similar functionality<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
Publications related to this module go here. Links to pdfs would be useful.<br />
For extensions: link to the source code repository and additional documentation<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
{{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
If you are documenting a CLI, the category should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-category|xmlurl=http://path/to/YOURMODULENAME.xml }}</pre><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Pohlhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/EMSegment_Command-line&diff=23686Documentation/4.0/Modules/EMSegment Command-line2011-12-11T19:30:53Z<p>Pohl: /* Use Cases, Examples, Tutorials */</p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work was funded by the ARRA Supplement to the Neuroimage Analysis Center (NAC), funded by the National Institutes of Health. Information on NAC can be obtained from the [http://nac.spl.harvard.edu/pages/Overview NAC website].<br><br />
Author: Kilian Pohl, UPenn <br><br />
Contributor1: Daniel Haehn, UPENN<br><br />
Contact: Kilian Pohl, <email>pohl.kilian@gmail.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:UPenn-logo.png|University of Pennsylvania<br />
|Image:Logo-splnew.jpg|Surgical Planning Laboratory <br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
{{documentation/{{documentation/version}}/module-description|xmlurl=http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/EMSegment/CommandLineApplication/EMSegmentCommandLine.xml?revision=16914&view=co}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
<br />
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.<br />
<br />
This module is especially appropriate for segmenting large quantity of data by scripted/batch processing. It requires predefined parameter set, and new target/atlas images can be specified on command line.<br />
<br />
* A full Tutorial for all three EMSegment modules<br />
<br />
These slides and data describe the Slicer3 implementation of all three EMSegment modules and demonstrate their use. A recent (later than 7Jan08) version of Slicer3 is required to run the test data.<br />
<br />
[[Media:EMSegTutorial-AHM2008.ppt | Slides]] - [[Media:EMSegTutorial-AHM2008.zip | Data]]<br />
<br />
* Export EMSEG_TUTORIAL_DIR environment variable ( e.g. <PATH TO TUTORIAL> = /tmp/EMSegmentTutorial-Jan2008/ ) <br />
export EMSEG_TUTORIAL_DIR=<PATH_TO_TUTORIAL><br />
<br />
===Quick Tour of Features and Use===<br />
<br />
The above EMSegment tutorial data set demonstrates the use of the command line interface. <br />
<br />
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]]<br />
# MRML Scene: Select the mrml scene for the tutorial parameter set<br />
# Result Labelmap: Select a new image filename for output labelmap<br />
# Target Volumes: Select input target volumes (Multiple files can be selected at one time)<br />
# Click `Apply’<br />
<br />
Here are some basic examples to run this module from command line directly<br />
<br />
* Export the Slicer3_HOME environment variable ( e.g. <PATH_TO_SLICER> = /tmp/3DSlicer/Slicer3-build/ )<br />
export Slicer3_HOME=<PATH_TO_SLICER><br />
<br />
* Run the executable to see the documentation<br />
${Slicer3_HOME}/Slicer3 --launch $Slicer3_HOME/lib/Slicer3/Plugins/EMSegmentCommandLine --help<br />
<br />
* Run the segmentation algorithm with tutorial data<br />
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.<br />
<br />
source ${Slicer3_HOME}/bin/Slicer3SetupPaths.sh<br />
RUN_NAME=BrainTutorial-Defaults<br />
mkdir -p $EMSEG_TUTORIAL_DIR/Working/$RUN_NAME<br />
${Slicer3_HOME}/Slicer3 --launch $Slicer3_HOME/lib/Slicer3/Plugins/EMSegmentCommandLine \<br />
--verbose \<br />
--mrmlSceneFileName $EMSEG_TUTORIAL_DIR/EMSeg-Brain-MRT1T2.mrml \<br />
--intermediateResultsDirectory $EMSEG_TUTORIAL_DIR/Working/$RUN_NAME \<br />
--resultVolumeFileName $EMSEG_TUTORIAL_DIR/VolumeData_Output/Segmentation-$RUN_NAME.nhdr \<br />
<br />
* Run the segmentation algorithm with new data<br />
The other script, "BrainTutorial-SetTarget1.sh" demonstrate how to run the EMSegmenter on new<br />
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).<br />
<br />
source ${Slicer3_HOME}/bin/Slicer3SetupPaths.sh<br />
RUN_NAME=BrainTutorial-SetTarget<br />
mkdir -p $EMSEG_TUTORIAL_DIR/Working/$RUN_NAME<br />
${Slicer3_HOME}/Slicer3 --launch $Slicer3_HOME/lib/Slicer3/Plugins/EMSegmentCommandLine \<br />
--verbose \<br />
--mrmlSceneFileName $EMSEG_TUTORIAL_DIR/EMSeg-Brain-MRT1T2.mrml \<br />
--targetVolumeFileNames \<br />
$EMSEG_TUTORIAL_DIR/VolumeData_Input/Target/t1.nhdr,$EMSEG_TUTORIAL_DIR/VolumeData_Input/Target/t2.nhdr \<br />
--resultVolumeFileName \<br />
VolumeData_Output/Segmentation-$RUN_NAME.nhdr \<br />
--intermediateResultsDirectory \<br />
$EMSEG_TUTORIAL_DIR/Working/$RUN_NAME \<br />
<br />
* Run the MRI-Human-Brain task<br />
<br />
source ${Slicer3_HOME}/bin/Slicer3SetupPaths.sh<br />
${Slicer3_HOME}/Slicer3 --launch $Slicer3_HOME/lib/Slicer3/Plugins/EMSegmentCommandLine \<br />
--verbose \<br />
--mrmlSceneFileName \<br />
$Slicer3_HOME/share/Slicer3/Modules/EMSegment/Tasks/MRI-Human-Brain.mrml \<br />
--targetVolumeFileNames \<br />
$Slicer3_HOME/../Slicer3/Modules/EMSegment/Testing/TestData/MiscVolumeData/MRIHumanBrain_T1_aligned.nrrd \<br />
--resultVolumeFileName \<br />
/tmp/Result_MRI-Human-Brain.nhdr \<br />
<br />
Most frequently used for these scenarios:<br />
<br />
<br />
<br />
* Use Case 1:<br />
* Use Case 2:<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
Links to tutorials that use this module<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
A list of all the panels in the interface, their features, what they mean, and how to use them. For instance:<br />
<br />
{|style="width: 100%"<br />
|<br />
* Input panel1:<br />
** First input<br />
** Second input<br />
* Parameters panel:<br />
** First parameter<br />
** Second parameter<br />
* Output panel:<br />
** First output<br />
** Second output<br />
* Viewing panel:<br />
| align="right" |<br />
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 1]]<br />
|-<br />
|<br />
* Input panel2:<br />
** First input<br />
** Second input<br />
* Parameters panel:<br />
** First parameter<br />
** Second parameter<br />
* Output panel:<br />
** First output<br />
** Second output<br />
* Viewing panel:<br />
| align="right" |<br />
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 2]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
* Point to other modules that have similar functionality<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
Publications related to this module go here. Links to pdfs would be useful.<br />
For extensions: link to the source code repository and additional documentation<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
{{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
If you are documenting a CLI, the category should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-category|xmlurl=http://path/to/YOURMODULENAME.xml }}</pre><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Pohlhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/EMSegment_Command-line&diff=23685Documentation/4.0/Modules/EMSegment Command-line2011-12-11T19:30:11Z<p>Pohl: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work was funded by the ARRA Supplement to the Neuroimage Analysis Center (NAC), funded by the National Institutes of Health. Information on NAC can be obtained from the [http://nac.spl.harvard.edu/pages/Overview NAC website].<br><br />
Author: Kilian Pohl, UPenn <br><br />
Contributor1: Daniel Haehn, UPENN<br><br />
Contact: Kilian Pohl, <email>pohl.kilian@gmail.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:UPenn-logo.png|University of Pennsylvania<br />
|Image:Logo-splnew.jpg|Surgical Planning Laboratory <br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
{{documentation/{{documentation/version}}/module-description|xmlurl=http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/EMSegment/CommandLineApplication/EMSegmentCommandLine.xml?revision=16914&view=co}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
<br />
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.<br />
<br />
===Use Cases, Examples, Tutorials===<br />
<br />
This module is especially appropriate for segmenting large quantity of data by scripted/batch processing. It requires predefined parameter set, and new target/atlas images can be specified on command line.<br />
<br />
* A full Tutorial for all three EMSegment modules<br />
<br />
These slides and data describe the Slicer3 implementation of all three EMSegment modules and demonstrate their use. A recent (later than 7Jan08) version of Slicer3 is required to run the test data.<br />
<br />
[[Media:EMSegTutorial-AHM2008.ppt | Slides]] - [[Media:EMSegTutorial-AHM2008.zip | Data]]<br />
<br />
* Export EMSEG_TUTORIAL_DIR environment variable ( e.g. <PATH TO TUTORIAL> = /tmp/EMSegmentTutorial-Jan2008/ ) <br />
export EMSEG_TUTORIAL_DIR=<PATH_TO_TUTORIAL><br />
<br />
===Quick Tour of Features and Use===<br />
<br />
The above EMSegment tutorial data set demonstrates the use of the command line interface. <br />
<br />
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]]<br />
# MRML Scene: Select the mrml scene for the tutorial parameter set<br />
# Result Labelmap: Select a new image filename for output labelmap<br />
# Target Volumes: Select input target volumes (Multiple files can be selected at one time)<br />
# Click `Apply’<br />
<br />
Here are some basic examples to run this module from command line directly<br />
<br />
* Export the Slicer3_HOME environment variable ( e.g. <PATH_TO_SLICER> = /tmp/3DSlicer/Slicer3-build/ )<br />
export Slicer3_HOME=<PATH_TO_SLICER><br />
<br />
* Run the executable to see the documentation<br />
${Slicer3_HOME}/Slicer3 --launch $Slicer3_HOME/lib/Slicer3/Plugins/EMSegmentCommandLine --help<br />
<br />
* Run the segmentation algorithm with tutorial data<br />
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.<br />
<br />
source ${Slicer3_HOME}/bin/Slicer3SetupPaths.sh<br />
RUN_NAME=BrainTutorial-Defaults<br />
mkdir -p $EMSEG_TUTORIAL_DIR/Working/$RUN_NAME<br />
${Slicer3_HOME}/Slicer3 --launch $Slicer3_HOME/lib/Slicer3/Plugins/EMSegmentCommandLine \<br />
--verbose \<br />
--mrmlSceneFileName $EMSEG_TUTORIAL_DIR/EMSeg-Brain-MRT1T2.mrml \<br />
--intermediateResultsDirectory $EMSEG_TUTORIAL_DIR/Working/$RUN_NAME \<br />
--resultVolumeFileName $EMSEG_TUTORIAL_DIR/VolumeData_Output/Segmentation-$RUN_NAME.nhdr \<br />
<br />
* Run the segmentation algorithm with new data<br />
The other script, "BrainTutorial-SetTarget1.sh" demonstrate how to run the EMSegmenter on new<br />
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).<br />
<br />
source ${Slicer3_HOME}/bin/Slicer3SetupPaths.sh<br />
RUN_NAME=BrainTutorial-SetTarget<br />
mkdir -p $EMSEG_TUTORIAL_DIR/Working/$RUN_NAME<br />
${Slicer3_HOME}/Slicer3 --launch $Slicer3_HOME/lib/Slicer3/Plugins/EMSegmentCommandLine \<br />
--verbose \<br />
--mrmlSceneFileName $EMSEG_TUTORIAL_DIR/EMSeg-Brain-MRT1T2.mrml \<br />
--targetVolumeFileNames \<br />
$EMSEG_TUTORIAL_DIR/VolumeData_Input/Target/t1.nhdr,$EMSEG_TUTORIAL_DIR/VolumeData_Input/Target/t2.nhdr \<br />
--resultVolumeFileName \<br />
VolumeData_Output/Segmentation-$RUN_NAME.nhdr \<br />
--intermediateResultsDirectory \<br />
$EMSEG_TUTORIAL_DIR/Working/$RUN_NAME \<br />
<br />
* Run the MRI-Human-Brain task<br />
<br />
source ${Slicer3_HOME}/bin/Slicer3SetupPaths.sh<br />
${Slicer3_HOME}/Slicer3 --launch $Slicer3_HOME/lib/Slicer3/Plugins/EMSegmentCommandLine \<br />
--verbose \<br />
--mrmlSceneFileName \<br />
$Slicer3_HOME/share/Slicer3/Modules/EMSegment/Tasks/MRI-Human-Brain.mrml \<br />
--targetVolumeFileNames \<br />
$Slicer3_HOME/../Slicer3/Modules/EMSegment/Testing/TestData/MiscVolumeData/MRIHumanBrain_T1_aligned.nrrd \<br />
--resultVolumeFileName \<br />
/tmp/Result_MRI-Human-Brain.nhdr \<br />
<br />
Most frequently used for these scenarios:<br />
<br />
<br />
<br />
* Use Case 1:<br />
* Use Case 2:<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
Links to tutorials that use this module<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
A list of all the panels in the interface, their features, what they mean, and how to use them. For instance:<br />
<br />
{|style="width: 100%"<br />
|<br />
* Input panel1:<br />
** First input<br />
** Second input<br />
* Parameters panel:<br />
** First parameter<br />
** Second parameter<br />
* Output panel:<br />
** First output<br />
** Second output<br />
* Viewing panel:<br />
| align="right" |<br />
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 1]]<br />
|-<br />
|<br />
* Input panel2:<br />
** First input<br />
** Second input<br />
* Parameters panel:<br />
** First parameter<br />
** Second parameter<br />
* Output panel:<br />
** First output<br />
** Second output<br />
* Viewing panel:<br />
| align="right" |<br />
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 2]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
* Point to other modules that have similar functionality<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
Publications related to this module go here. Links to pdfs would be useful.<br />
For extensions: link to the source code repository and additional documentation<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
{{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
If you are documenting a CLI, the category should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-category|xmlurl=http://path/to/YOURMODULENAME.xml }}</pre><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Pohlhttps://www.slicer.org/w/index.php?title=Documentation/4.0&diff=23681Documentation/4.02011-12-10T16:31:03Z<p>Pohl: /* Utilities */</p>
<hr />
<div>__NOTOC__<br />
<br />
<!-- TODO: Create a template that will list all documentation links --><br />
<small><span class="versionlist">[[Documentation/4.0|4.0]] [[Documentation/3.6|3.6]] [[Documentation/3.5|3.5]] [[Documentation/3.4|3.4]] [[Documentation/3.2|3.2]] [[Documentation|ALL VERSIONS]]</span></small><br />
<br />
=Table of Content=<br />
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"<br />
|-<br />
! width="33%"|<br />
! |<br />
! width="33%"|<br />
! |<br />
! width="33%"|<br />
|- <br />
|valign="top"|<br />
<br />
===Slicer Application===<br />
----<br />
*[[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI| Main Application GUI]]<br />
<br />
*[[Documentation/{{documentation/version}}/SlicerApplication/KeyboardShortcuts | "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak)<br />
<br />
*[[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration | Computer configurations]]<br />
*[[Documentation/{{documentation/version}}/SlicerApplication/LoadingData | Loading]] or [[Documentation/{{documentation/version}}/SlicerApplication/SavingData | Saving]] data and listing of [[Documentation/{{documentation/version}}/SlicerApplication/SupportedDataFormat | supported data formats]]. (Julien Finet)<br />
<!-- : scenes, DICOM, volumes, models, fiducials, transforms, etc. --><br />
<br />
*[[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]]<br />
<br />
===Mailing Lists===<br />
----<br />
* [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users Mailing list for users]<br />
:[http://slicer-users.65878.n3.nabble.com/ Search] in archives on nabble.com<br />
* [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-devel Mailing list for developers]<br />
:[http://slicer-devel.65872.n3.nabble.com/ Search] in archives on nabble.com<br />
<br />
<!--<br />
*[[Modules:ExtensionsManagementWizard-Documentation-4.0| Extensions Management Wizard]] (xx)<br />
--><br />
<br />
|bgcolor="#CCCCCC"|<br />
|valign="top"|<br />
<br />
===Module Categories ===<br />
----<br />
* [[#Core Modules|Core Modules]]<br />
* [[#Wizards|Wizards]]<br />
* [[#Informatics|Informatics]]<br />
* [[#Registration|Registration]]<br />
* [[#Segmentation|Segmentation]]<br />
* [[#Quantification|Quantification]]<br />
* [[#Diffusion|Diffusion]]<br />
* [[#IGT|IGT]]<br />
* [[#Filtering|Filtering]]<br />
* [[#Surface Models|Surface Models]]<br />
* [[#Converters|Converters]]<br />
* [[#Endoscopy|Endoscopy]]<br />
* [[#Developer Tools|Developer Tools]]<br />
* [[#Legacy|Legacy]]<br />
* [[#Utilities|Utility]]<br />
|bgcolor="#CCCCCC"|<br />
|valign="top"|<br />
<br />
===Miscellaneous===<br />
----<br />
<!-- * [[Documentation/{{documentation/version}}/ImageGallery|Image gallery]] --><br />
<br />
* [[Slicer4:VisualBlog|Visual blog]]<br />
: Set of screenshots showing Slicer in action.<br />
<br />
<!--<br />
* [[Documents and links]]<br />
: Set of presentations made on Slicer and document talking about it.<br />
<br />
--><br />
* [[Documentation/4.0/Training|Training pages]]<br />
: Information on how to use Slicer {{documentation/version}}<br />
<br />
* [[Documentation/{{documentation/version}}/FAQ|FAQ]]<br />
: Set of common questions/answers<br />
<br />
* [[Documentation/{{documentation/version}}/ReleaseNotes|Release Notes]]<br />
: Platform specific issues and considerations<br />
<br />
===Developers Corner===<br />
----<br />
* [[Documentation/{{documentation/version}}/Developers | Developers Information]]<br />
: Handy Developer Info<br />
|}<br />
<br />
=General Information=<br />
{|width="100%"<br />
|rowspan="3"|<br />
{{Infobox<br />
|name = 3D Slicer {{documentation/version}}<br />
|above = 3D Slicer<br />
|abovestyle = <br />
<br />
|image = [[File:3DSlicer4Logo-H-218X144.png|218px|alt=3D Slicer {{documentation/version}}]]<br />
|imagestyle = <br />
|headerstyle = background:#E7DCC3;<br />
|labelstyle = <br />
|datastyle = <br />
<br />
|header1 = Description<br />
|label1 = <br />
|data1 =<br />
|header2 =<br />
|label2 = <br />
|data2 = Research platform for the analysis and visualization of medical images, including image guided therapy.<br />
|header3 =<br />
|label3 = <br />
|data3 = Free and extensible open source package.<br />
|header4 =<br />
|label4 = Multi-platform<br />
|data4 = Linux, MacOSX, Windows<br />
|header5 =<br />
|label5 = Version<br />
|data5 = {{documentation/version}}<br />
|header6 =<br />
|label6 = License<br />
|data6 = [http://www.slicer.org/pages/LicenseText Contribution and Software License Agreement]<br />
}}<br />
|align="center"|<br />
[[{{collaborator|logo|slicer4}}|x350px]] <br />
|-<br />
|<br />
{{ombox<br />
|type=content<br />
|text=The {{documentation/version}} release of 3D Slicer contains significant changes both to the organization of the software and to the functionality. Please check the [[Documentation/{{documentation/version}}/Announcements | Announcement]] page for more details. The community contributing to Slicer {{documentation/version}} is acknowledged [http://www.slicer.org/pages/Acknowledgments here].<br />
}}<br />
|-<br />
|<br />
{{ombox | text = For information on how to obtain Slicer {{documentation/version}} please go to the [[Snapshots|Download Pages]]. }}<br />
|}<br />
<br />
=Modules by Category=<br />
==Core Modules==<br />
*[[Documentation/{{documentation/version}}/Modules/Annotations|Annotations]] (Nicole Aucoin) <br />
*[[Documentation/{{documentation/version}}/Modules/Colors|Colors]] (Nicole Aucoin) <br />
*[[Documentation/{{documentation/version}}/Modules/Data|Data]] (Julien Finet)<br />
*[[Documentation/{{documentation/version}}/Modules/DICOM|DICOM]] (Steve Pieper)<br />
*[[Documentation/{{documentation/version}}/Modules/Editor|Editor]] (Steve Pieper)<br />
*[[Documentation/{{documentation/version}}/Modules/Models|Models]] (Nicole Aucoin)<br />
*[[Documentation/{{documentation/version}}/Modules/SceneViews|SceneViews]] (Nicole Aucoin) <br />
*[[Documentation/{{documentation/version}}/Modules/Transforms|Transforms]] (Alex Yarmarkovich) <br />
*[[Documentation/{{documentation/version}}/Modules/ViewControllers|View Controllers]] (Jim Miller) <br />
*[[Documentation/{{documentation/version}}/Modules/Volumes|Volumes]] (Steve Pieper)<br />
*[[Documentation/{{documentation/version}}/Modules/VolumeRendering|Volume Rendering]] (Julien Finet)<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerWelcome|Welcome to Slicer]] (Wendy Plesniak)<br />
<br />
==Wizards==<br />
*[[Documentation/{{documentation/version}}/Modules/ChangeTracker|ChangeTracker]] (Andrey Fedorov)<br />
<br />
==Informatics==<br />
*[[Documentation/{{documentation/version}}/Modules/SampleData|Sample Data]] (Steve Pieper)<br />
<br />
==Registration==<br />
*[[Documentation/4.0/Modules/BRAINSFit|General Brainsfit Registration]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/BRAINSResample|Resample Image (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]<br />
*Specialized<br />
**[[Documentation/4.0/Modules/ACPCTransform|ACPC Transform]] (Nicole Aucoin)<br />
**[[Documentation/4.0/Modules/BRAINSDemonWarp|Demon Registration (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/TransformFromFiducials|Fiducial Registration (BRAINS)]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]<br />
**Vector Demon Registration (Hans Johnson)<br />
<br />
==Segmentation==<br />
*[[Documentation/4.0/Modules/EMSegment Easy|EMSegment Easy (no atlas)]] (Kilian Pohl) <br />
*[[Documentation/4.0/Modules/EMSegmenter|EMSegment (with atlas)]] (Kilian Pohl) <br />
*[[Documentation/4.0/Modules/Simple Region Growing|Simple Region Growing]] (Jim Miller, Harini Veeraraghavan) <br />
*Specialized<br />
**[[Documentation/4.0/EMSegment Command-line | EMSegment Command-line]] (Kilian Pohl) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/ForegroundMasking|Foreground Masking (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/MeshContourSegmentation|Mesh Contour Segmentation]] (Allen Tannenbaum) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/RobustStatisticsSegmenter|Robust Statistics Segmentation]] (Yi Gao)<br />
<br />
==Quantification==<br />
*[[Documentation/{{documentation/version}}/Modules/DataProbe|Data Probe]] (Steve Pieper)<br />
*[[Documentation/4.0/Modules/LabelStatistics|Label Statistics]] (Steve Pieper)<br />
*[[Documentation/4.0/Modules/SUVComputation|SUV Computation]] (Nicole Aucoin)<br />
* Change quantification<br />
** [[Documentation/4.0/Modules/IntensityDifferenceMetric|Intensity Difference Metric]] (Andrey Fedorov)<br />
<br />
==Diffusion== <br />
*DWI to Full Brain Tractography (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
*Denoising<br />
**Joint Rician LMMSE Image Filter (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**Rician LMMSE Image Filter (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
*Tractography<br />
**[[Documentation/4.0/Modules/TractographyDisplay|Tractography Display]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/TractographyFiducialSeeding|Tractography Fiducial Seeding]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/Seeding|Tractography Labelmap Seeding]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
*Utilities<br />
**[[Documentation/4.0/Modules/DiffusionTensorEstimation|Diffusion Tensor Estimation]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/DiffusionTensorMathematics|Diffusion Tensor Scalar Measurements]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/DiffusionWeightedMasking|Mask from Diffusion Weighted Images]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/ResampleDTI|Resample DTI Volume]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
==IGT==<br />
<br />
==Filtering==<br />
*[[Documentation/4.0/Modules/N4ITKBiasFieldCorrection | N4ITK Bias Field Correction]] (Andrey Fedorov)<br />
*[[Documentation/4.0/Modules/CheckerBoard|CheckerBoard]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/ExtractSkeleton|Extract Skeleton]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/HistogramMatching|Histogram Matching]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/ImageLabelCombine|Image Label Combine]] (Alex Yarmarkovich) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/ResampleScalarVectorDWIVolume|Resample Scalar/Vector/DWI Volume]] (Francois Budin) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/Threshold|Threshold Image]] (Nicole Aucoin) <br />
*[[Documentation/4.0/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*Resample Tools<br />
**[[Documentation/4.0/Modules/ResampleVolume|Resample Volume]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*Arithmetic <br />
**[[Documentation/4.0/Modules/Add| Add Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/Cast| Cast Image]] (Nicole Aucoin) <br />
**[[Documentation/4.0/Modules/Mask| Mask Image]] (Nicole Aucoin) <br />
**[[Documentation/4.0/Modules/Multiply| Multiply Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/Subtract| Subtract Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*Denoising<br />
**[[Documentation/4.0/Modules/GradientAnisotropicDiffusion |Gradient Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]] <br />
**[[Documentation/4.0/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/GaussianBlurImageFilter|Gaussian Blur]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/MedianImageFilter|Median Image Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*Morphology<br />
**[[Documentation/4.0/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole]] (Jim Miller)<br />
**[[Documentation/4.0/Modules/GrayscaleGrindPeakImageFilter|Grayscale Grind Peak]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
==Surface Models==<br />
*[[Documentation/4.0/Modules/GrayscaleModelMaker| Grayscale Model Maker]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*Label Map Smoothing<br />
*[[Documentation/4.0/Modules/MergeModels| Merge Models]] (Nicole Aucoin) <br />
*[[Documentation/4.0/Modules/ModelMaker| Model Maker]] (Nicole Aucoin) <br />
*[[Documentation/4.0/Modules/PolyDataToLabelmap| PolyData To LabelMap]] (Nicole Aucoin) <br />
*[[Documentation/4.0/Modules/ProbeVolumeWithModel| Probe Volume with Model (Paint)]] (Lauren O'Donnell) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
==Converters==<br />
*[[Documentation/4.0/Modules/ImageReadDicomWrite|Create Dicom Series]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/Crop Volume|Crop Volume]] (Andrey Fedorov)<br />
*[[Documentation/4.0/Modules/DicomToNrrdConverter|Dicom to Nrrd Converter]] (Jim Miller) <br />
*[[Documentation/4.0/Modules/OrientImage| Orient Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
==Endoscopy==<br />
*[[Documentation/4.0/Modules/Endoscopy|Endoscopy]] (Steve Pieper)<br />
<br />
==Developer Tools==<br />
*[[Documentation/4.0/Modules/Cameras|Cameras]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/EventBroker|Event Broker]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/ExecutionModelTour |Execution Model Tour]] (JC Fillion-Robin) [[image:UnderConstruction.png|tumb|10px]]<br />
*Module Template<br />
*Multiple Models Example<br />
*Performance Tests<br />
*Tractography<br />
<br />
==Legacy==<br />
*Converters<br />
**BSpline to Deformation Field<br />
*Diffusion<br />
**Denoising<br />
***Unbiased Non Local Means Filter for DWI<br />
*Filtering<br />
**[[Documentation/4.0/Modules/MRIBiasFieldCorrection|MRI Bias Field Correction]] (Sylvain Jaume) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/OtsuThresholdImageFilter|Otsu Threshold]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]<br />
**Resample Scalar Volume<br />
*Registration<br />
**[[Documentation/4.0/Modules/RigidRegistration|Rigid Registration]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/AffineRegistration|Affine Registration]] (Daniel Blezek) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/BSplineDeformableRegistration|Nonrigid BSpline Registration]] [[image:UnderConstruction.png|tumb|10px]]<br />
**Nonrigid BSpline Registration<br />
**Expert Automated Registration<br />
**[[Documentation/4.0/Modules/LinearRegistration|Linear Registration]] [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/TestGridTransformRegistration|Test Grid Transform Registration]] [[image:UnderConstruction.png|tumb|10px]]<br />
**Robust Multiresolution Affine Registration<br />
*Segmentation<br />
**[[Documentation/4.0/Modules/OtsuThresholdSegmentation|Otsu Threshold Segmentation]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
=Extensions=<br />
<br />
'''Introduction'''<br />
<br />
* Slicer Extensions are the "on-ramp" to the Slicer "highway". slicer Extensions provide a voluntary mechanism for anybody, including third parties, to extend the functionality of 3d Slicer.<br />
* While the '''Slicer license''' is suggested for extensions, it is '''not required'''. Please review the documentation of the extension carefully as some extensions might have a "non-Slicer" license.<br />
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. <br />
* In case of problems with extensions, please talk directly to the developers of the extensions.<br />
* Information for developers can be found [[Slicer4:Extensions|here]]. See [[Module:EndUserDocumentationTemplate-4.0|here]] for the end-user documentation template.<br />
* In Slicer 4, all new modules will begin as "Immature Extensions". They will progress to the status of "Mature Extensions", when they meet all the criteria listed below. In order to become part of the main Slicer distribution a discussion with the Slicer core team will have to be initiated after reaching the mature extension status. While extensions can be made available under many licenses, the main Slicer distribution will contain ONLY code under the slicer license, with no known IP liabilities.<br />
<br />
==Collections==<br />
Collections are groups of extensions that can be downloaded in a single operation. You can think of them as the equivalent to a playlist.<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
! id<br />
! Thumbnail<br />
! Name<br />
! Short Description<br />
! Maturity<br />
! Slicer License<br />
! Search terms<br />
! Contact Information<br />
|-<br />
| 1<br />
| [[Image:Slicervmtk logo.png|60px|lleft|Replace the image with your image, replace the generic documentation link with a link to your documentation|link=Module:EndUserDocumentationTemplate-4.0]] <br />
| MyCollection<br />
| This is a collection of extensions that will do something miraculous with your images<br />
| [[File:StableExtensionIcon.png|80px]]<br />
| [[File:SlicerLicenseIcon.png|80px]]<br />
| segmentation, level set<br />
| my-email at mit.edu<br />
|-<br />
|}<br />
<br />
<br />
<br />
<br />
==Table Of Extensions==<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
! id<br />
! Thumbnail<br />
! Name<br />
! Short Description<br />
! Maturity<br />
! Slicer License<br />
! Search terms<br />
! Contact Information<br />
|-<br />
| 1<br />
| [[Image:SkullStripperSurface-3-6.png|60px|lleft|Replace the image with your image, replace the generic documentation linke with a link to your documentation|link=Module:EndUserDocumentationTemplate-4.0]] <br />
| MyExtension<br />
| This is an extension that will do something wonderful with your data<br />
| [[File:ExperimentalExtensionIcon.png|80px]]<br />
| [[File:NoSlicerLicenseIcon.png|80px]]<br />
| filter, anisotropic<br />
| my-email at gmail.com<br />
|-<br />
| 2<br />
| [[Image:Slicervmtk logo.png|60px|lleft|Replace the image with your image, replace the generic documentation linke with a link to your documentation|link=Module:EndUserDocumentationTemplate-4.0]] <br />
| MyExtension<br />
| This is an extension that will do something miraculous with your images<br />
| [[File:StableExtensionIcon.png|80px]]<br />
| [[File:SlicerLicenseIcon.png|80px]]<br />
| segmentation, level set<br />
| my-email at mit.edu<br />
|-<br />
|}<br />
<br />
<br />
<br />
'''Caption for the table of extensions'''<br />
<gallery heights="50px" perrow="4"><br />
Image:SlicerLicenseIcon.png| Distributed under the [http://www.slicer.org/pages/LicenseText Slicer License]<br />
Image:NoSlicerLicenseIcon.png| Distributed under a Non Slicer License<br />
Image:ExperimentalExtensionIcon.png|Work in progress (aka mess)<br>Use with care<br>Might not work all the time<br>Might not be available for all platforms<br />
Image:StableExtensionIcon.png|Stable <br>Full documentation <br>Works as advertised <br>Compiles on all supported platforms<br>Email support works<br />
</gallery></div>Pohlhttps://www.slicer.org/w/index.php?title=EMSegmenter-Overview&diff=23680EMSegmenter-Overview2011-12-10T02:10:32Z<p>Pohl: /* Background */</p>
<hr />
<div>[[File:SlicerEMSegment-Large.png]]<br />
<br />
Overview<br />
=Background=<br />
<br />
* Some background materials: [http://wiki.na-mic.org/Wiki/index.php/EMSegmenter EMSegmenter history]<br />
<br />
*Pohl K, Bouix S, Nakamura M, Rohlfing T, McCarley R, Kikinis R, Grimson W, Shenton M, Wells W. [http://www.slicer.org/pages/Special:PubDB_View?dspaceid=608 A Hierarchical Algorithm for MR Brain Image Parcellation.] IEEE Transactions on Medical Imaging. 2007 Sept;26(9):1201-1212. [[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib]]<br />
<br />
=Documentation=<br />
<br />
{|<br />
|align="left"|<br />
*[[Modules:EMSegmenter-3.6|EM Segmenter 3.6]]<br />
*[[Modules:EMSegment-Command-Line3.6|EM Segment Command-Line 3.6]]<br />
*[[EMSegmenter-Tasks|Library of example solutions]]<br />
*[[EMSegmenter-UseCaseAdvertisement|UseCaseAdvertisement]]<br />
|[[image:Screen Shot 2011-08-04 at 4.39.55 PM.png|400px|right|thumb|See at this link for the [[EMSegmenter-Tasks|library of EM example solutions]]]]<br />
|-<br />
|}<br />
<br />
=Development=<br />
<br />
* [http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerEM ARRA]<br />
* [http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerEM:Developer Slicer4 Development]<br />
* [http://www.slicer.org/slicerWiki/index.php/Slicer4:EMSegment Slicer4 Developer]<br />
* [https://sbia-infr-vweb.uphs.upenn.edu/wiki/index.php/EMSegmenter SBIA internal]<br />
<br />
=FAQ=<br />
<br />
Please send questions to the public mailing list for users of the 3D slicer program.<br />
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users<br />
<br />
=Buglist=<br />
[http://www.na-mic.org/Bug/view_all_bug_page.php Links]to known bugs in the Slicer3 bug tracker. Please expand the search options, select EMSegmenter in the category, and press apply filter<br />
<br />
=Dashboard=<br />
* [http://www.cdash.org/CDash/index.php?project=Slicer3 Slicer3 Dashboard]<br />
* [http://www.cdash.org/CDash/index.php?project=Slicer4 Slicer4 Dashboard]</div>Pohlhttps://www.slicer.org/w/index.php?title=Modules:EMSegmenter-3.6&diff=23679Modules:EMSegmenter-3.62011-12-10T02:09:48Z<p>Pohl: /* References */</p>
<hr />
<div>[[EMSegmenter-Overview|Return to EMSegmenter Overview Page]]<br />
<br />
[[Documentation-3.6|Return to Slicer 3.6 Documentation]]<br />
<br />
[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]<br />
<br />
__NOTOC__<br />
===EMSegmenter===<br />
EMSegmenter<br />
<br />
== General Information ==<br />
===Module Type & Category===<br />
<br />
Type: Interactive <br />
<br />
Category: Segmentation<br />
<br />
===Authors, Collaborators & Contact===<br />
* Daniel Haehn, UPenn<br />
* Dominique Belhachemi, UPenn<br />
* Kilian Pohl: UPenn<br />
* Contact: Kilian Pohl <pohl@csail.mit.edu><br />
<br />
===Module Description===<br />
[[Image:EMSegmenterLogo.png|thumb|width=200px|Hierarchical Model of the EMSegmenter]]<br />
This module is designed for users who perform atlas based medical image segmentation. The module can be operated in <B>two</B> modes: <br><br />
An <B>advanced mode (Button: Adjust Parameters)</B> that allows users to parameterize the tool to specific segmentation tasks and a <B>simple mode (Button: Use Existing Setting)</B> which is designed for users who would like to apply the predefined parameterization to new data with a minimal amount of user interaction. One can also apply the parameterization to medical scans via the command-line executable <B>EMSegmentCommandLine</B>. The remainder of this sections describes the work flow of the two modes in further detail:<br />
<br />
== Usage ==<br />
The purpose of the module is to configure the algorithm to automatically segment anatomical structures in medical images. First the user has to specify parameters defining the image protocol and the anatomical structures of interests. This process results in a template that the module uses to automatically segment large data sets. The template is composed of atlas data and a non-trivial collection of parameters for the EMSegment algorithm. <br />
<br />
Once the parameters are specified, the target images are segmented<br />
using the EM Segmentation algorithm (Pohl et al. TMI 2007). If the results are<br />
satisfactory, the template is saved and can be used later to segment<br />
new images (via the GUI or batch processing). If the results are<br />
unsatisfactory, the parameters can be modified and the segmentation<br />
re-run.<br />
<br />
One important aspect of the project is the workflow wizard. This wizard simplifies the module by dividing the complicated template specification task into a number of smaller, intuitive steps. The wizard allows to [[EMSegmenter-CreateTask|create tasks]] and to use them to analyze data sets.<br />
<br />
There are multiple [[EMSegmenter-Tasks|'''predefined tasks''']] which are ready to use.<br />
<br />
=== Simple Mode ===<br />
The work flow is defined by only two steps.<br />
==== Step 1: Define Task ====<br />
Select an already existing task and click on the "Use Existing Settings" button to use for the simple mode in the pop up window.<br />
A MRML file defining parameters of the algorithm specific to the task as well atlas data are automatically downloaded for existing Tasks.<br />
==== Step 2: Define Input Channels ====<br />
In this step the user specifies the scans to be segmented as well as the check list associated with the preprocessing.<br />
A click on the 'Segment' button is enough to start the pre-processing and the subsequent segmentation.<br />
<br />
=== Advanced Mode ===<br />
Unlike the Simple mode, the advanced mode is defined by nine steps which one can navigate via the "Back", "Next", or "Segment" button. The Segment button jumps right away to the last step of the work flow and segments the medical scans into the structures of interests. <br />
==== Step 1: Define Task ====<br />
Select an already existing task or define a new one. Click on the button "Adjust Parameters" for the advanced mode in the pop up window. A MRML file defining parameters of the algorithm specific to the task as well atlas data are automatically downloaded for existing Tasks.<br />
==== Step 2: Define Input Channel ====<br />
Define the number of input channels as well as the name of each channel and the corresponding scan associated with the channel. If using multiple input channel(scans) which are not aligned with each other then check on the check-box button "Align input scans".<br />
==== Step 3: Define Anatomical Tree ====<br />
The user specifies the hierarchical relationship between the anatomical structures. The tree will refine the complex segmentation task into a set of easier segmentation problems. A sub-classes is added to an existing structure by right-clicking on the structure and selecting "Add sub-class". The name, label, and color of a structure are modified by selecting the structure in the tree and then defining these attributes in the panel below.<br />
==== Step 4: Define Atlas ====<br />
In this step, the user links the probabilistic atlases to the anatomical structures in the tree by first highlighting the structure and then selecting the volume representing the probability map of that structure in the panel below. We note that the probabilistic atlas of structures with sub-structures is defined by the atlases of the sub-structures and thus is not explicitly defined. <br />
==== Step 5: Edit Registration Parameters ====<br />
The atlas is in general not aligned to the specific patient scans defined in Step 2. The user assigns in this step the scans of the atlas corresponding to the input channels in Step 2 as well as the type of registration (Affine / Deformable) and the interpolation. <br />
==== Step 6: Define Preprocessing ==== <br />
[[Image:EMSegmenter_DisplayClassDistribution.png | thumb|width=200px|Graph showing intensity distributions of a set of anatomical structures]] This step is defined via a task specific Tcl file that configures the preprocessing pipeline of the input scans and the atlas. Complete the step by going through the task specific check list, clicking on the 'Next' button, and clicking on the 'Yes' button of the pop up window. One can define a new preprocessing pipeline by specifying the pipeline via a Tcl file, placing the file in Slicer3-build/share/Slicer3/Modules/EMSegment/Tasks and listing the file name in the task specific MRML file.<br />
<br />
==== Step 7: Specify Intensity Distribution ==== <br />
Refining the intensity distribution for each structure of interest is often a critical step in the parameterization of the segmentation algorithm. The panel includes an overview window that shows the distribution in a 1D and 2D graph (press "Plot Distributions" to view the graph). By placing the mouse cursor in the 2D viewers the corresponding intensity value is shown in the graph.<br />
<br />
==== Step 8: Edit Node-based Parameters ====<br />
Users specify the relative to weight of a node in the tree with respect to other structures which are children of the same parent node. The first tab also specifies the weight of the input channels as well as the atlases. The value 'Alpha' specifies the smoothing applied to the structure (via MRFs). The second tab (Stopping Condition) lists the number of iterations associated with the segmentation task. By default, the Bias iteration is set to -1 which means that it is performed each iteration. If the value is greater -1 then the inhomogeneity computation is stopped after n iterations. The third tab specifies printing out intermediate results, which are saved in the working directory specified in the next step <br />
==== Step 9: Define Miscellaneous Parameters ====<br />
This panels lists the general parameters necessary for segmenting images. Users can specify a region of interest to speed up the segmentation algorithm. Pressing the 'Segment' button creates a label map of the anatomical structures.<br />
<br />
===Use Cases, Examples & Tutorials ===<br />
<br />
* EMSegmenter Tutorial for 3D Slicer 3.6.2<br />
** [[Media:EMSegmenterTutorialSimpleMode-2010-Dec.pdf | Simple Mode]] - [[Media:MRIHumanBrain_T1_aligned.nrrd | Tutorial Data]]<br />
** [[Media:EMSegmenterTutorialAdvancedMode-2010-Dec.pdf | Advanced Mode]] - [[Media:MRIHumanBrain_T1_aligned.nrrd | Tutorial Data]]<br />
<br />
* EMSegmenter Tutorial for 3D Slicer 3.6.3<br />
** [[Media:EMSegmenterTutorialSimpleMode-Slicer-3.6.3-1.pdf | Simple Mode]] - [[Media:MRIHumanBrain_T1_aligned.nrrd | Tutorial Data]]<br />
** [[Media:EMSegmenterTutorialAdvancedMode-Slicer-3.6.3-1.pdf | Advanced Mode]] - [[Media:MRIHumanBrain_T1_aligned.nrrd | Tutorial Data]]<br />
<br />
<br />
* A full Tutorial for all two EMSegment modules<br />
<br />
These slides and data describe the Slicer3 implementation of the two EMSegment GUI and command-line modules and demonstrate their use.<br />
<br />
[[Media:EMSegTutorial-AHM2008.ppt | Tutorial Slides]] - [[Media:EMSegTutorial-AHM2008.zip | Tutorial Data]]<br />
<br />
* Another detailed training tutorial on EMSegment algorithm and the Slicer3 EMSegment module.<br />
<br />
[http://wiki.na-mic.org/Wiki/images/2/2f/AutomaticSegmentation_SoniaPujol_Munich2008.ppt Tutorial Slides] - <br />
[http://wiki.na-mic.org/Wiki/images/b/b7/AutomaticSegmentation.tar.gz Training Data]<br />
<br />
== Development ==<br />
<br />
The overall design of the EMSegment module is described in the AHM2008 [[Media:EMSegTutorial-AHM2008.ppt |slides]].<br />
<br />
The module is implemented as a programmatic Slicer3 module because it<br />
requires a large degree of interaction with the user, the data stored<br />
in the MRML tree, and the Slicer3 GUI itself. Because the MRML node<br />
structure is rather complicated (for example the anatomical tissue<br />
hierarchy and a large number of interdependent nodes) the Logic class<br />
is solely responsible for maintaining and accessing these nodes. The<br />
Logic class provides an API that the GUI code uses to access and<br />
modify data. The Logic class also wraps the algorithm code itself.<br />
<br />
===Notes from the Developer(s)===<br />
<br />
N/A<br />
<br />
===Dependencies===<br />
<br />
Slicer3 base modules.<br />
<br />
<br />
===Tests===<br />
<br />
On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:<br />
<br />
* [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/EMSegment/Testing/vtkEMSegmentBlackBoxSegmentationTest.cxx vtkEMSegmentBlackBoxSegmentationTest ]<br />
* [http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/EMSegment/Testing/vtkEMSegmentMRMLManagerTest.cxx vtkEMSegmentMRMLManagerTest ]<br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/EMSegment/Testing/vtkEMSegmentPreprocessingManagerTest.cxx vtkEMSegmentPreprocessingManagerTest ]<br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/EMSegment/Testing/vtkEMSegmentReadWriteMRMLTest.cxx vtkEMSegmentReadWriteMRMLTest ]<br />
*[http://viewvc.slicer.org/viewcvs.cgi/trunk/Modules/EMSegment/Testing/vtkEMSegmentTestUtilities.cxx vtkEMSegmentTestUtilities ]<br />
<br />
===Known bugs===<br />
<br />
* [http://www.na-mic.org/Bug/view_all_bug_page.php Links ] to known bugs in the Slicer3 bug tracker. Please expand the search options, select EMSegmenter in the category, and press apply filter<br />
<br />
===Usability issues===<br />
Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.<br />
<br />
===Source code & documentation===<br />
<br />
[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ Links] for the module.<br />
*[http://www.na-mic.org/ViewVC/index.cgi/trunk/Modules/EMSegment/ View EMSegment Code]<br />
*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]<br />
<br />
== More Information == <br />
*For more information about the EM Segmenter project see the [[EMSegmenter-Overview| EMSegmenter Wiki page here]]<br />
<br />
===Acknowledgment===<br />
We thank Andriy Fedorov and Alexander Zaitsev for pointing to and fixing issues in the early development.<br />
Funding for the EMSegment module was provided by NA-MIC and NAC (PI: Ron Kikinis).<br />
<br />
===References===<br />
*Pohl K, Bouix S, Nakamura M, Rohlfing T, McCarley R, Kikinis R, Grimson W, Shenton M, Wells W. [http://www.slicer.org/pages/Special:PubDB_View?dspaceid=608 A Hierarchical Algorithm for MR Brain Image Parcellation.] IEEE Transactions on Medical Imaging. 2007 Sept;26(9):1201-1212. [[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib]]</div>Pohlhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/EMSegmenter&diff=23678Documentation/4.0/Modules/EMSegmenter2011-12-10T02:08:46Z<p>Pohl: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work was funded by the ARRA Supplement to the Neuroimage Analysis Center (NAC), funded by the National Institutes of Health. Information on NAC can be obtained from the [http://nac.spl.harvard.edu/pages/Overview NAC website].<br><br />
Author: Kilian Pohl, UPenn <br><br />
Contributor1: Daniel Haehn, UPENN<br><br />
Contact: Kilian Pohl, <email>pohl.kilian@gmail.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:UPenn-logo.png|University of Pennsylvania<br />
|Image:Logo-splnew.jpg|Surgical Planning Laboratory <br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<br />
[[Image:EMSegmenterLogo.png|thumb|width=200px|Hierarchical Model of the EMSegmenter]]<br />
This module is designed for users who perform atlas based medical image segmentation. The module can be operated in <B>two</B> modes: <br><br />
An <B>advanced mode (Button: Adjust Parameters)</B> that allows users to parameterize the tool to specific segmentation tasks and a <B>simple mode (Button: Use Existing Setting)</B> which is designed for users who would like to apply the predefined parameterization to new data with a minimal amount of user interaction. One can also apply the parameterization to medical scans via the command-line executable <B>EMSegmentCommandLine</B>. The remainder of this sections describes the work flow of the two modes in further detail:<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The purpose of the module is to configure the algorithm to automatically segment anatomical structures in medical images. First the user has to specify parameters defining the image protocol and the anatomical structures of interests. This process results in a template that the module uses to automatically segment large data sets. The template is composed of atlas data and a non-trivial collection of parameters for the EMSegment algorithm. <br />
<br />
Once the parameters are specified, the target images are segmented<br />
using the EM Segmentation algorithm (Pohl et al. TMI 2007). If the results are<br />
satisfactory, the template is saved and can be used later to segment<br />
new images (via the GUI or batch processing). If the results are<br />
unsatisfactory, the parameters can be modified and the segmentation<br />
re-run.<br />
<br />
One important aspect of the project is the workflow wizard. This wizard simplifies the module by dividing the complicated template specification task into a number of smaller, intuitive steps. The wizard allows to [[EMSegmenter-CreateTask|create tasks]] and to use them to analyze data sets.<br />
<br />
There are multiple [[EMSegmenter-Tasks|'''predefined tasks''']] which are ready to use.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
* EMSegmenter Tutorial for 3D Slicer 3.6.2<br />
** [[Media:EMSegmenterTutorialSimpleMode-2010-Dec.pdf | Simple Mode]] - [[Media:MRIHumanBrain_T1_aligned.nrrd | Tutorial Data]]<br />
** [[Media:EMSegmenterTutorialAdvancedMode-2010-Dec.pdf | Advanced Mode]] - [[Media:MRIHumanBrain_T1_aligned.nrrd | Tutorial Data]]<br />
<br />
* EMSegmenter Tutorial for 3D Slicer 3.6.3<br />
** [[Media:EMSegmenterTutorialSimpleMode-Slicer-3.6.3-1.pdf | Simple Mode]] - [[Media:MRIHumanBrain_T1_aligned.nrrd | Tutorial Data]]<br />
** [[Media:EMSegmenterTutorialAdvancedMode-Slicer-3.6.3-1.pdf | Advanced Mode]] - [[Media:MRIHumanBrain_T1_aligned.nrrd | Tutorial Data]]<br />
<br />
<br />
* A full Tutorial for the two EMSegment modules<br />
<br />
These slides and data describe the Slicer3 implementation of the two EMSegment GUI and command-line modules and demonstrate their use.<br />
<br />
[[Media:EMSegTutorial-AHM2008.ppt | Tutorial Slides]] - [[Media:EMSegTutorial-AHM2008.zip | Tutorial Data]]<br />
<br />
* Another detailed training tutorial on EMSegment algorithm and the Slicer3 EMSegment module.<br />
<br />
[http://wiki.na-mic.org/Wiki/images/2/2f/AutomaticSegmentation_SoniaPujol_Munich2008.ppt Tutorial Slides] - <br />
[http://wiki.na-mic.org/Wiki/images/b/b7/AutomaticSegmentation.tar.gz Training Data]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
[[image:EMwithAtlas-2011-11-25.png|400px]]<br />
<br />
=== Simple Mode ===<br />
The work flow is defined by only two steps.<br />
==== Step 1: Define Task ====<br />
Select an already existing task and click on the "Use Existing Settings" button to use for the simple mode in the pop up window.<br />
A MRML file defining parameters of the algorithm specific to the task as well atlas data are automatically downloaded for existing Tasks.<br />
==== Step 2: Define Input Channels ====<br />
In this step the user specifies the scans to be segmented as well as the check list associated with the preprocessing.<br />
A click on the 'Segment' button is enough to start the pre-processing and the subsequent segmentation.<br />
<br />
=== Advanced Mode ===<br />
Unlike the Simple mode, the advanced mode is defined by nine steps which one can navigate via the "Back", "Next", or "Segment" button. The Segment button jumps right away to the last step of the work flow and segments the medical scans into the structures of interests. <br />
==== Step 1: Define Task ====<br />
Select an already existing task or define a new one. Click on the button "Adjust Parameters" for the advanced mode in the pop up window. A MRML file defining parameters of the algorithm specific to the task as well atlas data are automatically downloaded for existing Tasks.<br />
==== Step 2: Define Input Channel ====<br />
Define the number of input channels as well as the name of each channel and the corresponding scan associated with the channel. If using multiple input channel(scans) which are not aligned with each other then check on the check-box button "Align input scans".<br />
==== Step 3: Define Anatomical Tree ====<br />
The user specifies the hierarchical relationship between the anatomical structures. The tree will refine the complex segmentation task into a set of easier segmentation problems. A sub-classes is added to an existing structure by right-clicking on the structure and selecting "Add sub-class". The name, label, and color of a structure are modified by selecting the structure in the tree and then defining these attributes in the panel below.<br />
==== Step 4: Define Atlas ====<br />
In this step, the user links the probabilistic atlases to the anatomical structures in the tree by first highlighting the structure and then selecting the volume representing the probability map of that structure in the panel below. We note that the probabilistic atlas of structures with sub-structures is defined by the atlases of the sub-structures and thus is not explicitly defined. <br />
==== Step 5: Edit Registration Parameters ====<br />
The atlas is in general not aligned to the specific patient scans defined in Step 2. The user assigns in this step the scans of the atlas corresponding to the input channels in Step 2 as well as the type of registration (Affine / Deformable) and the interpolation. <br />
==== Step 6: Define Preprocessing ==== <br />
[[Image:EMSegmenter_DisplayClassDistribution.png | thumb|width=200px|Graph showing intensity distributions of a set of anatomical structures]] This step is defined via a task specific Tcl file that configures the preprocessing pipeline of the input scans and the atlas. Complete the step by going through the task specific check list, clicking on the 'Next' button, and clicking on the 'Yes' button of the pop up window. One can define a new preprocessing pipeline by specifying the pipeline via a Tcl file, placing the file in Slicer3-build/share/Slicer3/Modules/EMSegment/Tasks and listing the file name in the task specific MRML file.<br />
<br />
==== Step 7: Specify Intensity Distribution ==== <br />
Refining the intensity distribution for each structure of interest is often a critical step in the parameterization of the segmentation algorithm. It includes an overview window that shows the distribution in a 1D and 2D graph (press "Plot Distributions" to view the graph). By placing the mouse cursor in the 2D viewers the corresponding intensity value is shown in the graph.<br />
<br />
==== Step 8: Edit Node-based Parameters ====<br />
Users specify the relative to weight of a node in the tree with respect to other structures which are children of the same parent node. The first tab also specifies the weight of the input channels as well as the atlases. The value 'Alpha' specifies the smoothing applied to the structure (via MRFs). The second tab (Stopping Condition) lists the number of iterations associated with the segmentation task. By default, the Bias iteration is set to -1 which means that it is performed each iteration. If the value is greater -1 then the inhomogeneity computation is stopped after n iterations. The third tab specifies printing out intermediate results, which are saved in the working directory specified in the next step <br />
==== Step 9: Define Miscellaneous Parameters ====<br />
This panels lists the general parameters necessary for segmenting images. Users can specify a region of interest to speed up the segmentation algorithm. Pressing the 'Segment' button creates a label map of the anatomical structures.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
Please visit the [[ Documentation/4.0#Segmentation | segmentation section ]] for similar modules <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
*Pohl K, Bouix S, Nakamura M, Rohlfing T, McCarley R, Kikinis R, Grimson W, Shenton M, Wells W. [http://www.slicer.org/pages/Special:PubDB_View?dspaceid=608 A Hierarchical Algorithm for MR Brain Image Parcellation.] IEEE Transactions on Medical Imaging. 2007 Sept;26(9):1201-1212. [[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}} <br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
{{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
If you are documenting a CLI, the category should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-category|xmlurl=http://path/to/YOURMODULENAME.xml }}</pre><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Pohlhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/EMSegment_Easy&diff=23677Documentation/4.0/Modules/EMSegment Easy2011-12-10T02:07:55Z<p>Pohl: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work was funded by the ARRA Supplement to the Neuroimage Analysis Center (NAC), funded by the National Institutes of Health. Information on NAC can be obtained from the [http://nac.spl.harvard.edu/pages/Overview NAC website].<br><br />
Author: Kilian Pohl, UPenn <br><br />
Contributor1: Daniel Haehn, UPENN<br><br />
Contact: Kilian Pohl, <email>pohl.kilian@gmail.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:UPenn-logo.png|University of Pennsylvania<br />
|Image:Logo-splnew.jpg|Surgical Planning Laboratory <br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<br />
This module is designed for users who want to do a quick intensity based image segmentation. The remainder of this sections describes the work flow of the two modes in further detail: <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
MR image segmentation <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
=== Step 1: Define Input Datasets ===<br />
Define the volumes to be segmented. Each volume has to be from the subject and has to represent a different mode, such as T1 and FLAIR, than the other input volumes.<br />
<br />
=== Step 2: Define Structure ===<br />
The user specifies the number of structures to be segmented and the label of each structure. You can further add class to an existing structure by right-clicking on the structure and selecting "Add sub-class". The label and corresponding color of a structure are modified by selecting the structure in the tree.<br />
<br />
=== Step 3: Sampling and Class Weights === <br />
Define the intensity distribution for each structure of interest by taking samples in the image of interest. Users can also specify the relative to weight of a node in the tree with respect to other structures. If a class should be overestimated in the final label map then this can be adjusted by lowering the weight of that structure and repeating the segmentation.<br />
<br />
=== Step 4: Edit Node-based Parameters ===<br />
Users specify the relative to weight of a node in the tree with respect to other structures which are children of the same parent node. The first tab also specifies the weight of the input channels as well as the atlases. The value 'Alpha' specifies the smoothing applied to the structure (via MRFs). The second tab (Stopping Condition) lists the number of iterations associated with the segmentation task. By default, the Bias iteration is set to -1 which means that it is performed each iteration. If the value is greater -1 then the inhomogeneity computation is stopped after n iterations. The third tab specifies printing out intermediate results, which are saved in the working directory specified in the next step <br />
=== Step 5: Miscellaneous ===<br />
This panels allows the user to specify the region of interest to be segmented. Pressing the 'Segment' button starts the segmentation. <br />
<br />
Once the parameters are specified, the target images are segmented<br />
using the EM Segmentation algorithm (Pohl et al. TMI 2007). The label map with corresponding statistics is returned after successful completion of the algorithm. <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
Please visit the [[ Documentation/4.0#Segmentation | segmentation section ]] for similar modules <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}} <br />
*Pohl K, Bouix S, Nakamura M, Rohlfing T, McCarley R, Kikinis R, Grimson W, Shenton M, Wells W. [http://www.slicer.org/pages/Special:PubDB_View?dspaceid=608 A Hierarchical Algorithm for MR Brain Image Parcellation.] IEEE Transactions on Medical Imaging. 2007 Sept;26(9):1201-1212. [[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
{{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
If you are documenting a CLI, the category should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-category|xmlurl=http://path/to/YOURMODULENAME.xml }}</pre><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Pohlhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Announcements&diff=23601Documentation/4.0/Announcements2011-12-05T18:02:07Z<p>Pohl: /* Slicer Highlights */</p>
<hr />
<div> [[Documentation/{{documentation/version}}|Back to Documentation {{documentation/version}}]]<br />
{|width="100%"<br />
|<br />
__TOC__<br />
<br />
|align="right"|<br />
[[image:Slicer4Announcement-HiRes.png|right|{{documentation/version}}]]<br />
|}<br />
=Introduction= <br />
<br />
The [http://slicer.org/pages/Acknowledgments#Acknowledgments_Slicer_4.0 community] of Slicer developers is proud to announce the release of '''Slicer {{documentation/version}}'''.<br />
<br />
*Slicer {{documentation/version}} includes a major overhaul of the user interface, improved and simplified workflows for major tasks, simplified procedures for developers, and improved Python support.<br />
<br />
*Click here to [http://download.slicer.org/ download] Slicer {{documentation/version}} for different platforms and find pointers to the source code, mailing lists and bug tracker. <br />
*Please note that Slicer continues to be a research package and is not intended for clinical use. Testing of functionality is an ongoing activity with high priority, however, some features of Slicer4 are not fully tested.<br />
*The [[Documentation/{{documentation/version}}/Training|Slicer Training page]] provides a series of courses for learning how to use Slicer4. The portfolio contains self-guided presentation and sample data sets. <br />
<br />
The main [http://www.slicer.org slicer.org] pages provide a guided tour to the application, training materials, and the development community. New users should start there because we try to keep the pages organized and up to date.<br />
<br />
=Our Philosophy=<br />
Slicer is a community platform created for the purpose of subject specific image analysis and visualization. <br />
<br />
* Multi-modality imaging including, MRI, CT, US, nuclear medicine, and microscopy<br />
* Multi organ from head to toe<br />
* Bidirectional interface for devices<br />
* Expandable and interfaced to multiple toolkits<br />
<br />
There is no restriction on use, but permissions and compliance with rules are responsibility of users. For details on the license see [http://www.slicer.org/cgi-bin/License/SlicerLicenseForm.pl here]<br />
<br />
=Slicer Highlights=<br />
<gallery caption="Slicer 4.0 - New and Improved Modules" widths="250px" heights="150px" perrow="3"><br />
Image:MainGui-2011-11-25.png|[[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI|Main GUI]]<br />
Image:Prostate multiparametric visualization Slicer4.png|Layouts<br />
Image:Tumor-Volume-Rendering-PostGad-2011.png|[[Documentation/{{documentation/version}}/Modules/VolumeRendering|Volume Rendering]]<br />
Image:Editor-2011-11-24.png|[[Documentation/{{documentation/version}}/Modules/Editor|Editor]]<br />
Image:2011-11-12-CroppingWholeBrainTractography.png|[[Documentation/{{documentation/version}}/Modules/TractographyDisplay|Diffusion: Fiber Display]]<br />
Image:Screen Shot 2011-11-02 at 1.52.42 PM.png|[[Documentation/{{documentation/version}}/Modules/Annotations|Annotations]]<br />
Image:SceneViews-2011-11-25.png|[[Documentation/{{documentation/version}}/Modules/SceneViews|Sceneviews]]<br />
Image:ViewControllers-2011-11-25.png|[[Documentation/{{documentation/version}}/Modules/ViewControllers|View controllers]]<br />
Image:VolumesModule-2011-11-25.png|[[Documentation/{{documentation/version}}/Modules/Volumes|Volume module]]<br />
Image:Slicer4-EMSegment-Overview.png|[[Documentation/{{documentation/version}}/Modules/EMSegmenter|EM segmenter]]<br />
Image:WelcomeModule-2011-11-25.png|[[Documentation/{{documentation/version}}/Modules/SlicerWelcome|Slicer welcome module]]<br />
Image:DataProbe-2011-11-25.png|[[Documentation/{{documentation/version}}/Modules/DataProbe|Data Probe]]<br />
Image:Selection 142.png|[[Documentation/{{documentation/version}}/Modules/DICOM|DICOM module]]<br />
Image:ModelsModule-2011-11-25.png|[[Documentation/{{documentation/version}}/Modules/Models|Models module]]<br />
Image:Slicer4 ChangeTracker Ad.png|[[Documentation/{{documentation/version}}/Modules/ChangeTracker|Changetracker]]<br />
</gallery><br />
<br />
=Slicer Extensions=<br />
Extension for Slicer {{documentation/version}} will become available in February of 2012.<br />
<br />
= Other Improvements, Additions & Documentation =<br />
<gallery caption="" widths="250px" heights="150px" perrow="3"><br />
image:<br />
</gallery></div>Pohlhttps://www.slicer.org/w/index.php?title=File:Slicer4-EMSegment-Overview.png&diff=23600File:Slicer4-EMSegment-Overview.png2011-12-05T18:01:16Z<p>Pohl: </p>
<hr />
<div></div>Pohlhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/EMSegment_Command-line&diff=23544Documentation/4.0/Modules/EMSegment Command-line2011-12-02T07:56:34Z<p>Pohl: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work was funded by the ARRA Supplement to the Neuroimage Analysis Center (NAC), funded by the National Institutes of Health. Information on NAC can be obtained from the [http://nac.spl.harvard.edu/pages/Overview NAC website].<br><br />
Author: Kilian Pohl, UPenn <br><br />
Contributor1: Daniel Haehn, UPENN<br><br />
Contact: Kilian Pohl, <email>pohl.kilian@gmail.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:UPenn-logo.png|University of Pennsylvania<br />
|Image:Logo-splnew.jpg|Surgical Planning Laboratory <br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
{{documentation/{{documentation/version}}/module-description|xmlurl=http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/EMSegment/CommandLineApplication/EMSegmentCommandLine.xml?revision=16914&view=co}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
Most frequently used for these scenarios:<br />
<br />
* Use Case 1:<br />
* Use Case 2:<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
Links to tutorials that use this module<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
A list of all the panels in the interface, their features, what they mean, and how to use them. For instance:<br />
<br />
{|style="width: 100%"<br />
|<br />
* Input panel1:<br />
** First input<br />
** Second input<br />
* Parameters panel:<br />
** First parameter<br />
** Second parameter<br />
* Output panel:<br />
** First output<br />
** Second output<br />
* Viewing panel:<br />
| align="right" |<br />
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 1]]<br />
|-<br />
|<br />
* Input panel2:<br />
** First input<br />
** Second input<br />
* Parameters panel:<br />
** First parameter<br />
** Second parameter<br />
* Output panel:<br />
** First output<br />
** Second output<br />
* Viewing panel:<br />
| align="right" |<br />
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 2]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
* Point to other modules that have similar functionality<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
Publications related to this module go here. Links to pdfs would be useful.<br />
For extensions: link to the source code repository and additional documentation<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
{{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
If you are documenting a CLI, the category should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-category|xmlurl=http://path/to/YOURMODULENAME.xml }}</pre><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Pohlhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/EMSegment_Command-line&diff=23543Documentation/4.0/Modules/EMSegment Command-line2011-12-02T07:55:07Z<p>Pohl: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work was funded by the ARRA Supplement to the Neuroimage Analysis Center (NAC), funded by the National Institutes of Health. Information on NAC can be obtained from the [http://nac.spl.harvard.edu/pages/Overview NAC website].<br><br />
Author: Kilian Pohl, UPenn <br><br />
Contributor1: Daniel Haehn, UPENN<br><br />
Contact: Kilian Pohl, <email>pohl.kilian@gmail.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:UPenn-logo.png|University of Pennsylvania<br />
|Image:Logo-splnew.jpg|Surgical Planning Laboratory <br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<!--- {{documentation/{{documentation/version}}/module-description|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|17347}} }} --><br />
Start:<br />
{{documentation/{{documentation/version}}/module-description|xmlurl=http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/EMSegment/CommandLineApplication/EMSegmentCommandLine.xml?revision=16914&view=co}}<br />
..End<br />
<br />
<!--- {{documentation/{{documentation/version}}/module-cli-xmlurl|http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/EMSegment/CommandLineApplication/EMSegmentCommandLine.xml?revision=16914&view=co}} --><br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description|xmlurl=http://path/to/YOURMODULE.xml }}</pre><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-description|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
Most frequently used for these scenarios:<br />
<br />
* Use Case 1:<br />
* Use Case 2:<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
Links to tutorials that use this module<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
A list of all the panels in the interface, their features, what they mean, and how to use them. For instance:<br />
<br />
{|style="width: 100%"<br />
|<br />
* Input panel1:<br />
** First input<br />
** Second input<br />
* Parameters panel:<br />
** First parameter<br />
** Second parameter<br />
* Output panel:<br />
** First output<br />
** Second output<br />
* Viewing panel:<br />
| align="right" |<br />
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 1]]<br />
|-<br />
|<br />
* Input panel2:<br />
** First input<br />
** Second input<br />
* Parameters panel:<br />
** First parameter<br />
** Second parameter<br />
* Output panel:<br />
** First output<br />
** Second output<br />
* Viewing panel:<br />
| align="right" |<br />
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 2]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
* Point to other modules that have similar functionality<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
Publications related to this module go here. Links to pdfs would be useful.<br />
For extensions: link to the source code repository and additional documentation<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
{{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
If you are documenting a CLI, the category should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-category|xmlurl=http://path/to/YOURMODULENAME.xml }}</pre><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Pohlhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/EMSegment_Command-line&diff=23442Documentation/4.0/Modules/EMSegment Command-line2011-11-29T02:01:59Z<p>Pohl: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work was funded by the ARRA Supplement to the Neuroimage Analysis Center (NAC), funded by the National Institutes of Health. Information on NAC can be obtained from the [http://nac.spl.harvard.edu/pages/Overview NAC website].<br><br />
Author: Kilian Pohl, UPenn <br><br />
Contributor1: Daniel Haehn, UPENN<br><br />
Contact: Kilian Pohl, <email>pohl.kilian@gmail.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:UPenn-logo.png|University of Pennsylvania<br />
|Image:Logo-splnew.jpg|Surgical Planning Laboratory <br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<!--- {{documentation/{{documentation/version}}/module-description|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|17347}} }} --><br />
Start:<br />
{{documentation/{{documentation/version}}/module-description|http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/EMSegment/CommandLineApplication/EMSegmentCommandLine.xml?revision=16914&view=co}}<br />
..End<br />
<br />
<!--- {{documentation/{{documentation/version}}/module-cli-xmlurl|http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/EMSegment/CommandLineApplication/EMSegmentCommandLine.xml?revision=16914&view=co}} --><br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description|xmlurl=http://path/to/YOURMODULE.xml }}</pre><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-description|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
Most frequently used for these scenarios:<br />
<br />
* Use Case 1:<br />
* Use Case 2:<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
Links to tutorials that use this module<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
A list of all the panels in the interface, their features, what they mean, and how to use them. For instance:<br />
<br />
{|style="width: 100%"<br />
|<br />
* Input panel1:<br />
** First input<br />
** Second input<br />
* Parameters panel:<br />
** First parameter<br />
** Second parameter<br />
* Output panel:<br />
** First output<br />
** Second output<br />
* Viewing panel:<br />
| align="right" |<br />
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 1]]<br />
|-<br />
|<br />
* Input panel2:<br />
** First input<br />
** Second input<br />
* Parameters panel:<br />
** First parameter<br />
** Second parameter<br />
* Output panel:<br />
** First output<br />
** Second output<br />
* Viewing panel:<br />
| align="right" |<br />
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 2]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
* Point to other modules that have similar functionality<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
Publications related to this module go here. Links to pdfs would be useful.<br />
For extensions: link to the source code repository and additional documentation<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
{{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
If you are documenting a CLI, the category should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-category|xmlurl=http://path/to/YOURMODULENAME.xml }}</pre><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Pohlhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/EMSegment_Command-line&diff=23441Documentation/4.0/Modules/EMSegment Command-line2011-11-29T00:38:45Z<p>Pohl: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work was funded by the ARRA Supplement to the Neuroimage Analysis Center (NAC), funded by the National Institutes of Health. Information on NAC can be obtained from the [http://nac.spl.harvard.edu/pages/Overview NAC website].<br><br />
Author: Kilian Pohl, UPenn <br><br />
Contributor1: Daniel Haehn, UPENN<br><br />
Contact: Kilian Pohl, <email>pohl.kilian@gmail.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:UPenn-logo.png|University of Pennsylvania<br />
|Image:Logo-splnew.jpg|Surgical Planning Laboratory <br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<!--- {{documentation/{{documentation/version}}/module-description|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|17347}} }} --><br />
<br />
{{documentation/{{documentation/version}}/module-description|http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/EMSegment/CommandLineApplication/EMSegmentCommandLine.xml?revision=16914&view=co}}<br />
<br />
<!--- {{documentation/{{documentation/version}}/module-cli-xmlurl|http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/EMSegment/CommandLineApplication/EMSegmentCommandLine.xml?revision=16914&view=co}} --><br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description|xmlurl=http://path/to/YOURMODULE.xml }}</pre><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-description|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
Most frequently used for these scenarios:<br />
<br />
* Use Case 1:<br />
* Use Case 2:<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
Links to tutorials that use this module<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
A list of all the panels in the interface, their features, what they mean, and how to use them. For instance:<br />
<br />
{|style="width: 100%"<br />
|<br />
* Input panel1:<br />
** First input<br />
** Second input<br />
* Parameters panel:<br />
** First parameter<br />
** Second parameter<br />
* Output panel:<br />
** First output<br />
** Second output<br />
* Viewing panel:<br />
| align="right" |<br />
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 1]]<br />
|-<br />
|<br />
* Input panel2:<br />
** First input<br />
** Second input<br />
* Parameters panel:<br />
** First parameter<br />
** Second parameter<br />
* Output panel:<br />
** First output<br />
** Second output<br />
* Viewing panel:<br />
| align="right" |<br />
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 2]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
* Point to other modules that have similar functionality<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
Publications related to this module go here. Links to pdfs would be useful.<br />
For extensions: link to the source code repository and additional documentation<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
{{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
If you are documenting a CLI, the category should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-category|xmlurl=http://path/to/YOURMODULENAME.xml }}</pre><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Pohlhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/EMSegment_Command-line&diff=23440Documentation/4.0/Modules/EMSegment Command-line2011-11-29T00:38:01Z<p>Pohl: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work was funded by the ARRA Supplement to the Neuroimage Analysis Center (NAC), funded by the National Institutes of Health. Information on NAC can be obtained from the [http://nac.spl.harvard.edu/pages/Overview NAC website].<br><br />
Author: Kilian Pohl, UPenn <br><br />
Contributor1: Daniel Haehn, UPENN<br><br />
Contact: Kilian Pohl, <email>pohl.kilian@gmail.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:UPenn-logo.png|University of Pennsylvania<br />
|Image:Logo-splnew.jpg|Surgical Planning Laboratory <br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<!--- {{documentation/{{documentation/version}}/module-description|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|17347}} }} --><br />
<br />
{{documentation/{{documentation/version}}/module-description|http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/EMSegment/CommandLineApplication/EMSegmentCommandLine.xml?revision=16914&view=co}}<br />
<br />
{{documentation/{{documentation/version}}/module-cli-xmlurl|http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/EMSegment/CommandLineApplication/EMSegmentCommandLine.xml?revision=16914&view=co}}<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description|xmlurl=http://path/to/YOURMODULE.xml }}</pre><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-description|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
Most frequently used for these scenarios:<br />
<br />
* Use Case 1:<br />
* Use Case 2:<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
Links to tutorials that use this module<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
A list of all the panels in the interface, their features, what they mean, and how to use them. For instance:<br />
<br />
{|style="width: 100%"<br />
|<br />
* Input panel1:<br />
** First input<br />
** Second input<br />
* Parameters panel:<br />
** First parameter<br />
** Second parameter<br />
* Output panel:<br />
** First output<br />
** Second output<br />
* Viewing panel:<br />
| align="right" |<br />
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 1]]<br />
|-<br />
|<br />
* Input panel2:<br />
** First input<br />
** Second input<br />
* Parameters panel:<br />
** First parameter<br />
** Second parameter<br />
* Output panel:<br />
** First output<br />
** Second output<br />
* Viewing panel:<br />
| align="right" |<br />
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 2]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
* Point to other modules that have similar functionality<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
Publications related to this module go here. Links to pdfs would be useful.<br />
For extensions: link to the source code repository and additional documentation<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
{{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
If you are documenting a CLI, the category should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-category|xmlurl=http://path/to/YOURMODULENAME.xml }}</pre><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Pohlhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/EMSegment_Command-line&diff=23439Documentation/4.0/Modules/EMSegment Command-line2011-11-29T00:28:59Z<p>Pohl: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work was funded by the ARRA Supplement to the Neuroimage Analysis Center (NAC), funded by the National Institutes of Health. Information on NAC can be obtained from the [http://nac.spl.harvard.edu/pages/Overview NAC website].<br><br />
Author: Kilian Pohl, UPenn <br><br />
Contributor1: Daniel Haehn, UPENN<br><br />
Contact: Kilian Pohl, <email>pohl.kilian@gmail.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:UPenn-logo.png|University of Pennsylvania<br />
|Image:Logo-splnew.jpg|Surgical Planning Laboratory <br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<!--- {{documentation/{{documentation/version}}/module-description|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|17347}} }} --><br />
<br />
{{documentation/{{documentation/version}}/module-description|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl||http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/EMSegment/CommandLineApplication/EMSegmentCommandLine.xml?revision=16914&view=co}}<br />
<br />
{{documentation/{{documentation/version}}/module-cli-xmlurl|http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/EMSegment/CommandLineApplication/EMSegmentCommandLine.xml?revision=16914&view=co}}<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description|xmlurl=http://path/to/YOURMODULE.xml }}</pre><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-description|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
Most frequently used for these scenarios:<br />
<br />
* Use Case 1:<br />
* Use Case 2:<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
Links to tutorials that use this module<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
A list of all the panels in the interface, their features, what they mean, and how to use them. For instance:<br />
<br />
{|style="width: 100%"<br />
|<br />
* Input panel1:<br />
** First input<br />
** Second input<br />
* Parameters panel:<br />
** First parameter<br />
** Second parameter<br />
* Output panel:<br />
** First output<br />
** Second output<br />
* Viewing panel:<br />
| align="right" |<br />
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 1]]<br />
|-<br />
|<br />
* Input panel2:<br />
** First input<br />
** Second input<br />
* Parameters panel:<br />
** First parameter<br />
** Second parameter<br />
* Output panel:<br />
** First output<br />
** Second output<br />
* Viewing panel:<br />
| align="right" |<br />
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 2]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
* Point to other modules that have similar functionality<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
Publications related to this module go here. Links to pdfs would be useful.<br />
For extensions: link to the source code repository and additional documentation<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
{{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
If you are documenting a CLI, the category should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-category|xmlurl=http://path/to/YOURMODULENAME.xml }}</pre><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Pohlhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/EMSegment_Command-line&diff=23438Documentation/4.0/Modules/EMSegment Command-line2011-11-29T00:24:53Z<p>Pohl: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work was funded by the ARRA Supplement to the Neuroimage Analysis Center (NAC), funded by the National Institutes of Health. Information on NAC can be obtained from the [http://nac.spl.harvard.edu/pages/Overview NAC website].<br><br />
Author: Kilian Pohl, UPenn <br><br />
Contributor1: Daniel Haehn, UPENN<br><br />
Contact: Kilian Pohl, <email>pohl.kilian@gmail.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:UPenn-logo.png|University of Pennsylvania<br />
|Image:Logo-splnew.jpg|Surgical Planning Laboratory <br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<!--- {{documentation/{{documentation/version}}/module-description|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|17347}} }} --><br />
<br />
{{documentation/{{documentation/version}}/module-description|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl||http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/EMSegment/CommandLineApplication/EMSegmentCommandLine.xml?revision=16914&view=co}}<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description|xmlurl=http://path/to/YOURMODULE.xml }}</pre><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-description|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
Most frequently used for these scenarios:<br />
<br />
* Use Case 1:<br />
* Use Case 2:<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
Links to tutorials that use this module<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
A list of all the panels in the interface, their features, what they mean, and how to use them. For instance:<br />
<br />
{|style="width: 100%"<br />
|<br />
* Input panel1:<br />
** First input<br />
** Second input<br />
* Parameters panel:<br />
** First parameter<br />
** Second parameter<br />
* Output panel:<br />
** First output<br />
** Second output<br />
* Viewing panel:<br />
| align="right" |<br />
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 1]]<br />
|-<br />
|<br />
* Input panel2:<br />
** First input<br />
** Second input<br />
* Parameters panel:<br />
** First parameter<br />
** Second parameter<br />
* Output panel:<br />
** First output<br />
** Second output<br />
* Viewing panel:<br />
| align="right" |<br />
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 2]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
* Point to other modules that have similar functionality<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
Publications related to this module go here. Links to pdfs would be useful.<br />
For extensions: link to the source code repository and additional documentation<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
{{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
If you are documenting a CLI, the category should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-category|xmlurl=http://path/to/YOURMODULENAME.xml }}</pre><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Pohlhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/EMSegment_Command-line&diff=23437Documentation/4.0/Modules/EMSegment Command-line2011-11-28T20:39:51Z<p>Pohl: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work was funded by the ARRA Supplement to the Neuroimage Analysis Center (NAC), funded by the National Institutes of Health. Information on NAC can be obtained from the [http://nac.spl.harvard.edu/pages/Overview NAC website].<br><br />
Author: Kilian Pohl, UPenn <br><br />
Contributor1: Daniel Haehn, UPENN<br><br />
Contact: Kilian Pohl, <email>pohl.kilian@gmail.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:UPenn-logo.png|University of Pennsylvania<br />
|Image:Logo-splnew.jpg|Surgical Planning Laboratory <br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description|xmlurl=http://path/to/YOURMODULE.xml }}</pre><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-description|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
Most frequently used for these scenarios:<br />
<br />
* Use Case 1:<br />
* Use Case 2:<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
Links to tutorials that use this module<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
A list of all the panels in the interface, their features, what they mean, and how to use them. For instance:<br />
<br />
{|style="width: 100%"<br />
|<br />
* Input panel1:<br />
** First input<br />
** Second input<br />
* Parameters panel:<br />
** First parameter<br />
** Second parameter<br />
* Output panel:<br />
** First output<br />
** Second output<br />
* Viewing panel:<br />
| align="right" |<br />
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 1]]<br />
|-<br />
|<br />
* Input panel2:<br />
** First input<br />
** Second input<br />
* Parameters panel:<br />
** First parameter<br />
** Second parameter<br />
* Output panel:<br />
** First output<br />
** Second output<br />
* Viewing panel:<br />
| align="right" |<br />
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 2]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
* Point to other modules that have similar functionality<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
Publications related to this module go here. Links to pdfs would be useful.<br />
For extensions: link to the source code repository and additional documentation<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
{{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
If you are documenting a CLI, the category should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-category|xmlurl=http://path/to/YOURMODULENAME.xml }}</pre><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Pohlhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/EMSegment_Command-line&diff=23436Documentation/4.0/Modules/EMSegment Command-line2011-11-28T20:37:38Z<p>Pohl: Created page with '<!-- ---------------------------- --> {{documentation/{{documentation/version}}/module-header}} <!-- ---------------------------- --> <!-- ---------------------------- --> {{doc…'</p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].<br><br />
Author: FIRSTNAME LASTNAME, AFFILIATION<br><br />
Contributor1: FIRSTNAME LASTNAME, AFFILIATION<br><br />
Contributor2: FIRSTNAME LASTNAME, AFFILIATION<br><br />
Contact: FIRSTNAME LASTNAME, <email>john@doe.org</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:Logo-isomics.png|Isomics, Inc. <- Replace this logo with yours<br />
|Image:Logo-splnew.jpg|Surgical Planning Laboratory <-Replace this logo with yours<br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
{{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].<br><br />
Author: FIRSTNAME LASTNAME, AFFILIATION<br><br />
Contributor1: FIRSTNAME LASTNAME, AFFILIATION<br><br />
Contributor2: FIRSTNAME LASTNAME, AFFILIATION<br><br />
Contact: FIRSTNAME LASTNAME, <email>john@doe.org</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:Logo-isomics.png|Isomics, Inc. <- Replace this logo with yours<br />
|Image:Logo-splnew.jpg|Surgical Planning Laboratory <-Replace this logo with yours<br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description|xmlurl=http://path/to/YOURMODULE.xml }}</pre><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-description|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
Most frequently used for these scenarios:<br />
<br />
* Use Case 1:<br />
* Use Case 2:<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
Links to tutorials that use this module<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
A list of all the panels in the interface, their features, what they mean, and how to use them. For instance:<br />
<br />
{|style="width: 100%"<br />
|<br />
* Input panel1:<br />
** First input<br />
** Second input<br />
* Parameters panel:<br />
** First parameter<br />
** Second parameter<br />
* Output panel:<br />
** First output<br />
** Second output<br />
* Viewing panel:<br />
| align="right" |<br />
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 1]]<br />
|-<br />
|<br />
* Input panel2:<br />
** First input<br />
** Second input<br />
* Parameters panel:<br />
** First parameter<br />
** Second parameter<br />
* Output panel:<br />
** First output<br />
** Second output<br />
* Viewing panel:<br />
| align="right" |<br />
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 2]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
* Point to other modules that have similar functionality<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
Publications related to this module go here. Links to pdfs would be useful.<br />
For extensions: link to the source code repository and additional documentation<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
{{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
If you are documenting a CLI, the category should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-category|xmlurl=http://path/to/YOURMODULENAME.xml }}</pre><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Pohlhttps://www.slicer.org/w/index.php?title=Documentation/4.0&diff=23435Documentation/4.02011-11-28T20:37:11Z<p>Pohl: /* Segmentation */</p>
<hr />
<div>__NOTOC__<br />
<br />
<!-- TODO: Create a template that will list all documentation links --><br />
<small><span class="versionlist">[[Documentation/4.0|4.0]] [[Documentation/3.6|3.6]] [[Documentation/3.5|3.5]] [[Documentation/3.4|3.4]] [[Documentation/3.2|3.2]] [[Documentation|ALL VERSIONS]]</span></small><br />
<br />
=Table of Content=<br />
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"<br />
|-<br />
! width="33%"|<br />
! |<br />
! width="33%"|<br />
! |<br />
! width="33%"|<br />
|- <br />
|valign="top"|<br />
<br />
===Slicer Application===<br />
----<br />
<big>'''<br />
*[[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI| Main Application GUI]] (Wendy Plesniak)<br />
<br />
*[[Documentation/{{documentation/version}}/SlicerApplication/KeyboardShortcuts | "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak)<br />
<br />
*[[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration | Computer configurations]] (Steve Pieper)<br />
<br />
*[[Documentation/{{documentation/version}}/SlicerApplication/LoadingData | Loading]] or [[Documentation/{{documentation/version}}/SlicerApplication/SavingData | Saving]] data and listing of [[Documentation/{{documentation/version}}/SlicerApplication/SupportedDataFormat | supported data formats]]. (Julien Finet)<br />
<!-- : scenes, DICOM, volumes, models, fiducials, transforms, etc. --><br />
<br />
*[[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]] (Curtis Lisle)''' <br />
</big><br />
<br />
===Mailing Lists===<br />
----<br />
* [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users Mailing list for users]<br />
* [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-devel Mailing list for developers]<br />
<br />
<!--<br />
*[[Modules:ExtensionsManagementWizard-Documentation-4.0| Extensions Management Wizard]] (xx)<br />
--><br />
<br />
|bgcolor="#CCCCCC"|<br />
|valign="top"|<br />
<br />
===Module Categories ===<br />
----<br />
<big>'''<br />
* [[#Core Modules|Core Modules]]<br />
* [[#Wizards|Wizards]]<br />
* [[#Informatics|Informatics]]<br />
* [[#Registration|Registration]]<br />
* [[#Segmentation|Segmentation]]<br />
* [[#Quantification|Quantification]]<br />
* [[#Diffusion|Diffusion]]<br />
* [[#IGT|IGT]]<br />
* [[#Filtering|Filtering]]<br />
* [[#Surface Models|Surface Models]]<br />
* [[#Converters|Converters]]<br />
* [[#Endoscopy|Endoscopy]]<br />
* [[#Developer Tools|Developer Tools]]<br />
* [[#Legacy|Legacy]]<br />
* [[#Utilities|Utility]]<br />
</big><br />
|bgcolor="#CCCCCC"|<br />
|valign="top"|<br />
<br />
===Miscellaneous===<br />
----<br />
<!-- * [[Documentation/{{documentation/version}}/ImageGallery|Image gallery]] --><br />
<br />
* [[Slicer4:VisualBlog|Visual blog]]<br />
: Set of screenshots showing Slicer in action.<br />
<br />
<!--<br />
* [[Documents and links]]<br />
: Set of presentations made on Slicer and document talking about it.<br />
<br />
--><br />
* [[Documentation/4.0/Training|Training pages]]<br />
: Information on how to use Slicer {{documentation/version}}<br />
<br />
* [[Documentation/{{documentation/version}}/FAQ|FAQ]]<br />
: Set of common questions/answers<br />
<br />
===Developers Corner===<br />
----<br />
* [[Documentation/{{documentation/version}}/Developers | Developers Information]]<br />
: Handy Developer Info<br />
|}<br />
<br />
=General Information=<br />
{|width="100%"<br />
|rowspan="3"|<br />
{{Infobox<br />
|name = 3D Slicer {{documentation/version}}<br />
|above = 3D Slicer<br />
|abovestyle = <br />
<br />
|image = [[File:3DSlicer4Logo-H-218X144.png|218px|alt=3D Slicer {{documentation/version}}]]<br />
|imagestyle = <br />
|headerstyle = background:#E7DCC3;<br />
|labelstyle = <br />
|datastyle = <br />
<br />
|header1 = Description<br />
|label1 = <br />
|data1 =<br />
|header2 =<br />
|label2 = <br />
|data2 = Research platform for the analysis and visualization of medical images, including image guided therapy.<br />
|header3 =<br />
|label3 = <br />
|data3 = Free and extensible open source package.<br />
|header4 =<br />
|label4 = Multi-platform<br />
|data4 = Linux, MacOSX, Windows<br />
|header5 =<br />
|label5 = Version<br />
|data5 = {{documentation/version}}<br />
|header6 =<br />
|label6 = License<br />
|data6 = [http://www.slicer.org/pages/LicenseText Contribution and Software License Agreement]<br />
}}<br />
|align="center"|<br />
[[{{collaborator|logo|slicer4}}|x350px]] <br />
|-<br />
|<br />
{{ombox<br />
|type=content<br />
|text=The {{documentation/version}} release of 3D Slicer contains significant changes both to the organization of the software and to the functionality. Please check the [[Documentation/{{documentation/version}}/Announcements | Announcement page]] for more details. The community contributing to Slicer {{documentation/version}} is [[Documentation/{{documentation/version}}/Acknowledgment Team|acknowledged here]].<br />
}}<br />
|-<br />
|<br />
{{ombox | text = For information on how to obtain Slicer {{documentation/version}} please go to the [[Snapshots|Download Pages]]. }}<br />
|}<br />
<br />
=Requirements for Modules=<br />
* The module is '''feature complete''', i.e. it does everything that it advertises<br />
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.<br />
* The module is fully documented. [[Documentation/{{documentation/version}}/Modules/YOURMODULENAME|Template]] and [[Documentation/{{documentation/version}}/HowTo|How-to]] for the end user documentation.<br />
* The module complies with [[Documentation-Rons-Rules-For-Tools|Rons rules for tool]] and the style guide lines, including [[Slicer3:Human_Interface_and_Style_Guide_for_Developers#Colors:_application_palettes|color palette]].<br />
* Use logos listed in the [[Template:Collaborator|Collaborators Template]].<br />
<br />
=Modules by Category=<br />
==Core Modules==<br />
*[[Documentation/{{documentation/version}}/Modules/Annotations|Annotations]] (Nicole Aucoin) <br />
*[[Documentation/{{documentation/version}}/Modules/Colors|Colors]] (Nicole Aucoin) <br />
*[[Documentation/{{documentation/version}}/Modules/Data|Data]] (Julien Finet)<br />
*[[Documentation/{{documentation/version}}/Modules/DICOM|DICOM]] (Steve Pieper)<br />
*[[Documentation/{{documentation/version}}/Modules/Editor|Editor]] (Steve Pieper)<br />
*[[Documentation/{{documentation/version}}/Modules/Models|Models]] (Nicole Aucoin)<br />
*[[Documentation/{{documentation/version}}/Modules/SceneViews|SceneViews]] (Nicole Aucoin) <br />
*[[Documentation/{{documentation/version}}/Modules/Transforms|Transforms]] (Alex Yarmarkovich) <br />
*[[Documentation/{{documentation/version}}/Modules/ViewControllers|View Controllers]] (Jim Miller) <br />
*[[Documentation/{{documentation/version}}/Modules/Volumes|Volumes]] (Steve Pieper)<br />
*[[Documentation/{{documentation/version}}/Modules/VolumeRendering|Volume Rendering]] (Julien Finet)<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerWelcome|Welcome to Slicer]] (Wendy Plesniak)<br />
<br />
==Wizards==<br />
*[[Documentation/{{documentation/version}}/Modules/ChangeTracker|ChangeTracker]] (Andrey Fedorov)<br />
<br />
==Informatics==<br />
*[[Documentation/{{documentation/version}}/Modules/SampleData|Sample Data]] (Steve Pieper)<br />
<br />
==Registration==<br />
*[[Documentation/4.0/Modules/BRAINSFit|General Brainsfit Registration]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/BRAINSResample|Resample Image (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]<br />
*Specialized<br />
**[[Documentation/4.0/Modules/ACPCTransform|ACPC Transform]] (Nicole Aucoin)<br />
**[[Documentation/4.0/Modules/BRAINSDemonWarp|Demon Registration (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/TransformFromFiducials|Fiducial Registration (BRAINS)]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]<br />
**Vector Demon Registration (Hans Johnson)<br />
<br />
==Segmentation==<br />
*[[Documentation/4.0/Modules/EMSegment Easy|EMSegment Easy (no atlas)]] (Kilian Pohl) <br />
*[[Documentation/4.0/Modules/EMSegmenter|EMSegment (with atlas)]] (Kilian Pohl) <br />
*[[Documentation/4.0/Modules/Simple Region Growing|Simple Region Growing]] (Jim Miller, Harini Veeraraghavan) <br />
*Specialized<br />
**[[Documentation/4.0/EMSegment Command-line | EMSegment Command-line]] (Kilian Pohl) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/ForegroundMasking|Foreground Masking (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/MeshContourSegmentation|Mesh Contour Segmentation]] (Allen Tannenbaum) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/RobustStatisticsSegmenter|Robust Statistics Segmentation]] (Yi Gao)<br />
<br />
==Quantification==<br />
*[[Documentation/{{documentation/version}}/Modules/DataProbe|Data Probe]] (Steve Pieper)<br />
*[[Documentation/4.0/Modules/LabelStatistics|Label Statistics]] (Steve Pieper)<br />
*[[Documentation/4.0/Modules/SUVComputation|SUV Computation]] (Nicole Aucoin)<br />
* Change quantification<br />
** [[Documentation/4.0/Modules/IntensityDifferenceMetric|Intensity Difference Metric]] (Andrey Fedorov)<br />
<br />
==Diffusion== <br />
*DWI to Full Brain Tractography (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
*Denoising<br />
**Joint Rician LMMSE Image Filter (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**Rician LMMSE Image Filter (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
*Tractography<br />
**[[Documentation/4.0/Modules/TractographyDisplay|Tractography Display]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/TractographyFiducialSeeding|Tractography Fiducial Seeding]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/Seeding|Tractography Labelmap Seeding]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
*Utilities<br />
**[[Documentation/4.0/Modules/DiffusionTensorEstimation|Diffusion Tensor Estimation]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/DiffusionTensorMathematics|Diffusion Tensor Scalar Measurements]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/DiffusionWeightedMasking|Mask from Diffusion Weighted Images]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/ResampleDTI|Resample DTI Volume]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
==IGT==<br />
<br />
==Filtering==<br />
*[[Documentation/4.0/Modules/N4ITKBiasFieldCorrection | N4ITK Bias Field Correction]] (Andrey Fedorov)<br />
*[[Documentation/4.0/Modules/CheckerBoard|CheckerBoard]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/ExtractSkeleton|Extract Skeleton]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/HistogramMatching|Histogram Matching]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/ImageLabelCombine|Image Label Combine]] (Alex Yarmarkovich) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/ResampleScalarVectorDWIVolume|Resample Scalar/Vector/DWI Volume]] (Francois Budin) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/Threshold|Threshold Image]] (Nicole Aucoin) <br />
*[[Documentation/4.0/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*Resample Tools<br />
**[[Documentation/4.0/Modules/ResampleVolume|Resample Volume]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*Arithmetic <br />
**[[Documentation/4.0/Modules/Add| Add Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/Cast| Cast Image]] (Nicole Aucoin) <br />
**[[Documentation/4.0/Modules/Mask| Mask Image]] (Nicole Aucoin) <br />
**[[Documentation/4.0/Modules/Multiply| Multiply Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/Subtract| Subtract Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*Denoising<br />
**[[Documentation/4.0/Modules/GradientAnisotropicDiffusion |Gradient Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]] <br />
**[[Documentation/4.0/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/GaussianBlurImageFilter|Gaussian Blur]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/MedianImageFilter|Median Image Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*Morphology<br />
**[[Documentation/4.0/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole]] (Jim Miller)<br />
**[[Documentation/4.0/Modules/GrayscaleGrindPeakImageFilter|Grayscale Grind Peak]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
==Surface Models==<br />
*[[Documentation/4.0/Modules/GrayscaleModelMaker| Grayscale Model Maker]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*Label Map Smoothing<br />
*[[Documentation/4.0/Modules/MergeModels| Merge Models]] (Nicole Aucoin) <br />
*[[Documentation/4.0/Modules/ModelMaker| Model Maker]] (Nicole Aucoin) <br />
*[[Documentation/4.0/Modules/PolyDataToLabelmap| PolyData To LabelMap]] (Nicole Aucoin) <br />
*[[Documentation/4.0/Modules/ProbeVolumeWithModel| Probe Volume with Model (Paint)]] (Lauren O'Donnell) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
==Converters==<br />
*[[Documentation/4.0/Modules/ImageReadDicomWrite|Create Dicom Series]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/Crop Volume|Crop Volume]] (Andrey Fedorov)<br />
*[[Documentation/4.0/Modules/DicomToNrrdConverter|Dicom to Nrrd Converter]] (Jim Miller) <br />
*[[Documentation/4.0/Modules/OrientImage| Orient Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
==Endoscopy==<br />
*[[Documentation/4.0/Modules/Endoscopy|Endoscopy]] (Steve Pieper)<br />
<br />
==Developer Tools==<br />
*[[Documentation/4.0/Modules/Cameras|Cameras]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/EventBroker|Event Broker]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/ExecutionModelTour |Execution Model Tour]] (JC Fillion-Robin) [[image:UnderConstruction.png|tumb|10px]]<br />
*Module Template<br />
*Multiple Models Example<br />
*Performance Tests<br />
*Tractography<br />
<br />
==Legacy==<br />
*Converters<br />
**BSpline to Deformation Field<br />
*Diffusion<br />
**Denoising<br />
***Unbiased Non Local Means Filter for DWI<br />
*Filtering<br />
**[[Documentation/4.0/Modules/MRIBiasFieldCorrection|MRI Bias Field Correction]] (Sylvain Jaume) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/OtsuThresholdImageFilter|Otsu Threshold]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]<br />
**Resample Scalar Volume<br />
*Registration<br />
**[[Documentation/4.0/Modules/RigidRegistration|Rigid Registration]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/AffineRegistration|Affine Registration]] (Daniel Blezek) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/BSplineDeformableRegistration|Nonrigid BSpline Registration]] [[image:UnderConstruction.png|tumb|10px]]<br />
**Nonrigid BSpline Registration<br />
**Expert Automated Registration<br />
**[[Documentation/4.0/Modules/LinearRegistration|Linear Registration]] [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/TestGridTransformRegistration|Test Grid Transform Registration]] [[image:UnderConstruction.png|tumb|10px]]<br />
**Robust Multiresolution Affine Registration<br />
*Segmentation<br />
**[[Documentation/4.0/Modules/OtsuThresholdSegmentation|Otsu Threshold Segmentation]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
==Utilities==<br />
*Transform MRML Files to NewSegmenter Standard<br />
<br />
=Extensions=<br />
<br />
'''Introduction'''<br />
<br />
* Slicer Extensions are the "on-ramp" to the Slicer "highway". slicer Extensions provide a voluntary mechanism for anybody, including third parties, to extend the functionality of 3d Slicer.<br />
* While the '''Slicer license''' is suggested for extensions, it is '''not required'''. Please review the documentation of the extension carefully as some extensions might have a "non-Slicer" license.<br />
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. <br />
* In case of problems with extensions, please talk directly to the developers of the extensions.<br />
* Information for developers can be found [[Slicer4:Extensions|here]]. See [[Module:EndUserDocumentationTemplate-4.0|here]] for the end-user documentation template.<br />
* In Slicer 4, all new modules will begin as "Immature Extensions". They will progress to the status of "Mature Extensions", when they meet all the criteria listed below. In order to become part of the main Slicer distribution a discussion with the Slicer core team will have to be initiated after reaching the mature extension status. While extensions can be made available under many licenses, the main Slicer distribution will contain ONLY code under the slicer license, with no known IP liabilities.<br />
<br />
==Collections==<br />
Collections are groups of extensions that can be downloaded in a single operation. You can think of them as the equivalent to a playlist.<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
! id<br />
! Thumbnail<br />
! Name<br />
! Short Description<br />
! Maturity<br />
! Slicer License<br />
! Search terms<br />
! Contact Information<br />
|-<br />
| 1<br />
| [[Image:Slicervmtk logo.png|60px|lleft|Replace the image with your image, replace the generic documentation link with a link to your documentation|link=Module:EndUserDocumentationTemplate-4.0]] <br />
| MyCollection<br />
| This is a collection of extensions that will do something miraculous with your images<br />
| [[File:StableExtensionIcon.png|80px]]<br />
| [[File:SlicerLicenseIcon.png|80px]]<br />
| segmentation, level set<br />
| my-email at mit.edu<br />
|-<br />
|}<br />
<br />
<br />
<br />
<br />
==Table Of Extensions==<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
! id<br />
! Thumbnail<br />
! Name<br />
! Short Description<br />
! Maturity<br />
! Slicer License<br />
! Search terms<br />
! Contact Information<br />
|-<br />
| 1<br />
| [[Image:SkullStripperSurface-3-6.png|60px|lleft|Replace the image with your image, replace the generic documentation linke with a link to your documentation|link=Module:EndUserDocumentationTemplate-4.0]] <br />
| MyExtension<br />
| This is an extension that will do something wonderful with your data<br />
| [[File:ExperimentalExtensionIcon.png|80px]]<br />
| [[File:NoSlicerLicenseIcon.png|80px]]<br />
| filter, anisotropic<br />
| my-email at gmail.com<br />
|-<br />
| 2<br />
| [[Image:Slicervmtk logo.png|60px|lleft|Replace the image with your image, replace the generic documentation linke with a link to your documentation|link=Module:EndUserDocumentationTemplate-4.0]] <br />
| MyExtension<br />
| This is an extension that will do something miraculous with your images<br />
| [[File:StableExtensionIcon.png|80px]]<br />
| [[File:SlicerLicenseIcon.png|80px]]<br />
| segmentation, level set<br />
| my-email at mit.edu<br />
|-<br />
|}<br />
<br />
<br />
<br />
'''Caption for the table of extensions'''<br />
<gallery heights="50px" perrow="4"><br />
Image:SlicerLicenseIcon.png| Distributed under the [http://www.slicer.org/pages/LicenseText Slicer License]<br />
Image:NoSlicerLicenseIcon.png| Distributed under a Non Slicer License<br />
Image:ExperimentalExtensionIcon.png|Work in progress (aka mess)<br>Use with care<br>Might not work all the time<br>Might not be available for all platforms<br />
Image:StableExtensionIcon.png|Stable <br>Full documentation <br>Works as advertised <br>Compiles on all supported platforms<br>Email support works<br />
</gallery></div>Pohlhttps://www.slicer.org/w/index.php?title=Documentation/4.0&diff=23434Documentation/4.02011-11-28T20:34:48Z<p>Pohl: /* Segmentation */</p>
<hr />
<div>__NOTOC__<br />
<br />
<!-- TODO: Create a template that will list all documentation links --><br />
<small><span class="versionlist">[[Documentation/4.0|4.0]] [[Documentation/3.6|3.6]] [[Documentation/3.5|3.5]] [[Documentation/3.4|3.4]] [[Documentation/3.2|3.2]] [[Documentation|ALL VERSIONS]]</span></small><br />
<br />
=Table of Content=<br />
{| border="0" align="center" width="100%" valign="top" cellspacing="7" cellpadding="2"<br />
|-<br />
! width="33%"|<br />
! |<br />
! width="33%"|<br />
! |<br />
! width="33%"|<br />
|- <br />
|valign="top"|<br />
<br />
===Slicer Application===<br />
----<br />
<big>'''<br />
*[[Documentation/{{documentation/version}}/SlicerApplication/MainApplicationGUI| Main Application GUI]] (Wendy Plesniak)<br />
<br />
*[[Documentation/{{documentation/version}}/SlicerApplication/KeyboardShortcuts | "Hot-keys" and Keyboard Shortcuts]] (Wendy Plesniak)<br />
<br />
*[[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration | Computer configurations]] (Steve Pieper)<br />
<br />
*[[Documentation/{{documentation/version}}/SlicerApplication/LoadingData | Loading]] or [[Documentation/{{documentation/version}}/SlicerApplication/SavingData | Saving]] data and listing of [[Documentation/{{documentation/version}}/SlicerApplication/SupportedDataFormat | supported data formats]]. (Julien Finet)<br />
<!-- : scenes, DICOM, volumes, models, fiducials, transforms, etc. --><br />
<br />
*[[Documentation/{{documentation/version}}/SlicerApplication/StereoViewing | Setting up and using stereoscopic viewing]] (Curtis Lisle)''' <br />
</big><br />
<br />
===Mailing Lists===<br />
----<br />
* [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users Mailing list for users]<br />
* [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-devel Mailing list for developers]<br />
<br />
<!--<br />
*[[Modules:ExtensionsManagementWizard-Documentation-4.0| Extensions Management Wizard]] (xx)<br />
--><br />
<br />
|bgcolor="#CCCCCC"|<br />
|valign="top"|<br />
<br />
===Module Categories ===<br />
----<br />
<big>'''<br />
* [[#Core Modules|Core Modules]]<br />
* [[#Wizards|Wizards]]<br />
* [[#Informatics|Informatics]]<br />
* [[#Registration|Registration]]<br />
* [[#Segmentation|Segmentation]]<br />
* [[#Quantification|Quantification]]<br />
* [[#Diffusion|Diffusion]]<br />
* [[#IGT|IGT]]<br />
* [[#Filtering|Filtering]]<br />
* [[#Surface Models|Surface Models]]<br />
* [[#Converters|Converters]]<br />
* [[#Endoscopy|Endoscopy]]<br />
* [[#Developer Tools|Developer Tools]]<br />
* [[#Legacy|Legacy]]<br />
* [[#Utilities|Utility]]<br />
</big><br />
|bgcolor="#CCCCCC"|<br />
|valign="top"|<br />
<br />
===Miscellaneous===<br />
----<br />
<!-- * [[Documentation/{{documentation/version}}/ImageGallery|Image gallery]] --><br />
<br />
* [[Slicer4:VisualBlog|Visual blog]]<br />
: Set of screenshots showing Slicer in action.<br />
<br />
<!--<br />
* [[Documents and links]]<br />
: Set of presentations made on Slicer and document talking about it.<br />
<br />
--><br />
* [[Documentation/4.0/Training|Training pages]]<br />
: Information on how to use Slicer {{documentation/version}}<br />
<br />
* [[Documentation/{{documentation/version}}/FAQ|FAQ]]<br />
: Set of common questions/answers<br />
<br />
===Developers Corner===<br />
----<br />
* [[Documentation/{{documentation/version}}/Developers | Developers Information]]<br />
: Handy Developer Info<br />
|}<br />
<br />
=General Information=<br />
{|width="100%"<br />
|rowspan="3"|<br />
{{Infobox<br />
|name = 3D Slicer {{documentation/version}}<br />
|above = 3D Slicer<br />
|abovestyle = <br />
<br />
|image = [[File:3DSlicer4Logo-H-218X144.png|218px|alt=3D Slicer {{documentation/version}}]]<br />
|imagestyle = <br />
|headerstyle = background:#E7DCC3;<br />
|labelstyle = <br />
|datastyle = <br />
<br />
|header1 = Description<br />
|label1 = <br />
|data1 =<br />
|header2 =<br />
|label2 = <br />
|data2 = Research platform for the analysis and visualization of medical images, including image guided therapy.<br />
|header3 =<br />
|label3 = <br />
|data3 = Free and extensible open source package.<br />
|header4 =<br />
|label4 = Multi-platform<br />
|data4 = Linux, MacOSX, Windows<br />
|header5 =<br />
|label5 = Version<br />
|data5 = {{documentation/version}}<br />
|header6 =<br />
|label6 = License<br />
|data6 = [http://www.slicer.org/pages/LicenseText Contribution and Software License Agreement]<br />
}}<br />
|align="center"|<br />
[[{{collaborator|logo|slicer4}}|x350px]] <br />
|-<br />
|<br />
{{ombox<br />
|type=content<br />
|text=The {{documentation/version}} release of 3D Slicer contains significant changes both to the organization of the software and to the functionality. Please check the [[Documentation/{{documentation/version}}/Announcements | Announcement page]] for more details. The community contributing to Slicer {{documentation/version}} is [[Documentation/{{documentation/version}}/Acknowledgment Team|acknowledged here]].<br />
}}<br />
|-<br />
|<br />
{{ombox | text = For information on how to obtain Slicer {{documentation/version}} please go to the [[Snapshots|Download Pages]]. }}<br />
|}<br />
<br />
=Requirements for Modules=<br />
* The module is '''feature complete''', i.e. it does everything that it advertises<br />
* The module has a '''test'''. See [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Execution_Model_Testing '''here'''] for more information.<br />
* The module is fully documented. [[Documentation/{{documentation/version}}/Modules/YOURMODULENAME|Template]] and [[Documentation/{{documentation/version}}/HowTo|How-to]] for the end user documentation.<br />
* The module complies with [[Documentation-Rons-Rules-For-Tools|Rons rules for tool]] and the style guide lines, including [[Slicer3:Human_Interface_and_Style_Guide_for_Developers#Colors:_application_palettes|color palette]].<br />
* Use logos listed in the [[Template:Collaborator|Collaborators Template]].<br />
<br />
=Modules by Category=<br />
==Core Modules==<br />
*[[Documentation/{{documentation/version}}/Modules/Annotations|Annotations]] (Nicole Aucoin) <br />
*[[Documentation/{{documentation/version}}/Modules/Colors|Colors]] (Nicole Aucoin) <br />
*[[Documentation/{{documentation/version}}/Modules/Data|Data]] (Julien Finet)<br />
*[[Documentation/{{documentation/version}}/Modules/DICOM|DICOM]] (Steve Pieper)<br />
*[[Documentation/{{documentation/version}}/Modules/Editor|Editor]] (Steve Pieper)<br />
*[[Documentation/{{documentation/version}}/Modules/Models|Models]] (Nicole Aucoin)<br />
*[[Documentation/{{documentation/version}}/Modules/SceneViews|SceneViews]] (Nicole Aucoin) <br />
*[[Documentation/{{documentation/version}}/Modules/Transforms|Transforms]] (Alex Yarmarkovich) <br />
*[[Documentation/{{documentation/version}}/Modules/ViewControllers|View Controllers]] (Jim Miller) <br />
*[[Documentation/{{documentation/version}}/Modules/Volumes|Volumes]] (Steve Pieper)<br />
*[[Documentation/{{documentation/version}}/Modules/VolumeRendering|Volume Rendering]] (Julien Finet)<br />
*[[Documentation/{{documentation/version}}/Modules/SlicerWelcome|Welcome to Slicer]] (Wendy Plesniak)<br />
<br />
==Wizards==<br />
*[[Documentation/{{documentation/version}}/Modules/ChangeTracker|ChangeTracker]] (Andrey Fedorov)<br />
<br />
==Informatics==<br />
*[[Documentation/{{documentation/version}}/Modules/SampleData|Sample Data]] (Steve Pieper)<br />
<br />
==Registration==<br />
*[[Documentation/4.0/Modules/BRAINSFit|General Brainsfit Registration]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/BRAINSResample|Resample Image (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]<br />
*Specialized<br />
**[[Documentation/4.0/Modules/ACPCTransform|ACPC Transform]] (Nicole Aucoin)<br />
**[[Documentation/4.0/Modules/BRAINSDemonWarp|Demon Registration (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/TransformFromFiducials|Fiducial Registration (BRAINS)]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]<br />
**Vector Demon Registration (Hans Johnson)<br />
<br />
==Segmentation==<br />
*[[Documentation/4.0/Modules/EMSegment Easy|EMSegment Easy (no atlas)]] (Kilian Pohl) <br />
*[[Documentation/4.0/Modules/EMSegmenter|EMSegment (with atlas)]] (Kilian Pohl) <br />
*[[Documentation/4.0/Modules/Simple Region Growing|Simple Region Growing]] (Jim Miller, Harini Veeraraghavan) <br />
*Specialized<br />
**EMSegment Command-line (Kilian Pohl) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/ForegroundMasking|Foreground Masking (BRAINS)]] (Hans Johnson) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/MeshContourSegmentation|Mesh Contour Segmentation]] (Allen Tannenbaum) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/RobustStatisticsSegmenter|Robust Statistics Segmentation]] (Yi Gao)<br />
<br />
==Quantification==<br />
*[[Documentation/{{documentation/version}}/Modules/DataProbe|Data Probe]] (Steve Pieper)<br />
*[[Documentation/4.0/Modules/LabelStatistics|Label Statistics]] (Steve Pieper)<br />
*[[Documentation/4.0/Modules/SUVComputation|SUV Computation]] (Nicole Aucoin)<br />
* Change quantification<br />
** [[Documentation/4.0/Modules/IntensityDifferenceMetric|Intensity Difference Metric]] (Andrey Fedorov)<br />
<br />
==Diffusion== <br />
*DWI to Full Brain Tractography (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
*Denoising<br />
**Joint Rician LMMSE Image Filter (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**Rician LMMSE Image Filter (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
*Tractography<br />
**[[Documentation/4.0/Modules/TractographyDisplay|Tractography Display]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/TractographyFiducialSeeding|Tractography Fiducial Seeding]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/Seeding|Tractography Labelmap Seeding]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
*Utilities<br />
**[[Documentation/4.0/Modules/DiffusionTensorEstimation|Diffusion Tensor Estimation]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/DiffusionTensorMathematics|Diffusion Tensor Scalar Measurements]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/DiffusionWeightedMasking|Mask from Diffusion Weighted Images]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/ResampleDTI|Resample DTI Volume]] (Demian Wasserman) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
==IGT==<br />
<br />
==Filtering==<br />
*[[Documentation/4.0/Modules/N4ITKBiasFieldCorrection | N4ITK Bias Field Correction]] (Andrey Fedorov)<br />
*[[Documentation/4.0/Modules/CheckerBoard|CheckerBoard]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/ExtractSkeleton|Extract Skeleton]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/HistogramMatching|Histogram Matching]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/ImageLabelCombine|Image Label Combine]] (Alex Yarmarkovich) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/ResampleScalarVectorDWIVolume|Resample Scalar/Vector/DWI Volume]] (Francois Budin) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/Threshold|Threshold Image]] (Nicole Aucoin) <br />
*[[Documentation/4.0/Modules/VotingBinaryHoleFillingImageFilter|Voting Binary Hole Filling]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*Resample Tools<br />
**[[Documentation/4.0/Modules/ResampleVolume|Resample Volume]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*Arithmetic <br />
**[[Documentation/4.0/Modules/Add| Add Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/Cast| Cast Image]] (Nicole Aucoin) <br />
**[[Documentation/4.0/Modules/Mask| Mask Image]] (Nicole Aucoin) <br />
**[[Documentation/4.0/Modules/Multiply| Multiply Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/Subtract| Subtract Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*Denoising<br />
**[[Documentation/4.0/Modules/GradientAnisotropicDiffusion |Gradient Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]] <br />
**[[Documentation/4.0/Modules/CurvatureAnisotropicDiffusion|Curvature Anisotropic Diffusion]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/GaussianBlurImageFilter|Gaussian Blur]] (Stephen Aylward) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/MedianImageFilter|Median Image Filter]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*Morphology<br />
**[[Documentation/4.0/Modules/GrayscaleFillHoleImageFilter|Grayscale Fill Hole]] (Jim Miller)<br />
**[[Documentation/4.0/Modules/GrayscaleGrindPeakImageFilter|Grayscale Grind Peak]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
==Surface Models==<br />
*[[Documentation/4.0/Modules/GrayscaleModelMaker| Grayscale Model Maker]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*Label Map Smoothing<br />
*[[Documentation/4.0/Modules/MergeModels| Merge Models]] (Nicole Aucoin) <br />
*[[Documentation/4.0/Modules/ModelMaker| Model Maker]] (Nicole Aucoin) <br />
*[[Documentation/4.0/Modules/PolyDataToLabelmap| PolyData To LabelMap]] (Nicole Aucoin) <br />
*[[Documentation/4.0/Modules/ProbeVolumeWithModel| Probe Volume with Model (Paint)]] (Lauren O'Donnell) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
==Converters==<br />
*[[Documentation/4.0/Modules/ImageReadDicomWrite|Create Dicom Series]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/Crop Volume|Crop Volume]] (Andrey Fedorov)<br />
*[[Documentation/4.0/Modules/DicomToNrrdConverter|Dicom to Nrrd Converter]] (Jim Miller) <br />
*[[Documentation/4.0/Modules/OrientImage| Orient Images]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
==Endoscopy==<br />
*[[Documentation/4.0/Modules/Endoscopy|Endoscopy]] (Steve Pieper)<br />
<br />
==Developer Tools==<br />
*[[Documentation/4.0/Modules/Cameras|Cameras]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/EventBroker|Event Broker]] (Julien Finet) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/ExecutionModelTour |Execution Model Tour]] (JC Fillion-Robin) [[image:UnderConstruction.png|tumb|10px]]<br />
*Module Template<br />
*Multiple Models Example<br />
*Performance Tests<br />
*Tractography<br />
<br />
==Legacy==<br />
*Converters<br />
**BSpline to Deformation Field<br />
*Diffusion<br />
**Denoising<br />
***Unbiased Non Local Means Filter for DWI<br />
*Filtering<br />
**[[Documentation/4.0/Modules/MRIBiasFieldCorrection|MRI Bias Field Correction]] (Sylvain Jaume) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/OtsuThresholdImageFilter|Otsu Threshold]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]<br />
**Resample Scalar Volume<br />
*Registration<br />
**[[Documentation/4.0/Modules/RigidRegistration|Rigid Registration]] (Jim Miller) [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/AffineRegistration|Affine Registration]] (Daniel Blezek) [[image:UnderConstruction.png|tumb|10px]]<br />
*[[Documentation/4.0/Modules/BSplineDeformableRegistration|Nonrigid BSpline Registration]] [[image:UnderConstruction.png|tumb|10px]]<br />
**Nonrigid BSpline Registration<br />
**Expert Automated Registration<br />
**[[Documentation/4.0/Modules/LinearRegistration|Linear Registration]] [[image:UnderConstruction.png|tumb|10px]]<br />
**[[Documentation/4.0/Modules/TestGridTransformRegistration|Test Grid Transform Registration]] [[image:UnderConstruction.png|tumb|10px]]<br />
**Robust Multiresolution Affine Registration<br />
*Segmentation<br />
**[[Documentation/4.0/Modules/OtsuThresholdSegmentation|Otsu Threshold Segmentation]] (Bill Lorensen) [[image:UnderConstruction.png|tumb|10px]]<br />
<br />
==Utilities==<br />
*Transform MRML Files to NewSegmenter Standard<br />
<br />
=Extensions=<br />
<br />
'''Introduction'''<br />
<br />
* Slicer Extensions are the "on-ramp" to the Slicer "highway". slicer Extensions provide a voluntary mechanism for anybody, including third parties, to extend the functionality of 3d Slicer.<br />
* While the '''Slicer license''' is suggested for extensions, it is '''not required'''. Please review the documentation of the extension carefully as some extensions might have a "non-Slicer" license.<br />
* For a subset of extensions, you can use the extension wizard in Slicer to find their webpages and to install/uninstall individual extensions. <br />
* In case of problems with extensions, please talk directly to the developers of the extensions.<br />
* Information for developers can be found [[Slicer4:Extensions|here]]. See [[Module:EndUserDocumentationTemplate-4.0|here]] for the end-user documentation template.<br />
* In Slicer 4, all new modules will begin as "Immature Extensions". They will progress to the status of "Mature Extensions", when they meet all the criteria listed below. In order to become part of the main Slicer distribution a discussion with the Slicer core team will have to be initiated after reaching the mature extension status. While extensions can be made available under many licenses, the main Slicer distribution will contain ONLY code under the slicer license, with no known IP liabilities.<br />
<br />
==Collections==<br />
Collections are groups of extensions that can be downloaded in a single operation. You can think of them as the equivalent to a playlist.<br />
<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
! id<br />
! Thumbnail<br />
! Name<br />
! Short Description<br />
! Maturity<br />
! Slicer License<br />
! Search terms<br />
! Contact Information<br />
|-<br />
| 1<br />
| [[Image:Slicervmtk logo.png|60px|lleft|Replace the image with your image, replace the generic documentation link with a link to your documentation|link=Module:EndUserDocumentationTemplate-4.0]] <br />
| MyCollection<br />
| This is a collection of extensions that will do something miraculous with your images<br />
| [[File:StableExtensionIcon.png|80px]]<br />
| [[File:SlicerLicenseIcon.png|80px]]<br />
| segmentation, level set<br />
| my-email at mit.edu<br />
|-<br />
|}<br />
<br />
<br />
<br />
<br />
==Table Of Extensions==<br />
{| class="wikitable sortable labelpage labelpagetable" border="1"<br />
|-<br />
! id<br />
! Thumbnail<br />
! Name<br />
! Short Description<br />
! Maturity<br />
! Slicer License<br />
! Search terms<br />
! Contact Information<br />
|-<br />
| 1<br />
| [[Image:SkullStripperSurface-3-6.png|60px|lleft|Replace the image with your image, replace the generic documentation linke with a link to your documentation|link=Module:EndUserDocumentationTemplate-4.0]] <br />
| MyExtension<br />
| This is an extension that will do something wonderful with your data<br />
| [[File:ExperimentalExtensionIcon.png|80px]]<br />
| [[File:NoSlicerLicenseIcon.png|80px]]<br />
| filter, anisotropic<br />
| my-email at gmail.com<br />
|-<br />
| 2<br />
| [[Image:Slicervmtk logo.png|60px|lleft|Replace the image with your image, replace the generic documentation linke with a link to your documentation|link=Module:EndUserDocumentationTemplate-4.0]] <br />
| MyExtension<br />
| This is an extension that will do something miraculous with your images<br />
| [[File:StableExtensionIcon.png|80px]]<br />
| [[File:SlicerLicenseIcon.png|80px]]<br />
| segmentation, level set<br />
| my-email at mit.edu<br />
|-<br />
|}<br />
<br />
<br />
<br />
'''Caption for the table of extensions'''<br />
<gallery heights="50px" perrow="4"><br />
Image:SlicerLicenseIcon.png| Distributed under the [http://www.slicer.org/pages/LicenseText Slicer License]<br />
Image:NoSlicerLicenseIcon.png| Distributed under a Non Slicer License<br />
Image:ExperimentalExtensionIcon.png|Work in progress (aka mess)<br>Use with care<br>Might not work all the time<br>Might not be available for all platforms<br />
Image:StableExtensionIcon.png|Stable <br>Full documentation <br>Works as advertised <br>Compiles on all supported platforms<br>Email support works<br />
</gallery></div>Pohlhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/EMSegmenter&diff=23171Documentation/4.0/Modules/EMSegmenter2011-11-23T20:05:41Z<p>Pohl: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work was funded by the ARRA Supplement to the Neuroimage Analysis Center (NAC), funded by the National Institutes of Health. Information on NAC can be obtained from the [http://nac.spl.harvard.edu/pages/Overview NAC website].<br><br />
Author: Kilian Pohl, UPenn <br><br />
Contributor1: Daniel Haehn, UPENN<br><br />
Contact: Kilian Pohl, <email>pohl.kilian@gmail.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:UPenn-logo.png|University of Pennsylvania<br />
|Image:Logo-splnew.jpg|Surgical Planning Laboratory <br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<br />
[[Image:EMSegmenterLogo.png|thumb|width=200px|Hierarchical Model of the EMSegmenter]]<br />
This module is designed for users who perform atlas based medical image segmentation. The module can be operated in <B>two</B> modes: <br><br />
An <B>advanced mode (Button: Adjust Parameters)</B> that allows users to parameterize the tool to specific segmentation tasks and a <B>simple mode (Button: Use Existing Setting)</B> which is designed for users who would like to apply the predefined parameterization to new data with a minimal amount of user interaction. One can also apply the parameterization to medical scans via the command-line executable <B>EMSegmentCommandLine</B>. The remainder of this sections describes the work flow of the two modes in further detail:<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The purpose of the module is to configure the algorithm to automatically segment anatomical structures in medical images. First the user has to specify parameters defining the image protocol and the anatomical structures of interests. This process results in a template that the module uses to automatically segment large data sets. The template is composed of atlas data and a non-trivial collection of parameters for the EMSegment algorithm. <br />
<br />
Once the parameters are specified, the target images are segmented<br />
using the EM Segmentation algorithm (Pohl et al. TMI 2007). If the results are<br />
satisfactory, the template is saved and can be used later to segment<br />
new images (via the GUI or batch processing). If the results are<br />
unsatisfactory, the parameters can be modified and the segmentation<br />
re-run.<br />
<br />
One important aspect of the project is the workflow wizard. This wizard simplifies the module by dividing the complicated template specification task into a number of smaller, intuitive steps. The wizard allows to [[EMSegmenter-CreateTask|create tasks]] and to use them to analyze data sets.<br />
<br />
There are multiple [[EMSegmenter-Tasks|'''predefined tasks''']] which are ready to use.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
* EMSegmenter Tutorial for 3D Slicer 3.6.2<br />
** [[Media:EMSegmenterTutorialSimpleMode-2010-Dec.pdf | Simple Mode]] - [[Media:MRIHumanBrain_T1_aligned.nrrd | Tutorial Data]]<br />
** [[Media:EMSegmenterTutorialAdvancedMode-2010-Dec.pdf | Advanced Mode]] - [[Media:MRIHumanBrain_T1_aligned.nrrd | Tutorial Data]]<br />
<br />
* EMSegmenter Tutorial for 3D Slicer 3.6.3<br />
** [[Media:EMSegmenterTutorialSimpleMode-Slicer-3.6.3-1.pdf | Simple Mode]] - [[Media:MRIHumanBrain_T1_aligned.nrrd | Tutorial Data]]<br />
** [[Media:EMSegmenterTutorialAdvancedMode-Slicer-3.6.3-1.pdf | Advanced Mode]] - [[Media:MRIHumanBrain_T1_aligned.nrrd | Tutorial Data]]<br />
<br />
<br />
* A full Tutorial for the two EMSegment modules<br />
<br />
These slides and data describe the Slicer3 implementation of the two EMSegment GUI and command-line modules and demonstrate their use.<br />
<br />
[[Media:EMSegTutorial-AHM2008.ppt | Tutorial Slides]] - [[Media:EMSegTutorial-AHM2008.zip | Tutorial Data]]<br />
<br />
* Another detailed training tutorial on EMSegment algorithm and the Slicer3 EMSegment module.<br />
<br />
[http://wiki.na-mic.org/Wiki/images/2/2f/AutomaticSegmentation_SoniaPujol_Munich2008.ppt Tutorial Slides] - <br />
[http://wiki.na-mic.org/Wiki/images/b/b7/AutomaticSegmentation.tar.gz Training Data]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
=== Simple Mode ===<br />
The work flow is defined by only two steps.<br />
==== Step 1: Define Task ====<br />
Select an already existing task and click on the "Use Existing Settings" button to use for the simple mode in the pop up window.<br />
A MRML file defining parameters of the algorithm specific to the task as well atlas data are automatically downloaded for existing Tasks.<br />
==== Step 2: Define Input Channels ====<br />
In this step the user specifies the scans to be segmented as well as the check list associated with the preprocessing.<br />
A click on the 'Segment' button is enough to start the pre-processing and the subsequent segmentation.<br />
<br />
=== Advanced Mode ===<br />
Unlike the Simple mode, the advanced mode is defined by nine steps which one can navigate via the "Back", "Next", or "Segment" button. The Segment button jumps right away to the last step of the work flow and segments the medical scans into the structures of interests. <br />
==== Step 1: Define Task ====<br />
Select an already existing task or define a new one. Click on the button "Adjust Parameters" for the advanced mode in the pop up window. A MRML file defining parameters of the algorithm specific to the task as well atlas data are automatically downloaded for existing Tasks.<br />
==== Step 2: Define Input Channel ====<br />
Define the number of input channels as well as the name of each channel and the corresponding scan associated with the channel. If using multiple input channel(scans) which are not aligned with each other then check on the check-box button "Align input scans".<br />
==== Step 3: Define Anatomical Tree ====<br />
The user specifies the hierarchical relationship between the anatomical structures. The tree will refine the complex segmentation task into a set of easier segmentation problems. A sub-classes is added to an existing structure by right-clicking on the structure and selecting "Add sub-class". The name, label, and color of a structure are modified by selecting the structure in the tree and then defining these attributes in the panel below.<br />
==== Step 4: Define Atlas ====<br />
In this step, the user links the probabilistic atlases to the anatomical structures in the tree by first highlighting the structure and then selecting the volume representing the probability map of that structure in the panel below. We note that the probabilistic atlas of structures with sub-structures is defined by the atlases of the sub-structures and thus is not explicitly defined. <br />
==== Step 5: Edit Registration Parameters ====<br />
The atlas is in general not aligned to the specific patient scans defined in Step 2. The user assigns in this step the scans of the atlas corresponding to the input channels in Step 2 as well as the type of registration (Affine / Deformable) and the interpolation. <br />
==== Step 6: Define Preprocessing ==== <br />
[[Image:EMSegmenter_DisplayClassDistribution.png | thumb|width=200px|Graph showing intensity distributions of a set of anatomical structures]] This step is defined via a task specific Tcl file that configures the preprocessing pipeline of the input scans and the atlas. Complete the step by going through the task specific check list, clicking on the 'Next' button, and clicking on the 'Yes' button of the pop up window. One can define a new preprocessing pipeline by specifying the pipeline via a Tcl file, placing the file in Slicer3-build/share/Slicer3/Modules/EMSegment/Tasks and listing the file name in the task specific MRML file.<br />
<br />
==== Step 7: Specify Intensity Distribution ==== <br />
Refining the intensity distribution for each structure of interest is often a critical step in the parameterization of the segmentation algorithm. It includes an overview window that shows the distribution in a 1D and 2D graph (press "Plot Distributions" to view the graph). By placing the mouse cursor in the 2D viewers the corresponding intensity value is shown in the graph.<br />
<br />
==== Step 8: Edit Node-based Parameters ====<br />
Users specify the relative to weight of a node in the tree with respect to other structures which are children of the same parent node. The first tab also specifies the weight of the input channels as well as the atlases. The value 'Alpha' specifies the smoothing applied to the structure (via MRFs). The second tab (Stopping Condition) lists the number of iterations associated with the segmentation task. By default, the Bias iteration is set to -1 which means that it is performed each iteration. If the value is greater -1 then the inhomogeneity computation is stopped after n iterations. The third tab specifies printing out intermediate results, which are saved in the working directory specified in the next step <br />
==== Step 9: Define Miscellaneous Parameters ====<br />
This panels lists the general parameters necessary for segmenting images. Users can specify a region of interest to speed up the segmentation algorithm. Pressing the 'Segment' button creates a label map of the anatomical structures.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
Please visit the [[ Documentation/4.0#Segmentation | segmentation section ]] for similar modules <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
* Wells III W.M., Grimson W.E.L., Kikinis R., Jolesz F.A. [http://www.spl.harvard.edu/publications/item/view/847 Adaptive segmentation of MRI data.] IEEE Trans Med Imaging. 1996; 15(4):429-442.<br />
<br />
* Pohl K.M., Fisher III J.W., Grimson W.E.L., Kikinis R., Wells III W.M. [http://www.spl.harvard.edu/publications/item/view/58 A Bayesian model for joint segmentation and registration.] Neuroimage. 2006 May 15;31(1):228-39.<br />
<br />
*Pohl K, Bouix S, Nakamura M, Rohlfing T, McCarley R, Kikinis R, Grimson W, Shenton M, Wells W. [http://www.slicer.org/pages/Special:PubDB_View?dspaceid=608 A Hierarchical Algorithm for MR Brain Image Parcellation.] IEEE Transactions on Medical Imaging. 2007 Sept;26(9):1201-1212. [[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}} <br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
{{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
If you are documenting a CLI, the category should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-category|xmlurl=http://path/to/YOURMODULENAME.xml }}</pre><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Pohlhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/EMSegment_Easy&diff=23170Documentation/4.0/Modules/EMSegment Easy2011-11-23T20:04:42Z<p>Pohl: /* Step 5: Define Miscellaneous Parameters */</p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work was funded by the ARRA Supplement to the Neuroimage Analysis Center (NAC), funded by the National Institutes of Health. Information on NAC can be obtained from the [http://nac.spl.harvard.edu/pages/Overview NAC website].<br><br />
Author: Kilian Pohl, UPenn <br><br />
Contributor1: Daniel Haehn, UPENN<br><br />
Contact: Kilian Pohl, <email>pohl.kilian@gmail.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:UPenn-logo.png|University of Pennsylvania<br />
|Image:Logo-splnew.jpg|Surgical Planning Laboratory <br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<br />
This module is designed for users who want to do a quick intensity based image segmentation. The remainder of this sections describes the work flow of the two modes in further detail: <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
MR image segmentation <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
=== Step 1: Define Input Datasets ===<br />
Define the volumes to be segmented. Each volume has to be from the subject and has to represent a different mode, such as T1 and FLAIR, than the other input volumes.<br />
<br />
=== Step 2: Define Structure ===<br />
The user specifies the number of structures to be segmented and the label of each structure. You can further add class to an existing structure by right-clicking on the structure and selecting "Add sub-class". The label and corresponding color of a structure are modified by selecting the structure in the tree.<br />
<br />
=== Step 3: Sampling and Class Weights === <br />
Define the intensity distribution for each structure of interest by taking samples in the image of interest. Users can also specify the relative to weight of a node in the tree with respect to other structures. If a class should be overestimated in the final label map then this can be adjusted by lowering the weight of that structure and repeating the segmentation.<br />
<br />
=== Step 4: Edit Node-based Parameters ===<br />
Users specify the relative to weight of a node in the tree with respect to other structures which are children of the same parent node. The first tab also specifies the weight of the input channels as well as the atlases. The value 'Alpha' specifies the smoothing applied to the structure (via MRFs). The second tab (Stopping Condition) lists the number of iterations associated with the segmentation task. By default, the Bias iteration is set to -1 which means that it is performed each iteration. If the value is greater -1 then the inhomogeneity computation is stopped after n iterations. The third tab specifies printing out intermediate results, which are saved in the working directory specified in the next step <br />
=== Step 5: Miscellaneous ===<br />
This panels allows the user to specify the region of interest to be segmented. Pressing the 'Segment' button starts the segmentation. <br />
<br />
Once the parameters are specified, the target images are segmented<br />
using the EM Segmentation algorithm (Pohl et al. TMI 2007). The label map with corresponding statistics is returned after successful completion of the algorithm. <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
Please visit the [[ Documentation/4.0#Segmentation | segmentation section ]] for similar modules <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
* Wells III W.M., Grimson W.E.L., Kikinis R., Jolesz F.A. [http://www.spl.harvard.edu/publications/item/view/847 Adaptive segmentation of MRI data.] IEEE Trans Med Imaging. 1996; 15(4):429-442.<br />
<br />
* Pohl K.M., Fisher III J.W., Grimson W.E.L., Kikinis R., Wells III W.M. [http://www.spl.harvard.edu/publications/item/view/58 A Bayesian model for joint segmentation and registration.] Neuroimage. 2006 May 15;31(1):228-39.<br />
<br />
*Pohl K, Bouix S, Nakamura M, Rohlfing T, McCarley R, Kikinis R, Grimson W, Shenton M, Wells W. [http://www.slicer.org/pages/Special:PubDB_View?dspaceid=608 A Hierarchical Algorithm for MR Brain Image Parcellation.] IEEE Transactions on Medical Imaging. 2007 Sept;26(9):1201-1212. [[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
{{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
If you are documenting a CLI, the category should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-category|xmlurl=http://path/to/YOURMODULENAME.xml }}</pre><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Pohlhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/EMSegment_Easy&diff=23169Documentation/4.0/Modules/EMSegment Easy2011-11-23T20:02:59Z<p>Pohl: /* Step 3: Specify Intensity Distribution */</p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work was funded by the ARRA Supplement to the Neuroimage Analysis Center (NAC), funded by the National Institutes of Health. Information on NAC can be obtained from the [http://nac.spl.harvard.edu/pages/Overview NAC website].<br><br />
Author: Kilian Pohl, UPenn <br><br />
Contributor1: Daniel Haehn, UPENN<br><br />
Contact: Kilian Pohl, <email>pohl.kilian@gmail.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:UPenn-logo.png|University of Pennsylvania<br />
|Image:Logo-splnew.jpg|Surgical Planning Laboratory <br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<br />
This module is designed for users who want to do a quick intensity based image segmentation. The remainder of this sections describes the work flow of the two modes in further detail: <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
MR image segmentation <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
=== Step 1: Define Input Datasets ===<br />
Define the volumes to be segmented. Each volume has to be from the subject and has to represent a different mode, such as T1 and FLAIR, than the other input volumes.<br />
<br />
=== Step 2: Define Structure ===<br />
The user specifies the number of structures to be segmented and the label of each structure. You can further add class to an existing structure by right-clicking on the structure and selecting "Add sub-class". The label and corresponding color of a structure are modified by selecting the structure in the tree.<br />
<br />
=== Step 3: Sampling and Class Weights === <br />
Define the intensity distribution for each structure of interest by taking samples in the image of interest. Users can also specify the relative to weight of a node in the tree with respect to other structures. If a class should be overestimated in the final label map then this can be adjusted by lowering the weight of that structure and repeating the segmentation.<br />
<br />
=== Step 4: Edit Node-based Parameters ===<br />
Users specify the relative to weight of a node in the tree with respect to other structures which are children of the same parent node. The first tab also specifies the weight of the input channels as well as the atlases. The value 'Alpha' specifies the smoothing applied to the structure (via MRFs). The second tab (Stopping Condition) lists the number of iterations associated with the segmentation task. By default, the Bias iteration is set to -1 which means that it is performed each iteration. If the value is greater -1 then the inhomogeneity computation is stopped after n iterations. The third tab specifies printing out intermediate results, which are saved in the working directory specified in the next step <br />
=== Step 5: Define Miscellaneous Parameters ===<br />
This panels lists the general parameters necessary for segmenting images. Users can specify a region of interest to speed up the segmentation algorithm. Pressing the 'Segment' button creates a label map of the anatomical structures.<br />
<br />
Once the parameters are specified, the target images are segmented<br />
using the EM Segmentation algorithm (Pohl et al. TMI 2007). The label map with corresponding statistics is returned after successful completion of the algorithm. <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
Please look at [[ Documentation/4.0#Segmentation | Segmentation]] section<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
* Wells III W.M., Grimson W.E.L., Kikinis R., Jolesz F.A. [http://www.spl.harvard.edu/publications/item/view/847 Adaptive segmentation of MRI data.] IEEE Trans Med Imaging. 1996; 15(4):429-442.<br />
<br />
* Pohl K.M., Fisher III J.W., Grimson W.E.L., Kikinis R., Wells III W.M. [http://www.spl.harvard.edu/publications/item/view/58 A Bayesian model for joint segmentation and registration.] Neuroimage. 2006 May 15;31(1):228-39.<br />
<br />
*Pohl K, Bouix S, Nakamura M, Rohlfing T, McCarley R, Kikinis R, Grimson W, Shenton M, Wells W. [http://www.slicer.org/pages/Special:PubDB_View?dspaceid=608 A Hierarchical Algorithm for MR Brain Image Parcellation.] IEEE Transactions on Medical Imaging. 2007 Sept;26(9):1201-1212. [[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
{{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
If you are documenting a CLI, the category should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-category|xmlurl=http://path/to/YOURMODULENAME.xml }}</pre><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Pohlhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/EMSegment_Easy&diff=23168Documentation/4.0/Modules/EMSegment Easy2011-11-23T19:59:44Z<p>Pohl: /* Step 2: Define Anatomical Tree */</p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work was funded by the ARRA Supplement to the Neuroimage Analysis Center (NAC), funded by the National Institutes of Health. Information on NAC can be obtained from the [http://nac.spl.harvard.edu/pages/Overview NAC website].<br><br />
Author: Kilian Pohl, UPenn <br><br />
Contributor1: Daniel Haehn, UPENN<br><br />
Contact: Kilian Pohl, <email>pohl.kilian@gmail.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:UPenn-logo.png|University of Pennsylvania<br />
|Image:Logo-splnew.jpg|Surgical Planning Laboratory <br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<br />
This module is designed for users who want to do a quick intensity based image segmentation. The remainder of this sections describes the work flow of the two modes in further detail: <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
MR image segmentation <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
=== Step 1: Define Input Datasets ===<br />
Define the volumes to be segmented. Each volume has to be from the subject and has to represent a different mode, such as T1 and FLAIR, than the other input volumes.<br />
<br />
=== Step 2: Define Structure ===<br />
The user specifies the number of structures to be segmented and the label of each structure. You can further add class to an existing structure by right-clicking on the structure and selecting "Add sub-class". The label and corresponding color of a structure are modified by selecting the structure in the tree.<br />
<br />
=== Step 3: Specify Intensity Distribution === <br />
Defining the intensity distribution for each structure of interest through taking samples in the image of interest<br />
=== Step 4: Edit Node-based Parameters ===<br />
Users specify the relative to weight of a node in the tree with respect to other structures which are children of the same parent node. The first tab also specifies the weight of the input channels as well as the atlases. The value 'Alpha' specifies the smoothing applied to the structure (via MRFs). The second tab (Stopping Condition) lists the number of iterations associated with the segmentation task. By default, the Bias iteration is set to -1 which means that it is performed each iteration. If the value is greater -1 then the inhomogeneity computation is stopped after n iterations. The third tab specifies printing out intermediate results, which are saved in the working directory specified in the next step <br />
=== Step 5: Define Miscellaneous Parameters ===<br />
This panels lists the general parameters necessary for segmenting images. Users can specify a region of interest to speed up the segmentation algorithm. Pressing the 'Segment' button creates a label map of the anatomical structures.<br />
<br />
Once the parameters are specified, the target images are segmented<br />
using the EM Segmentation algorithm (Pohl et al. TMI 2007). The label map with corresponding statistics is returned after successful completion of the algorithm. <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
Please look at [[ Documentation/4.0#Segmentation | Segmentation]] section<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
* Wells III W.M., Grimson W.E.L., Kikinis R., Jolesz F.A. [http://www.spl.harvard.edu/publications/item/view/847 Adaptive segmentation of MRI data.] IEEE Trans Med Imaging. 1996; 15(4):429-442.<br />
<br />
* Pohl K.M., Fisher III J.W., Grimson W.E.L., Kikinis R., Wells III W.M. [http://www.spl.harvard.edu/publications/item/view/58 A Bayesian model for joint segmentation and registration.] Neuroimage. 2006 May 15;31(1):228-39.<br />
<br />
*Pohl K, Bouix S, Nakamura M, Rohlfing T, McCarley R, Kikinis R, Grimson W, Shenton M, Wells W. [http://www.slicer.org/pages/Special:PubDB_View?dspaceid=608 A Hierarchical Algorithm for MR Brain Image Parcellation.] IEEE Transactions on Medical Imaging. 2007 Sept;26(9):1201-1212. [[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
{{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
If you are documenting a CLI, the category should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-category|xmlurl=http://path/to/YOURMODULENAME.xml }}</pre><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Pohlhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/EMSegment_Easy&diff=23167Documentation/4.0/Modules/EMSegment Easy2011-11-23T19:57:42Z<p>Pohl: /* Step 1: Define Input Datasets */</p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work was funded by the ARRA Supplement to the Neuroimage Analysis Center (NAC), funded by the National Institutes of Health. Information on NAC can be obtained from the [http://nac.spl.harvard.edu/pages/Overview NAC website].<br><br />
Author: Kilian Pohl, UPenn <br><br />
Contributor1: Daniel Haehn, UPENN<br><br />
Contact: Kilian Pohl, <email>pohl.kilian@gmail.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:UPenn-logo.png|University of Pennsylvania<br />
|Image:Logo-splnew.jpg|Surgical Planning Laboratory <br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<br />
This module is designed for users who want to do a quick intensity based image segmentation. The remainder of this sections describes the work flow of the two modes in further detail: <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
MR image segmentation <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
=== Step 1: Define Input Datasets ===<br />
Define the volumes to be segmented. Each volume has to be from the subject and has to represent a different mode, such as T1 and FLAIR, than the other input volumes.<br />
<br />
=== Step 2: Define Anatomical Tree ===<br />
The user specifies the hierarchical relationship between the anatomical structures. The tree will refine the complex segmentation task into a set of easier segmentation problems. A sub-classes is added to an existing structure by right-clicking on the structure and selecting "Add sub-class". The name, label, and color of a structure are modified by selecting the structure in the tree and then defining these attributes in the panel below.<br />
=== Step 3: Specify Intensity Distribution === <br />
Defining the intensity distribution for each structure of interest through taking samples in the image of interest<br />
=== Step 4: Edit Node-based Parameters ===<br />
Users specify the relative to weight of a node in the tree with respect to other structures which are children of the same parent node. The first tab also specifies the weight of the input channels as well as the atlases. The value 'Alpha' specifies the smoothing applied to the structure (via MRFs). The second tab (Stopping Condition) lists the number of iterations associated with the segmentation task. By default, the Bias iteration is set to -1 which means that it is performed each iteration. If the value is greater -1 then the inhomogeneity computation is stopped after n iterations. The third tab specifies printing out intermediate results, which are saved in the working directory specified in the next step <br />
=== Step 5: Define Miscellaneous Parameters ===<br />
This panels lists the general parameters necessary for segmenting images. Users can specify a region of interest to speed up the segmentation algorithm. Pressing the 'Segment' button creates a label map of the anatomical structures.<br />
<br />
Once the parameters are specified, the target images are segmented<br />
using the EM Segmentation algorithm (Pohl et al. TMI 2007). The label map with corresponding statistics is returned after successful completion of the algorithm. <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
Please look at [[ Documentation/4.0#Segmentation | Segmentation]] section<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
* Wells III W.M., Grimson W.E.L., Kikinis R., Jolesz F.A. [http://www.spl.harvard.edu/publications/item/view/847 Adaptive segmentation of MRI data.] IEEE Trans Med Imaging. 1996; 15(4):429-442.<br />
<br />
* Pohl K.M., Fisher III J.W., Grimson W.E.L., Kikinis R., Wells III W.M. [http://www.spl.harvard.edu/publications/item/view/58 A Bayesian model for joint segmentation and registration.] Neuroimage. 2006 May 15;31(1):228-39.<br />
<br />
*Pohl K, Bouix S, Nakamura M, Rohlfing T, McCarley R, Kikinis R, Grimson W, Shenton M, Wells W. [http://www.slicer.org/pages/Special:PubDB_View?dspaceid=608 A Hierarchical Algorithm for MR Brain Image Parcellation.] IEEE Transactions on Medical Imaging. 2007 Sept;26(9):1201-1212. [[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
{{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
If you are documenting a CLI, the category should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-category|xmlurl=http://path/to/YOURMODULENAME.xml }}</pre><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Pohlhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/EMSegment_Easy&diff=23166Documentation/4.0/Modules/EMSegment Easy2011-11-23T19:57:14Z<p>Pohl: /* Step 1: Define Input Channel */</p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work was funded by the ARRA Supplement to the Neuroimage Analysis Center (NAC), funded by the National Institutes of Health. Information on NAC can be obtained from the [http://nac.spl.harvard.edu/pages/Overview NAC website].<br><br />
Author: Kilian Pohl, UPenn <br><br />
Contributor1: Daniel Haehn, UPENN<br><br />
Contact: Kilian Pohl, <email>pohl.kilian@gmail.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:UPenn-logo.png|University of Pennsylvania<br />
|Image:Logo-splnew.jpg|Surgical Planning Laboratory <br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<br />
This module is designed for users who want to do a quick intensity based image segmentation. The remainder of this sections describes the work flow of the two modes in further detail: <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
MR image segmentation <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
=== Step 1: Define Input Datasets ===<br />
Define the volumes to be segmented. Each volume has to be from the subject and has to represent a different mode, such as T1 and FLAIR, than the other input volumes. If using multiple modes which are not aligned with each other then check on the check-box button "Align input scans".<br />
<br />
=== Step 2: Define Anatomical Tree ===<br />
The user specifies the hierarchical relationship between the anatomical structures. The tree will refine the complex segmentation task into a set of easier segmentation problems. A sub-classes is added to an existing structure by right-clicking on the structure and selecting "Add sub-class". The name, label, and color of a structure are modified by selecting the structure in the tree and then defining these attributes in the panel below.<br />
=== Step 3: Specify Intensity Distribution === <br />
Defining the intensity distribution for each structure of interest through taking samples in the image of interest<br />
=== Step 4: Edit Node-based Parameters ===<br />
Users specify the relative to weight of a node in the tree with respect to other structures which are children of the same parent node. The first tab also specifies the weight of the input channels as well as the atlases. The value 'Alpha' specifies the smoothing applied to the structure (via MRFs). The second tab (Stopping Condition) lists the number of iterations associated with the segmentation task. By default, the Bias iteration is set to -1 which means that it is performed each iteration. If the value is greater -1 then the inhomogeneity computation is stopped after n iterations. The third tab specifies printing out intermediate results, which are saved in the working directory specified in the next step <br />
=== Step 5: Define Miscellaneous Parameters ===<br />
This panels lists the general parameters necessary for segmenting images. Users can specify a region of interest to speed up the segmentation algorithm. Pressing the 'Segment' button creates a label map of the anatomical structures.<br />
<br />
Once the parameters are specified, the target images are segmented<br />
using the EM Segmentation algorithm (Pohl et al. TMI 2007). The label map with corresponding statistics is returned after successful completion of the algorithm. <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
Please look at [[ Documentation/4.0#Segmentation | Segmentation]] section<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
* Wells III W.M., Grimson W.E.L., Kikinis R., Jolesz F.A. [http://www.spl.harvard.edu/publications/item/view/847 Adaptive segmentation of MRI data.] IEEE Trans Med Imaging. 1996; 15(4):429-442.<br />
<br />
* Pohl K.M., Fisher III J.W., Grimson W.E.L., Kikinis R., Wells III W.M. [http://www.spl.harvard.edu/publications/item/view/58 A Bayesian model for joint segmentation and registration.] Neuroimage. 2006 May 15;31(1):228-39.<br />
<br />
*Pohl K, Bouix S, Nakamura M, Rohlfing T, McCarley R, Kikinis R, Grimson W, Shenton M, Wells W. [http://www.slicer.org/pages/Special:PubDB_View?dspaceid=608 A Hierarchical Algorithm for MR Brain Image Parcellation.] IEEE Transactions on Medical Imaging. 2007 Sept;26(9):1201-1212. [[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
{{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
If you are documenting a CLI, the category should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-category|xmlurl=http://path/to/YOURMODULENAME.xml }}</pre><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Pohlhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/EMSegment_Easy&diff=23165Documentation/4.0/Modules/EMSegment Easy2011-11-23T19:52:22Z<p>Pohl: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work was funded by the ARRA Supplement to the Neuroimage Analysis Center (NAC), funded by the National Institutes of Health. Information on NAC can be obtained from the [http://nac.spl.harvard.edu/pages/Overview NAC website].<br><br />
Author: Kilian Pohl, UPenn <br><br />
Contributor1: Daniel Haehn, UPENN<br><br />
Contact: Kilian Pohl, <email>pohl.kilian@gmail.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:UPenn-logo.png|University of Pennsylvania<br />
|Image:Logo-splnew.jpg|Surgical Planning Laboratory <br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<br />
This module is designed for users who want to do a quick intensity based image segmentation. The remainder of this sections describes the work flow of the two modes in further detail: <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
MR image segmentation <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
=== Step 1: Define Input Channel ===<br />
Define the number of input channels as well as the name of each channel and the corresponding scan associated with the channel. If using multiple input channel(scans) which are not aligned with each other then check on the check-box button "Align input scans".<br />
=== Step 2: Define Anatomical Tree ===<br />
The user specifies the hierarchical relationship between the anatomical structures. The tree will refine the complex segmentation task into a set of easier segmentation problems. A sub-classes is added to an existing structure by right-clicking on the structure and selecting "Add sub-class". The name, label, and color of a structure are modified by selecting the structure in the tree and then defining these attributes in the panel below.<br />
=== Step 3: Specify Intensity Distribution === <br />
Defining the intensity distribution for each structure of interest through taking samples in the image of interest<br />
=== Step 4: Edit Node-based Parameters ===<br />
Users specify the relative to weight of a node in the tree with respect to other structures which are children of the same parent node. The first tab also specifies the weight of the input channels as well as the atlases. The value 'Alpha' specifies the smoothing applied to the structure (via MRFs). The second tab (Stopping Condition) lists the number of iterations associated with the segmentation task. By default, the Bias iteration is set to -1 which means that it is performed each iteration. If the value is greater -1 then the inhomogeneity computation is stopped after n iterations. The third tab specifies printing out intermediate results, which are saved in the working directory specified in the next step <br />
=== Step 5: Define Miscellaneous Parameters ===<br />
This panels lists the general parameters necessary for segmenting images. Users can specify a region of interest to speed up the segmentation algorithm. Pressing the 'Segment' button creates a label map of the anatomical structures.<br />
<br />
Once the parameters are specified, the target images are segmented<br />
using the EM Segmentation algorithm (Pohl et al. TMI 2007). The label map with corresponding statistics is returned after successful completion of the algorithm. <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
Please look at [[ Documentation/4.0#Segmentation | Segmentation]] section<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
* Wells III W.M., Grimson W.E.L., Kikinis R., Jolesz F.A. [http://www.spl.harvard.edu/publications/item/view/847 Adaptive segmentation of MRI data.] IEEE Trans Med Imaging. 1996; 15(4):429-442.<br />
<br />
* Pohl K.M., Fisher III J.W., Grimson W.E.L., Kikinis R., Wells III W.M. [http://www.spl.harvard.edu/publications/item/view/58 A Bayesian model for joint segmentation and registration.] Neuroimage. 2006 May 15;31(1):228-39.<br />
<br />
*Pohl K, Bouix S, Nakamura M, Rohlfing T, McCarley R, Kikinis R, Grimson W, Shenton M, Wells W. [http://www.slicer.org/pages/Special:PubDB_View?dspaceid=608 A Hierarchical Algorithm for MR Brain Image Parcellation.] IEEE Transactions on Medical Imaging. 2007 Sept;26(9):1201-1212. [[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
{{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
If you are documenting a CLI, the category should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-category|xmlurl=http://path/to/YOURMODULENAME.xml }}</pre><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Pohlhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/EMSegment_Easy&diff=23164Documentation/4.0/Modules/EMSegment Easy2011-11-23T19:51:43Z<p>Pohl: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work was funded by the ARRA Supplement to the Neuroimage Analysis Center (NAC), funded by the National Institutes of Health. Information on NAC can be obtained from the [http://nac.spl.harvard.edu/pages/Overview NAC website].<br><br />
Author: Kilian Pohl, UPenn <br><br />
Contributor1: Daniel Haehn, UPENN<br><br />
Contact: Kilian Pohl, <email>pohl.kilian@gmail.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:UPenn-logo.png|University of Pennsylvania<br />
|Image:Logo-splnew.jpg|Surgical Planning Laboratory <br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<br />
This module is designed for users who want to do a quick intensity based image segmentation. The remainder of this sections describes the work flow of the two modes in further detail: <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
MR image segmentation <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
=== Step 1: Define Input Channel ===<br />
Define the number of input channels as well as the name of each channel and the corresponding scan associated with the channel. If using multiple input channel(scans) which are not aligned with each other then check on the check-box button "Align input scans".<br />
=== Step 2: Define Anatomical Tree ===<br />
The user specifies the hierarchical relationship between the anatomical structures. The tree will refine the complex segmentation task into a set of easier segmentation problems. A sub-classes is added to an existing structure by right-clicking on the structure and selecting "Add sub-class". The name, label, and color of a structure are modified by selecting the structure in the tree and then defining these attributes in the panel below.<br />
=== Step 3: Specify Intensity Distribution === <br />
Defining the intensity distribution for each structure of interest through taking samples in the image of interest<br />
=== Step 4: Edit Node-based Parameters ===<br />
Users specify the relative to weight of a node in the tree with respect to other structures which are children of the same parent node. The first tab also specifies the weight of the input channels as well as the atlases. The value 'Alpha' specifies the smoothing applied to the structure (via MRFs). The second tab (Stopping Condition) lists the number of iterations associated with the segmentation task. By default, the Bias iteration is set to -1 which means that it is performed each iteration. If the value is greater -1 then the inhomogeneity computation is stopped after n iterations. The third tab specifies printing out intermediate results, which are saved in the working directory specified in the next step <br />
=== Step 5: Define Miscellaneous Parameters ===<br />
This panels lists the general parameters necessary for segmenting images. Users can specify a region of interest to speed up the segmentation algorithm. Pressing the 'Segment' button creates a label map of the anatomical structures.<br />
<br />
Once the parameters are specified, the target images are segmented<br />
using the EM Segmentation algorithm (Pohl et al. TMI 2007). The label map with corresponding statistics is returned after successful completion of the algorithm. <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
Please look at [[ Documentation/4.0#Segmentation | Segmentation]] section<br />
<br />
* Point to other modules that have similar functionality<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
* Wells III W.M., Grimson W.E.L., Kikinis R., Jolesz F.A. [http://www.spl.harvard.edu/publications/item/view/847 Adaptive segmentation of MRI data.] IEEE Trans Med Imaging. 1996; 15(4):429-442.<br />
<br />
* Pohl K.M., Fisher III J.W., Grimson W.E.L., Kikinis R., Wells III W.M. [http://www.spl.harvard.edu/publications/item/view/58 A Bayesian model for joint segmentation and registration.] Neuroimage. 2006 May 15;31(1):228-39.<br />
<br />
*Pohl K, Bouix S, Nakamura M, Rohlfing T, McCarley R, Kikinis R, Grimson W, Shenton M, Wells W. [http://www.slicer.org/pages/Special:PubDB_View?dspaceid=608 A Hierarchical Algorithm for MR Brain Image Parcellation.] IEEE Transactions on Medical Imaging. 2007 Sept;26(9):1201-1212. [[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
{{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
If you are documenting a CLI, the category should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-category|xmlurl=http://path/to/YOURMODULENAME.xml }}</pre><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Pohlhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/EMSegmenter&diff=23163Documentation/4.0/Modules/EMSegmenter2011-11-23T19:47:38Z<p>Pohl: /* Step 7: Specify Intensity Distribution */</p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work was funded by the ARRA Supplement to the Neuroimage Analysis Center (NAC), funded by the National Institutes of Health. Information on NAC can be obtained from the [http://nac.spl.harvard.edu/pages/Overview NAC website].<br><br />
Author: Kilian Pohl, UPenn <br><br />
Contributor1: Daniel Haehn, UPENN<br><br />
Contact: Kilian Pohl, <email>pohl.kilian@gmail.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:UPenn-logo.png|University of Pennsylvania<br />
|Image:Logo-splnew.jpg|Surgical Planning Laboratory <br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
<br />
[[Image:EMSegmenterLogo.png|thumb|width=200px|Hierarchical Model of the EMSegmenter]]<br />
This module is designed for users who perform atlas based medical image segmentation. The module can be operated in <B>two</B> modes: <br><br />
An <B>advanced mode (Button: Adjust Parameters)</B> that allows users to parameterize the tool to specific segmentation tasks and a <B>simple mode (Button: Use Existing Setting)</B> which is designed for users who would like to apply the predefined parameterization to new data with a minimal amount of user interaction. One can also apply the parameterization to medical scans via the command-line executable <B>EMSegmentCommandLine</B>. The remainder of this sections describes the work flow of the two modes in further detail:<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
The purpose of the module is to configure the algorithm to automatically segment anatomical structures in medical images. First the user has to specify parameters defining the image protocol and the anatomical structures of interests. This process results in a template that the module uses to automatically segment large data sets. The template is composed of atlas data and a non-trivial collection of parameters for the EMSegment algorithm. <br />
<br />
Once the parameters are specified, the target images are segmented<br />
using the EM Segmentation algorithm (Pohl et al. TMI 2007). If the results are<br />
satisfactory, the template is saved and can be used later to segment<br />
new images (via the GUI or batch processing). If the results are<br />
unsatisfactory, the parameters can be modified and the segmentation<br />
re-run.<br />
<br />
One important aspect of the project is the workflow wizard. This wizard simplifies the module by dividing the complicated template specification task into a number of smaller, intuitive steps. The wizard allows to [[EMSegmenter-CreateTask|create tasks]] and to use them to analyze data sets.<br />
<br />
There are multiple [[EMSegmenter-Tasks|'''predefined tasks''']] which are ready to use.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
<br />
* EMSegmenter Tutorial for 3D Slicer 3.6.2<br />
** [[Media:EMSegmenterTutorialSimpleMode-2010-Dec.pdf | Simple Mode]] - [[Media:MRIHumanBrain_T1_aligned.nrrd | Tutorial Data]]<br />
** [[Media:EMSegmenterTutorialAdvancedMode-2010-Dec.pdf | Advanced Mode]] - [[Media:MRIHumanBrain_T1_aligned.nrrd | Tutorial Data]]<br />
<br />
* EMSegmenter Tutorial for 3D Slicer 3.6.3<br />
** [[Media:EMSegmenterTutorialSimpleMode-Slicer-3.6.3-1.pdf | Simple Mode]] - [[Media:MRIHumanBrain_T1_aligned.nrrd | Tutorial Data]]<br />
** [[Media:EMSegmenterTutorialAdvancedMode-Slicer-3.6.3-1.pdf | Advanced Mode]] - [[Media:MRIHumanBrain_T1_aligned.nrrd | Tutorial Data]]<br />
<br />
<br />
* A full Tutorial for the two EMSegment modules<br />
<br />
These slides and data describe the Slicer3 implementation of the two EMSegment GUI and command-line modules and demonstrate their use.<br />
<br />
[[Media:EMSegTutorial-AHM2008.ppt | Tutorial Slides]] - [[Media:EMSegTutorial-AHM2008.zip | Tutorial Data]]<br />
<br />
* Another detailed training tutorial on EMSegment algorithm and the Slicer3 EMSegment module.<br />
<br />
[http://wiki.na-mic.org/Wiki/images/2/2f/AutomaticSegmentation_SoniaPujol_Munich2008.ppt Tutorial Slides] - <br />
[http://wiki.na-mic.org/Wiki/images/b/b7/AutomaticSegmentation.tar.gz Training Data]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
=== Simple Mode ===<br />
The work flow is defined by only two steps.<br />
==== Step 1: Define Task ====<br />
Select an already existing task and click on the "Use Existing Settings" button to use for the simple mode in the pop up window.<br />
A MRML file defining parameters of the algorithm specific to the task as well atlas data are automatically downloaded for existing Tasks.<br />
==== Step 2: Define Input Channels ====<br />
In this step the user specifies the scans to be segmented as well as the check list associated with the preprocessing.<br />
A click on the 'Segment' button is enough to start the pre-processing and the subsequent segmentation.<br />
<br />
=== Advanced Mode ===<br />
Unlike the Simple mode, the advanced mode is defined by nine steps which one can navigate via the "Back", "Next", or "Segment" button. The Segment button jumps right away to the last step of the work flow and segments the medical scans into the structures of interests. <br />
==== Step 1: Define Task ====<br />
Select an already existing task or define a new one. Click on the button "Adjust Parameters" for the advanced mode in the pop up window. A MRML file defining parameters of the algorithm specific to the task as well atlas data are automatically downloaded for existing Tasks.<br />
==== Step 2: Define Input Channel ====<br />
Define the number of input channels as well as the name of each channel and the corresponding scan associated with the channel. If using multiple input channel(scans) which are not aligned with each other then check on the check-box button "Align input scans".<br />
==== Step 3: Define Anatomical Tree ====<br />
The user specifies the hierarchical relationship between the anatomical structures. The tree will refine the complex segmentation task into a set of easier segmentation problems. A sub-classes is added to an existing structure by right-clicking on the structure and selecting "Add sub-class". The name, label, and color of a structure are modified by selecting the structure in the tree and then defining these attributes in the panel below.<br />
==== Step 4: Define Atlas ====<br />
In this step, the user links the probabilistic atlases to the anatomical structures in the tree by first highlighting the structure and then selecting the volume representing the probability map of that structure in the panel below. We note that the probabilistic atlas of structures with sub-structures is defined by the atlases of the sub-structures and thus is not explicitly defined. <br />
==== Step 5: Edit Registration Parameters ====<br />
The atlas is in general not aligned to the specific patient scans defined in Step 2. The user assigns in this step the scans of the atlas corresponding to the input channels in Step 2 as well as the type of registration (Affine / Deformable) and the interpolation. <br />
==== Step 6: Define Preprocessing ==== <br />
[[Image:EMSegmenter_DisplayClassDistribution.png | thumb|width=200px|Graph showing intensity distributions of a set of anatomical structures]] This step is defined via a task specific Tcl file that configures the preprocessing pipeline of the input scans and the atlas. Complete the step by going through the task specific check list, clicking on the 'Next' button, and clicking on the 'Yes' button of the pop up window. One can define a new preprocessing pipeline by specifying the pipeline via a Tcl file, placing the file in Slicer3-build/share/Slicer3/Modules/EMSegment/Tasks and listing the file name in the task specific MRML file.<br />
<br />
==== Step 7: Specify Intensity Distribution ==== <br />
Refining the intensity distribution for each structure of interest is often a critical step in the parameterization of the segmentation algorithm. It includes an overview window that shows the distribution in a 1D and 2D graph (press "Plot Distributions" to view the graph). By placing the mouse cursor in the 2D viewers the corresponding intensity value is shown in the graph.<br />
<br />
==== Step 8: Edit Node-based Parameters ====<br />
Users specify the relative to weight of a node in the tree with respect to other structures which are children of the same parent node. The first tab also specifies the weight of the input channels as well as the atlases. The value 'Alpha' specifies the smoothing applied to the structure (via MRFs). The second tab (Stopping Condition) lists the number of iterations associated with the segmentation task. By default, the Bias iteration is set to -1 which means that it is performed each iteration. If the value is greater -1 then the inhomogeneity computation is stopped after n iterations. The third tab specifies printing out intermediate results, which are saved in the working directory specified in the next step <br />
==== Step 9: Define Miscellaneous Parameters ====<br />
This panels lists the general parameters necessary for segmenting images. Users can specify a region of interest to speed up the segmentation algorithm. Pressing the 'Segment' button creates a label map of the anatomical structures.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
* Please see <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
* Wells III W.M., Grimson W.E.L., Kikinis R., Jolesz F.A. [http://www.spl.harvard.edu/publications/item/view/847 Adaptive segmentation of MRI data.] IEEE Trans Med Imaging. 1996; 15(4):429-442.<br />
<br />
* Pohl K.M., Fisher III J.W., Grimson W.E.L., Kikinis R., Wells III W.M. [http://www.spl.harvard.edu/publications/item/view/58 A Bayesian model for joint segmentation and registration.] Neuroimage. 2006 May 15;31(1):228-39.<br />
<br />
*Pohl K, Bouix S, Nakamura M, Rohlfing T, McCarley R, Kikinis R, Grimson W, Shenton M, Wells W. [http://www.slicer.org/pages/Special:PubDB_View?dspaceid=608 A Hierarchical Algorithm for MR Brain Image Parcellation.] IEEE Transactions on Medical Imaging. 2007 Sept;26(9):1201-1212. [[http://people.csail.mit.edu/pohl/publications/journal-citation-bib.html#pohl07_3 bib]]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}} <br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
{{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
If you are documenting a CLI, the category should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-category|xmlurl=http://path/to/YOURMODULENAME.xml }}</pre><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Pohlhttps://www.slicer.org/w/index.php?title=Documentation/4.0/Modules/EMSegment_Easy&diff=23161Documentation/4.0/Modules/EMSegment Easy2011-11-23T19:32:43Z<p>Pohl: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work was funded by the ARRA Supplement to the Neuroimage Analysis Center (NAC), funded by the National Institutes of Health. Information on NAC can be obtained from the [http://nac.spl.harvard.edu/pages/Overview NAC website].<br><br />
Author: Kilian Pohl, UPenn <br><br />
Contributor1: Daniel Haehn, UPENN<br><br />
Contact: Kilian Pohl, <email>pohl.kilian@gmail.com</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:UPenn-logo.png|University of Pennsylvania<br />
|Image:Logo-splnew.jpg|Surgical Planning Laboratory <br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
{{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
{{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}<br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
This work is part of the National Alliance for Medical Image Computing (NA-MIC), funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 EB005149. Information on NA-MIC can be obtained from the [http://www.na-mic.org/ NA-MIC website].<br><br />
Author: FIRSTNAME LASTNAME, AFFILIATION<br><br />
Contributor1: FIRSTNAME LASTNAME, AFFILIATION<br><br />
Contributor2: FIRSTNAME LASTNAME, AFFILIATION<br><br />
Contact: FIRSTNAME LASTNAME, <email>john@doe.org</email><br><br />
{{documentation/{{documentation/version}}/module-introduction-row}}<br />
{{documentation/{{documentation/version}}/module-introduction-logo-gallery<br />
|Image:Logo-isomics.png|Isomics, Inc. <- Replace this logo with yours<br />
|Image:Logo-splnew.jpg|Surgical Planning Laboratory <-Replace this logo with yours<br />
}}<br />
{{documentation/{{documentation/version}}/module-introduction-end}}<br />
</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Module Description}}<br />
Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.<br />
<br />
<!-- ----------------------------------------------------------------- --><br />
<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
<!-- ----------------------------------------------------------------- --><br />
If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description|xmlurl=http://path/to/YOURMODULE.xml }}</pre><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-description|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<!-- ----------------------------------------------------------------- --><br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Use Cases}}<br />
Most frequently used for these scenarios:<br />
<br />
* Use Case 1:<br />
* Use Case 2:<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Tutorials}}<br />
Links to tutorials that use this module<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Panels and their use}}<br />
<br />
A list of all the panels in the interface, their features, what they mean, and how to use them. For instance:<br />
<br />
{|style="width: 100%"<br />
|<br />
* Input panel1:<br />
** First input<br />
** Second input<br />
* Parameters panel:<br />
** First parameter<br />
** Second parameter<br />
* Output panel:<br />
** First output<br />
** Second output<br />
* Viewing panel:<br />
| align="right" |<br />
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 1]]<br />
|-<br />
|<br />
* Input panel2:<br />
** First input<br />
** Second input<br />
* Parameters panel:<br />
** First parameter<br />
** Second parameter<br />
* Output panel:<br />
** First output<br />
** Second output<br />
* Viewing panel:<br />
| align="right" |<br />
[[Image:screenshotBlankNotOptional.png|thumb|280px|Name of panel 2]]<br />
|}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Similar Modules}}<br />
* Point to other modules that have similar functionality<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|References}}<br />
Publications related to this module go here. Links to pdfs would be useful.<br />
For extensions: link to the source code repository and additional documentation<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
<br />
<br />
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<!-- THE FOLLOWING SHOULD BE REMOVED FOR YOUR OWN MODULE DOCUMENTATION --><br />
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{{note}}The section above is generated using the following wiki code:<br />
<pre><br />
{{documentation/{{documentation/version}}/module-section|Information for Developers}}<br />
{{documentation/{{documentation/version}}/module-developerinfo|ModuleTemplate|type=Interactive|category=Example}}<br />
</pre><br />
<br />
If you are documenting a CLI, the category should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-category|xmlurl=http://path/to/YOURMODULENAME.xml }}</pre><br />
<br />
If your module is available in Slicer repository, the following template could be useful to obtain the corresponding URL:<br />
<pre>{{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}}</pre><br />
<br />
Using this later template, the final syntax would be:<br />
<pre>{{documentation/{{documentation/version}}/module-category|xmlurl={{documentation/{{documentation/version}}/module-cli-xmlurl|{{documentation/modulename}}|SVNREVISION}} }}</pre><br />
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<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-footer|category=Example}}<br />
<!-- ---------------------------- --></div>Pohl