Documentation/4.0/Developers/Build Instructions

2011-07-24T16:09:28Z

Belhachemi: /* STEP 0: Prerequisites */

[[Slicer4| Back to Slicer 4]]

The goal of the Super-Build is to provide a cross-platform build system that allows developers to quickly install and configure the multiple packages.

Where [[Slicer3:Build_Instructions|Slicer3's build system]] relied on a [[Slicer3:getbuildtest|custom build script called getbuildtest]], new features added to [http://www.cmake.org CMake], partly driven by slicer's requirements, allow porting of the scripts to rely more on native CMake functionality with the benefit that build script is more modular and general purpose.

== STEP 0: Prerequisites ==

Please check that the following tools are installed on your machine.

*Debian Squeeze user type:
sudo apt-get install gcc libX11-dev libXt-dev libgl1-mesa-dev libosmesa6-dev libglu1-mesa-dev git cmake cmake-curses-gui libqt4-dev subversion make g++
*Ubuntu users, just type the following line in a terminal
sudo apt-get install gcc libX11-dev libXt-dev libgl1-mesa-dev libosmesa6-dev libglu1-mesa-dev git cmake cmake-curses-gui
*CentOS user type:
yum install gcc-c++ libX11-devel libXt-devel make

*Mac
** git version >= 1.6.5
*** [http://git-scm.com/download Download and install Git]
**[http://www.cmake.org/cmake/resources/software.html CMake] version >= 2.8.2

* Linux prerequisites (''need to confirm'')
** gcc
** gcc-c++
** libX11
** libX11-devel (libX11-dev on Ubuntu 7.04)
** libXt-devel (libXt-dev on Ubuntu)
** opengl/mesa (libgl1-mesa-dev on Ubuntu) (and libosmesa6-dev on Ubuntu)
** glu (libglu1-mesa-dev on Ubuntu)
** git version >= 1.6.5
*** [http://git-scm.com/download Download Git]
*** install git: <code>sudo apt-get install git</code>. If <code>git --version</code> is inferior to 1.6.5, then:<code>sudo dpkg --install git-core_1.6.5-1~bpo50+1_amd64.deb</code>
**[http://www.cmake.org/cmake/resources/software.html CMake] version >= 2.8.2

* Windows prerequisites
** IDE:
*** Prefered: Microsoft Visual Studio 2008 or 2010 (including [http://www.microsoft.com/express/Downloads/#2010-Visual-CPP Express Edition])
*** Cygwin suite
**[http://www.cmake.org/cmake/resources/software.html CMake] version >= 2.8.2
** SVN
** CVS
** git version >= 1.6.5. [http://code.google.com/p/msysgit/ msysgit] is recommended. Using [http://code.google.com/p/tortoisegit/ TortoiseGit] is a plus.
* '''All Platforms: Qt.'''{{note}} Use one of the links provided in the table below to download the source code or binary of Qt. If required, you can download the source code and compile Qt using the instructions in [[Slicer4:Build_Instructions_for_QT|Slicer4: Build Instructions for Qt]].

{| border="1" style="margin-left: 20px;"
|- bgcolor="#FFFFCC"
!rowspan="3"|
!colspan="2" rowspan="2"|Linux
!colspan="2"|Mac
!colspan="2" rowspan="2"|Windows
|- bgcolor="#FFFFCC"
!colspan="1"|Tiger
!colspan="1"|Leopard, SnowLeopard
|- bgcolor="#FFFFCC"
!|32bits
!|64bits
!|32bits
!colspan="1"|64bits
!|32bits
!|64bits
|-
! bgcolor="#FFFFCC" | [http://get.qt.nokia.com/qt/source/ Qt source link]
|align="center" colspan="4"| [http://get.qt.nokia.com/qt/source/qt-everywhere-opensource-src-4.6.3.tar.gz 4.6.3]
|align="center" colspan="2"| [http://get.qt.nokia.com/qt/source/qt-everywhere-opensource-src-4.6.3.zip 4.6.3 (vs2008)] [http://get.qt.nokia.com/qt/source/qt-everywhere-opensource-src-4.7.3.zip 4.7.3 (vs2010)]
|-
! bgcolor="#FFFFCC" | [http://get.qt.nokia.com/qt/source/ Qt binary link]
|align="center" colspan="1"| [http://get.qt.nokia.com/qtsdk/qt-sdk-linux-x86-opensource-2010.05.bin x86_2010.05]
|align="center" colspan="1"| [http://get.qt.nokia.com/qtsdk/qt-sdk-linux-x86_64-opensource-2010.05.bin x86_64_2010.05]
|align="center" colspan="1"| [http://get.qt.nokia.com/qt/source/qt-mac-carbon-opensource-4.7.0.dmg carbon_4.7.0]
|align="center" colspan="1"| [http://get.qt.nokia.com/qtsdk/qt-sdk-mac-opensource-2010.05.dmg cocoa_4.7.0]
|align="center" colspan="1"| [http://get.qt.nokia.com/qt/source/qt-win-opensource-4.6.3-vs2008.exe 4.6.3 (vs2008)] [http://get.qt.nokia.com/qt/source/qt-win-opensource-4.7.3-vs2008.exe 4.7.3 (vs2010)]
|align="center" colspan="1"| -
|}

== Step1: Checkout slicer source files using subversion ==
For example:
<pre>
cd MyProjects
svn co http://svn.slicer.org/Slicer4/trunk Slicer4
</pre>

== Step2: Configure and generate Slicer solution files ==
You can configure and generate Slicer solution files using either ccmake or cmake-gui.
*cmake-gui (Recommended): Configure using default options.
{{note}}
#If you downloaded the Qt binary then qmake will be detected and all paths will be set automatically.
#If you built your own Qt (e.g. in Debug mode for use with the designer) set the QT_QMAKE_EXECUTABLE in cmake-gui.QT_QMAKE_EXECUTABLE should be set to the path of the qmake.exe file, which is inside the bin directory (for example, ./QT/qt-everywhere-opensource-src-4.7.3/bin/qmake.exe).

*ccmake (for linux/mac): Configure using the following commands. For developers, set the '''CMAKE_BUILD_TYPE''' to '''Debug'''.
<pre>
mkdir Slicer4-SuperBuild
cd Slicer4-SuperBuild
ccmake -DQT_QMAKE_EXECUTABLE:FILEPATH=/home/myself/qt-4.6.3/qt/bin/qmake ../Slicer4

</pre>

Two projects are generated by ccmake/cmake-gui. One of them is in the top-level bin directory Slicer4-Superbuild and the other one is in the subdirectory Slicer4-Superbuild/Slicer-build:

#The first project in Slicer4-Superbuild manages all the external dependencies of Slicer (VTK, ITK, Python, ...). To build Slicer for the first time, run make (or build the solution file in Visual Studio) in Slicer4-Superbuild, which will update and build the external libraries and if successful will then build the subproject Slicer-build. 
#The second project in Slicer4-Superbuild/Slicer-build is the "traditional" build directory of Slicer. After local changes in Slicer (or after an svn update on the source directory of Slicer), only running make (or building the solution file in Visual Studio) in Slicer4-Superuild/Slicer-build is necessary (the external libraries are considered built and up to date). 

{{warning}}
#For Windows users:Windows doesn't support path longer than 260 characters, please make sure that the total path name of your Slicer-build directory is no longer than 75 characters ( for example "c:\work\Slicer\Slicer-Superbuild" (32 characters) is fine)
#Warning: a lot of space disk is necessary to compile Slicer (>10GB on Windows)

== Step3: Build Slicer4 ==
After configuration, start the build process in the Slicer4-SuperBuild directory
*Linux / Mac: Run the following code:
<pre>
make -j<NUMBEROFCORES>
</pre>
*Windows: Open Slicer4-SuperBuild\Slicer.sln (or Slicer-4.0\Slicer4-SuperBuild\Slicer-build\Slicer.sln) in Visual Studio and build the ALL_BUILD project.

{{warning}}
# As it is indicated in Step2, if you make local changes in Slicer4, run make (or build the solution file in Visual Studio) in the directory Slicer4-Superuild/Slicer-build.
# If you would like to make local changes and debug your code in Debug mode in Visual Studio, use the Visual Studio Command Prompt to open the solution file in Slicer4-Superuild/Slicer-build:
#* Open Visual Studio Command Prompt
#* Go to the directory Slicer4-Superuild/Slicer-build
#* Write Slicer.exe --VisualStudio Slicer.sln

==Step4: Run Slicer4 ==
Run the launcher in Slicer4-SuperBuild/Slicer-build/Slicer (Slicer.exe on windows)

==Platform Notes==

* Linux Ubuntu: if you have odd rendering artifacts, try disabling visual effects (System/Appearance/Visual Effects)

Documentation/4.0/Developers/Build Instructions

2011-07-24T04:43:46Z

Belhachemi: /* STEP 0: Prerequisites */

[[Slicer4| Back to Slicer 4]]

The goal of the Super-Build is to provide a cross-platform build system that allows developers to quickly install and configure the multiple packages.

Where [[Slicer3:Build_Instructions|Slicer3's build system]] relied on a [[Slicer3:getbuildtest|custom build script called getbuildtest]], new features added to [http://www.cmake.org CMake], partly driven by slicer's requirements, allow porting of the scripts to rely more on native CMake functionality with the benefit that build script is more modular and general purpose.

== STEP 0: Prerequisites ==

Please check that the following tools are installed on your machine.

*Debian Squeeze user type:
sudo apt-get install gcc libX11-dev libXt-dev libgl1-mesa-dev libosmesa6-dev libglu1-mesa-dev git cmake cmake-curses-gui libqt4-dev subversion make g++
*Ubuntu users, just type the following line in a terminal
sudo apt-get install gcc libX11-dev libXt-dev libgl1-mesa-dev libosmesa6-dev libglu1-mesa-dev git cmake cmake-curses-gui

*Mac
** git version >= 1.6.5
*** [http://git-scm.com/download Download and install Git]
**[http://www.cmake.org/cmake/resources/software.html CMake] version >= 2.8.2

* Linux prerequisites (''need to confirm'')
** gcc
** gcc-c++
** libX11
** libX11-devel (libX11-dev on Ubuntu 7.04)
** libXt-devel (libXt-dev on Ubuntu)
** opengl/mesa (libgl1-mesa-dev on Ubuntu) (and libosmesa6-dev on Ubuntu)
** glu (libglu1-mesa-dev on Ubuntu)
** git version >= 1.6.5
*** [http://git-scm.com/download Download Git]
*** install git: <code>sudo apt-get install git</code>. If <code>git --version</code> is inferior to 1.6.5, then:<code>sudo dpkg --install git-core_1.6.5-1~bpo50+1_amd64.deb</code>
**[http://www.cmake.org/cmake/resources/software.html CMake] version >= 2.8.2

* Windows prerequisites
** IDE:
*** Prefered: Microsoft Visual Studio 2008 or 2010 (including [http://www.microsoft.com/express/Downloads/#2010-Visual-CPP Express Edition])
*** Cygwin suite
**[http://www.cmake.org/cmake/resources/software.html CMake] version >= 2.8.2
** SVN
** CVS
** git version >= 1.6.5. [http://code.google.com/p/msysgit/ msysgit] is recommended. Using [http://code.google.com/p/tortoisegit/ TortoiseGit] is a plus.
* '''All Platforms: Qt.'''{{note}} Use one of the links provided in the table below to download the source code or binary of Qt. If required, you can download the source code and compile Qt using the instructions in [[Slicer4:Build_Instructions_for_QT|Slicer4: Build Instructions for Qt]].

{| border="1" style="margin-left: 20px;"
|- bgcolor="#FFFFCC"
!rowspan="3"|
!colspan="2" rowspan="2"|Linux
!colspan="2"|Mac
!colspan="2" rowspan="2"|Windows
|- bgcolor="#FFFFCC"
!colspan="1"|Tiger
!colspan="1"|Leopard, SnowLeopard
|- bgcolor="#FFFFCC"
!|32bits
!|64bits
!|32bits
!colspan="1"|64bits
!|32bits
!|64bits
|-
! bgcolor="#FFFFCC" | [http://get.qt.nokia.com/qt/source/ Qt source link]
|align="center" colspan="4"| [http://get.qt.nokia.com/qt/source/qt-everywhere-opensource-src-4.6.3.tar.gz 4.6.3]
|align="center" colspan="2"| [http://get.qt.nokia.com/qt/source/qt-everywhere-opensource-src-4.6.3.zip 4.6.3 (vs2008)] [http://get.qt.nokia.com/qt/source/qt-everywhere-opensource-src-4.7.3.zip 4.7.3 (vs2010)]
|-
! bgcolor="#FFFFCC" | [http://get.qt.nokia.com/qt/source/ Qt binary link]
|align="center" colspan="1"| [http://get.qt.nokia.com/qtsdk/qt-sdk-linux-x86-opensource-2010.05.bin x86_2010.05]
|align="center" colspan="1"| [http://get.qt.nokia.com/qtsdk/qt-sdk-linux-x86_64-opensource-2010.05.bin x86_64_2010.05]
|align="center" colspan="1"| [http://get.qt.nokia.com/qt/source/qt-mac-carbon-opensource-4.7.0.dmg carbon_4.7.0]
|align="center" colspan="1"| [http://get.qt.nokia.com/qtsdk/qt-sdk-mac-opensource-2010.05.dmg cocoa_4.7.0]
|align="center" colspan="1"| [http://get.qt.nokia.com/qt/source/qt-win-opensource-4.6.3-vs2008.exe 4.6.3 (vs2008)] [http://get.qt.nokia.com/qt/source/qt-win-opensource-4.7.3-vs2008.exe 4.7.3 (vs2010)]
|align="center" colspan="1"| -
|}

== Step1: Checkout slicer source files using subversion ==
For example:
<pre>
cd MyProjects
svn co http://svn.slicer.org/Slicer4/trunk Slicer4
</pre>

== Step2: Configure and generate Slicer solution files ==
You can configure and generate Slicer solution files using either ccmake or cmake-gui.
*cmake-gui (Recommended): Configure using default options.
{{note}}
#If you downloaded the Qt binary then qmake will be detected and all paths will be set automatically.
#If you built your own Qt (e.g. in Debug mode for use with the designer) set the QT_QMAKE_EXECUTABLE in cmake-gui.QT_QMAKE_EXECUTABLE should be set to the path of the qmake.exe file, which is inside the bin directory (for example, ./QT/qt-everywhere-opensource-src-4.7.3/bin/qmake.exe).

*ccmake (for linux/mac): Configure using the following commands. For developers, set the '''CMAKE_BUILD_TYPE''' to '''Debug'''.
<pre>
mkdir Slicer4-SuperBuild
cd Slicer4-SuperBuild
ccmake -DQT_QMAKE_EXECUTABLE:FILEPATH=/home/myself/qt-4.6.3/qt/bin/qmake ../Slicer4

</pre>

Two projects are generated by ccmake/cmake-gui. One of them is in the top-level bin directory Slicer4-Superbuild and the other one is in the subdirectory Slicer4-Superbuild/Slicer-build:

#The first project in Slicer4-Superbuild manages all the external dependencies of Slicer (VTK, ITK, Python, ...). To build Slicer for the first time, run make (or build the solution file in Visual Studio) in Slicer4-Superbuild, which will update and build the external libraries and if successful will then build the subproject Slicer-build. 
#The second project in Slicer4-Superbuild/Slicer-build is the "traditional" build directory of Slicer. After local changes in Slicer (or after an svn update on the source directory of Slicer), only running make (or building the solution file in Visual Studio) in Slicer4-Superuild/Slicer-build is necessary (the external libraries are considered built and up to date). 

{{warning}}
#For Windows users:Windows doesn't support path longer than 260 characters, please make sure that the total path name of your Slicer-build directory is no longer than 75 characters ( for example "c:\work\Slicer\Slicer-Superbuild" (32 characters) is fine)
#Warning: a lot of space disk is necessary to compile Slicer (>10GB on Windows)

== Step3: Build Slicer4 ==
After configuration, start the build process in the Slicer4-SuperBuild directory
*Linux / Mac: Run the following code:
<pre>
make -j<NUMBEROFCORES>
</pre>
*Windows: Open Slicer4-SuperBuild\Slicer.sln (or Slicer-4.0\Slicer4-SuperBuild\Slicer-build\Slicer.sln) in Visual Studio and build the ALL_BUILD project.

{{warning}}
# As it is indicated in Step2, if you make local changes in Slicer4, run make (or build the solution file in Visual Studio) in the directory Slicer4-Superuild/Slicer-build.
# If you would like to make local changes and debug your code in Debug mode in Visual Studio, use the Visual Studio Command Prompt to open the solution file in Slicer4-Superuild/Slicer-build:
#* Open Visual Studio Command Prompt
#* Go to the directory Slicer4-Superuild/Slicer-build
#* Write Slicer.exe --VisualStudio Slicer.sln

==Step4: Run Slicer4 ==
Run the launcher in Slicer4-SuperBuild/Slicer-build/Slicer (Slicer.exe on windows)

==Platform Notes==

* Linux Ubuntu: if you have odd rendering artifacts, try disabling visual effects (System/Appearance/Visual Effects)

Documentation/4.0/Developers/Build Instructions

2011-07-24T04:36:20Z

Belhachemi: /* STEP 0: Prerequisites */

[[Slicer4| Back to Slicer 4]]

The goal of the Super-Build is to provide a cross-platform build system that allows developers to quickly install and configure the multiple packages.

Where [[Slicer3:Build_Instructions|Slicer3's build system]] relied on a [[Slicer3:getbuildtest|custom build script called getbuildtest]], new features added to [http://www.cmake.org CMake], partly driven by slicer's requirements, allow porting of the scripts to rely more on native CMake functionality with the benefit that build script is more modular and general purpose.

== STEP 0: Prerequisites ==

Please check that the following tools are installed on your machine.

*Mac
** git version >= 1.6.5
*** [http://git-scm.com/download Download and install Git]
**[http://www.cmake.org/cmake/resources/software.html CMake] version >= 2.8.2

* Linux prerequisites (''need to confirm'')
** Debian Squeeze user type: <code>sudo apt-get install gcc libX11-dev libXt-dev libgl1-mesa-dev libosmesa6-dev libglu1-mesa-dev git cmake cmake-curses-gui libqt4-dev subversion</code>
** Ubuntu users, just type the following line in a terminal <code>sudo apt-get install gcc libX11-dev libXt-dev libgl1-mesa-dev libosmesa6-dev libglu1-mesa-dev git cmake cmake-curses-gui</code>
** gcc
** gcc-c++
** libX11
** libX11-devel (libX11-dev on Ubuntu 7.04)
** libXt-devel (libXt-dev on Ubuntu)
** opengl/mesa (libgl1-mesa-dev on Ubuntu) (and libosmesa6-dev on Ubuntu)
** glu (libglu1-mesa-dev on Ubuntu)
** git version >= 1.6.5
*** [http://git-scm.com/download Download Git]
*** install git: <code>sudo apt-get install git</code>. If <code>git --version</code> is inferior to 1.6.5, then:<code>sudo dpkg --install git-core_1.6.5-1~bpo50+1_amd64.deb</code>
**[http://www.cmake.org/cmake/resources/software.html CMake] version >= 2.8.2

* Windows prerequisites
** IDE:
*** Prefered: Microsoft Visual Studio 2008 or 2010 (including [http://www.microsoft.com/express/Downloads/#2010-Visual-CPP Express Edition])
*** Cygwin suite
**[http://www.cmake.org/cmake/resources/software.html CMake] version >= 2.8.2
** SVN
** CVS
** git version >= 1.6.5. [http://code.google.com/p/msysgit/ msysgit] is recommended. Using [http://code.google.com/p/tortoisegit/ TortoiseGit] is a plus.
* '''All Platforms: Qt.'''{{note}} Use one of the links provided in the table below to download the source code or binary of Qt. If required, you can download the source code and compile Qt using the instructions in [[Slicer4:Build_Instructions_for_QT|Slicer4: Build Instructions for Qt]].

{| border="1" style="margin-left: 20px;"
|- bgcolor="#FFFFCC"
!rowspan="3"|
!colspan="2" rowspan="2"|Linux
!colspan="2"|Mac
!colspan="2" rowspan="2"|Windows
|- bgcolor="#FFFFCC"
!colspan="1"|Tiger
!colspan="1"|Leopard, SnowLeopard
|- bgcolor="#FFFFCC"
!|32bits
!|64bits
!|32bits
!colspan="1"|64bits
!|32bits
!|64bits
|-
! bgcolor="#FFFFCC" | [http://get.qt.nokia.com/qt/source/ Qt source link]
|align="center" colspan="4"| [http://get.qt.nokia.com/qt/source/qt-everywhere-opensource-src-4.6.3.tar.gz 4.6.3]
|align="center" colspan="2"| [http://get.qt.nokia.com/qt/source/qt-everywhere-opensource-src-4.6.3.zip 4.6.3 (vs2008)] [http://get.qt.nokia.com/qt/source/qt-everywhere-opensource-src-4.7.3.zip 4.7.3 (vs2010)]
|-
! bgcolor="#FFFFCC" | [http://get.qt.nokia.com/qt/source/ Qt binary link]
|align="center" colspan="1"| [http://get.qt.nokia.com/qtsdk/qt-sdk-linux-x86-opensource-2010.05.bin x86_2010.05]
|align="center" colspan="1"| [http://get.qt.nokia.com/qtsdk/qt-sdk-linux-x86_64-opensource-2010.05.bin x86_64_2010.05]
|align="center" colspan="1"| [http://get.qt.nokia.com/qt/source/qt-mac-carbon-opensource-4.7.0.dmg carbon_4.7.0]
|align="center" colspan="1"| [http://get.qt.nokia.com/qtsdk/qt-sdk-mac-opensource-2010.05.dmg cocoa_4.7.0]
|align="center" colspan="1"| [http://get.qt.nokia.com/qt/source/qt-win-opensource-4.6.3-vs2008.exe 4.6.3 (vs2008)] [http://get.qt.nokia.com/qt/source/qt-win-opensource-4.7.3-vs2008.exe 4.7.3 (vs2010)]
|align="center" colspan="1"| -
|}

== Step1: Checkout slicer source files using subversion ==
For example:
<pre>
cd MyProjects
svn co http://svn.slicer.org/Slicer4/trunk Slicer4
</pre>

== Step2: Configure and generate Slicer solution files ==
You can configure and generate Slicer solution files using either ccmake or cmake-gui.
*cmake-gui (Recommended): Configure using default options.
{{note}}
#If you downloaded the Qt binary then qmake will be detected and all paths will be set automatically.
#If you built your own Qt (e.g. in Debug mode for use with the designer) set the QT_QMAKE_EXECUTABLE in cmake-gui.QT_QMAKE_EXECUTABLE should be set to the path of the qmake.exe file, which is inside the bin directory (for example, ./QT/qt-everywhere-opensource-src-4.7.3/bin/qmake.exe).

*ccmake (for linux/mac): Configure using the following commands. For developers, set the '''CMAKE_BUILD_TYPE''' to '''Debug'''.
<pre>
mkdir Slicer4-SuperBuild
cd Slicer4-SuperBuild
ccmake -DQT_QMAKE_EXECUTABLE:FILEPATH=/home/myself/qt-4.6.3/qt/bin/qmake ../Slicer4

</pre>

Two projects are generated by ccmake/cmake-gui. One of them is in the top-level bin directory Slicer4-Superbuild and the other one is in the subdirectory Slicer4-Superbuild/Slicer-build:

#The first project in Slicer4-Superbuild manages all the external dependencies of Slicer (VTK, ITK, Python, ...). To build Slicer for the first time, run make (or build the solution file in Visual Studio) in Slicer4-Superbuild, which will update and build the external libraries and if successful will then build the subproject Slicer-build. 
#The second project in Slicer4-Superbuild/Slicer-build is the "traditional" build directory of Slicer. After local changes in Slicer (or after an svn update on the source directory of Slicer), only running make (or building the solution file in Visual Studio) in Slicer4-Superuild/Slicer-build is necessary (the external libraries are considered built and up to date). 

{{warning}}
#For Windows users:Windows doesn't support path longer than 260 characters, please make sure that the total path name of your Slicer-build directory is no longer than 75 characters ( for example "c:\work\Slicer\Slicer-Superbuild" (32 characters) is fine)
#Warning: a lot of space disk is necessary to compile Slicer (>10GB on Windows)

== Step3: Build Slicer4 ==
After configuration, start the build process in the Slicer4-SuperBuild directory
*Linux / Mac: Run the following code:
<pre>
make -j<NUMBEROFCORES>
</pre>
*Windows: Open Slicer4-SuperBuild\Slicer.sln (or Slicer-4.0\Slicer4-SuperBuild\Slicer-build\Slicer.sln) in Visual Studio and build the ALL_BUILD project.

{{warning}}
# As it is indicated in Step2, if you make local changes in Slicer4, run make (or build the solution file in Visual Studio) in the directory Slicer4-Superuild/Slicer-build.
# If you would like to make local changes and debug your code in Debug mode in Visual Studio, use the Visual Studio Command Prompt to open the solution file in Slicer4-Superuild/Slicer-build:
#* Open Visual Studio Command Prompt
#* Go to the directory Slicer4-Superuild/Slicer-build
#* Write Slicer.exe --VisualStudio Slicer.sln

==Step4: Run Slicer4 ==
Run the launcher in Slicer4-SuperBuild/Slicer-build/Slicer (Slicer.exe on windows)

==Platform Notes==

* Linux Ubuntu: if you have odd rendering artifacts, try disabling visual effects (System/Appearance/Visual Effects)

Documentation/4.0/Developers/Build Instructions

2011-07-24T04:34:50Z

Belhachemi: /* STEP 0: Prerequisites */

[[Slicer4| Back to Slicer 4]]

The goal of the Super-Build is to provide a cross-platform build system that allows developers to quickly install and configure the multiple packages.

Where [[Slicer3:Build_Instructions|Slicer3's build system]] relied on a [[Slicer3:getbuildtest|custom build script called getbuildtest]], new features added to [http://www.cmake.org CMake], partly driven by slicer's requirements, allow porting of the scripts to rely more on native CMake functionality with the benefit that build script is more modular and general purpose.

== STEP 0: Prerequisites ==

Please check that the following tools are installed on your machine.

*Mac
** git version >= 1.6.5
*** [http://git-scm.com/download Download and install Git]
**[http://www.cmake.org/cmake/resources/software.html CMake] version >= 2.8.2

* Linux prerequisites (''need to confirm'')
** Ubuntu users, just type the following line in a terminal <code>sudo apt-get install gcc libX11-dev libXt-dev libgl1-mesa-dev libosmesa6-dev libglu1-mesa-dev git cmake cmake-curses-gui</code>
** Debian Squeeze user type: <code>sudo apt-get install gcc libX11-dev libXt-dev libgl1-mesa-dev libosmesa6-dev libglu1-mesa-dev git cmake cmake-curses-gui libqt4-dev</code>
** gcc
** gcc-c++
** libX11
** libX11-devel (libX11-dev on Ubuntu 7.04)
** libXt-devel (libXt-dev on Ubuntu)
** opengl/mesa (libgl1-mesa-dev on Ubuntu) (and libosmesa6-dev on Ubuntu)
** glu (libglu1-mesa-dev on Ubuntu)
** git version >= 1.6.5
*** [http://git-scm.com/download Download Git]
*** install git: <code>sudo apt-get install git</code>. If <code>git --version</code> is inferior to 1.6.5, then:<code>sudo dpkg --install git-core_1.6.5-1~bpo50+1_amd64.deb</code>
**[http://www.cmake.org/cmake/resources/software.html CMake] version >= 2.8.2

* Windows prerequisites
** IDE:
*** Prefered: Microsoft Visual Studio 2008 or 2010 (including [http://www.microsoft.com/express/Downloads/#2010-Visual-CPP Express Edition])
*** Cygwin suite
**[http://www.cmake.org/cmake/resources/software.html CMake] version >= 2.8.2
** SVN
** CVS
** git version >= 1.6.5. [http://code.google.com/p/msysgit/ msysgit] is recommended. Using [http://code.google.com/p/tortoisegit/ TortoiseGit] is a plus.
* '''All Platforms: Qt.'''{{note}} Use one of the links provided in the table below to download the source code or binary of Qt. If required, you can download the source code and compile Qt using the instructions in [[Slicer4:Build_Instructions_for_QT|Slicer4: Build Instructions for Qt]].

{| border="1" style="margin-left: 20px;"
|- bgcolor="#FFFFCC"
!rowspan="3"|
!colspan="2" rowspan="2"|Linux
!colspan="2"|Mac
!colspan="2" rowspan="2"|Windows
|- bgcolor="#FFFFCC"
!colspan="1"|Tiger
!colspan="1"|Leopard, SnowLeopard
|- bgcolor="#FFFFCC"
!|32bits
!|64bits
!|32bits
!colspan="1"|64bits
!|32bits
!|64bits
|-
! bgcolor="#FFFFCC" | [http://get.qt.nokia.com/qt/source/ Qt source link]
|align="center" colspan="4"| [http://get.qt.nokia.com/qt/source/qt-everywhere-opensource-src-4.6.3.tar.gz 4.6.3]
|align="center" colspan="2"| [http://get.qt.nokia.com/qt/source/qt-everywhere-opensource-src-4.6.3.zip 4.6.3 (vs2008)] [http://get.qt.nokia.com/qt/source/qt-everywhere-opensource-src-4.7.3.zip 4.7.3 (vs2010)]
|-
! bgcolor="#FFFFCC" | [http://get.qt.nokia.com/qt/source/ Qt binary link]
|align="center" colspan="1"| [http://get.qt.nokia.com/qtsdk/qt-sdk-linux-x86-opensource-2010.05.bin x86_2010.05]
|align="center" colspan="1"| [http://get.qt.nokia.com/qtsdk/qt-sdk-linux-x86_64-opensource-2010.05.bin x86_64_2010.05]
|align="center" colspan="1"| [http://get.qt.nokia.com/qt/source/qt-mac-carbon-opensource-4.7.0.dmg carbon_4.7.0]
|align="center" colspan="1"| [http://get.qt.nokia.com/qtsdk/qt-sdk-mac-opensource-2010.05.dmg cocoa_4.7.0]
|align="center" colspan="1"| [http://get.qt.nokia.com/qt/source/qt-win-opensource-4.6.3-vs2008.exe 4.6.3 (vs2008)] [http://get.qt.nokia.com/qt/source/qt-win-opensource-4.7.3-vs2008.exe 4.7.3 (vs2010)]
|align="center" colspan="1"| -
|}

== Step1: Checkout slicer source files using subversion ==
For example:
<pre>
cd MyProjects
svn co http://svn.slicer.org/Slicer4/trunk Slicer4
</pre>

== Step2: Configure and generate Slicer solution files ==
You can configure and generate Slicer solution files using either ccmake or cmake-gui.
*cmake-gui (Recommended): Configure using default options.
{{note}}
#If you downloaded the Qt binary then qmake will be detected and all paths will be set automatically.
#If you built your own Qt (e.g. in Debug mode for use with the designer) set the QT_QMAKE_EXECUTABLE in cmake-gui.QT_QMAKE_EXECUTABLE should be set to the path of the qmake.exe file, which is inside the bin directory (for example, ./QT/qt-everywhere-opensource-src-4.7.3/bin/qmake.exe).

*ccmake (for linux/mac): Configure using the following commands. For developers, set the '''CMAKE_BUILD_TYPE''' to '''Debug'''.
<pre>
mkdir Slicer4-SuperBuild
cd Slicer4-SuperBuild
ccmake -DQT_QMAKE_EXECUTABLE:FILEPATH=/home/myself/qt-4.6.3/qt/bin/qmake ../Slicer4

</pre>

Two projects are generated by ccmake/cmake-gui. One of them is in the top-level bin directory Slicer4-Superbuild and the other one is in the subdirectory Slicer4-Superbuild/Slicer-build:

#The first project in Slicer4-Superbuild manages all the external dependencies of Slicer (VTK, ITK, Python, ...). To build Slicer for the first time, run make (or build the solution file in Visual Studio) in Slicer4-Superbuild, which will update and build the external libraries and if successful will then build the subproject Slicer-build. 
#The second project in Slicer4-Superbuild/Slicer-build is the "traditional" build directory of Slicer. After local changes in Slicer (or after an svn update on the source directory of Slicer), only running make (or building the solution file in Visual Studio) in Slicer4-Superuild/Slicer-build is necessary (the external libraries are considered built and up to date). 

{{warning}}
#For Windows users:Windows doesn't support path longer than 260 characters, please make sure that the total path name of your Slicer-build directory is no longer than 75 characters ( for example "c:\work\Slicer\Slicer-Superbuild" (32 characters) is fine)
#Warning: a lot of space disk is necessary to compile Slicer (>10GB on Windows)

== Step3: Build Slicer4 ==
After configuration, start the build process in the Slicer4-SuperBuild directory
*Linux / Mac: Run the following code:
<pre>
make -j<NUMBEROFCORES>
</pre>
*Windows: Open Slicer4-SuperBuild\Slicer.sln (or Slicer-4.0\Slicer4-SuperBuild\Slicer-build\Slicer.sln) in Visual Studio and build the ALL_BUILD project.

{{warning}}
# As it is indicated in Step2, if you make local changes in Slicer4, run make (or build the solution file in Visual Studio) in the directory Slicer4-Superuild/Slicer-build.
# If you would like to make local changes and debug your code in Debug mode in Visual Studio, use the Visual Studio Command Prompt to open the solution file in Slicer4-Superuild/Slicer-build:
#* Open Visual Studio Command Prompt
#* Go to the directory Slicer4-Superuild/Slicer-build
#* Write Slicer.exe --VisualStudio Slicer.sln

==Step4: Run Slicer4 ==
Run the launcher in Slicer4-SuperBuild/Slicer-build/Slicer (Slicer.exe on windows)

==Platform Notes==

* Linux Ubuntu: if you have odd rendering artifacts, try disabling visual effects (System/Appearance/Visual Effects)

Modules:AtlasCreator

2011-07-21T17:09:17Z

Belhachemi: /* The Command Line Interface */

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]

__NOTOC__
===AtlasCreator===

{|
|[[Image:ACguiStart.png|thumb|280px|Atlas Creator User Interface in '''simple mode''']]
|[[Image:ACexampleOutput.png|thumb|280px|Example of generated Atlases]]
|[[Image:ACcheckerboard.png|thumb|280px|Comparison of the alignment of two cases before and after Atlas Creation]]
|}

== General Information ==
===Module Type & Category===

Type: Built-in Loadable Module

Category: Registration

===Authors, Collaborators & Contact===
* Daniel Haehn, University of Pennsylvania
* Kilian Pohl, University of Pennsylvania
* Contact: Daniel Haehn (haehn@bwh.harvard.edu)

===Module Description===
The '''Atlas Creator module''' aligns images paired with segmentations to '''generate statistical atlases''' for several segmented structures.

'''Features''':
* Support for BRAINSFit/CMTK/Congeal toolkits for Registration and Resampling
* Fixed Registration against a template or Dynamic Registration against a mean image
* Normalization of output atlases to a given value
* auto-detection of Structures (labels)
* different Output Casts
* Principal Component Analysis
* Cluster Computation Mode
* using existing Transforms and skipping the Registration (f.e. to re-run a previous generation)

== Usage ==

This module supports different usage types and interfaces:
# '''[[Modules:AtlasCreator#simple|Simple Atlas Creation (HowTo)]]'''
# [[Modules:AtlasCreator#extended|The extended graphical user interface]]
# [[Modules:AtlasCreator#cli|The command line interface]]
# [[Modules:AtlasCreator#mrml|External invocation using the Atlas Creator MRML Node]]

===Use Cases, Examples===

''' Input Data Requirements '''

The Atlas Creator expects input data to be structured the following way:

* In general each original image is accompanied by a manual segmentation.
* The images and the segmentations have to be in two different folders but have matching filenames.
* All images and segmentations have to be in Slicer-readable format.
* For Example:
**./originals/case1.nrrd
**./originals/case2.nrrd
**./originals/case3.nrrd
**./segmentations/case1.nrrd
**./segmentations/case2.nrrd
**./segmentations/case3.nrrd


{| style="color:darkblue; background-color:lightgrey;" cellpadding="10" cellspacing="0" border="0"
|'''HowTo: Simple Atlas Creation'''
|-
|The following steps perform a Pair Fixed Registration against an automatic chosen template for automatically detected structures.
|-
|'''1.''' Select the directories containing the '''Original Images''' and the '''Segmentations''' in the Input/Output panel.
|-
|'''2.''' Select an '''Output Directory''' in the Input/Output panel. It makes sense to create a new directory to use for the Output.
|-
|'''3.''' Hit '''Start!'''
|-
|'''4.''' After some wait (minutes or hours!, depending on the number of input cases), the generated atlases and the used template will be loaded into 3D Slicer.
|}

'''Output Directory Structure'''

The ''Output Directory'' contains the following content after the Atlas Creator finished.

* '''./template.nrrd''' - The fixed or dynamic template
* '''./normalizedIntensityMapOfAligned.nrrd''' - An intensity map of all aligned cases, divided by the number of cases.
* '''./registered/''' - A directory containing the registered Original Images, if ''Delete Aligned Images'' is ''off''.
* '''./resampled/''' - A directory containing the resampled Segmentations used for the Atlas Creation, if ''Delete Aligned Segs.'' is ''off''.
* '''./transforms/''' - A directory containing the generated transforms as a result of the registration
* '''./atlasX.nrrd''' - Atlas for label X, if ''Activate PCA'' is ''off''.
* '''./atlasY.nrrd''' - Atlas for label Y, if ''Activate PCA'' is ''off''.
* '''./atlasZ.nrrd''' - Atlas for label Z, if ''Activate PCA'' is ''off''.
* '''./PCA/PCAX/''' - A directory containing generated PCA data for label X, if ''Activate PCA'' is ''on''.
* '''./PCA/PCAY/''' - A directory containing generated PCA data for label Y, if ''Activate PCA'' is ''on''.
* '''./PCA/PCAZ/''' - A directory containing generated PCA data for label Z, if ''Activate PCA'' is ''on''.
* ... more atlases depending on which structures were used

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


===='''The Extended Graphical User Interface'''====

[[Image:ACfullGui.png|thumb|360x360px|right|Atlas Creator User Interface in '''extended mode''']]
The Atlas Creator module is organized in panels from which only the ''Input/Output panel'' is expanded by default. Additional features are provided through an extended interface. This extended interface is divided into the ''Parameters'' panel and the ''Advanced'' panels which are collapsed by default.

'''Input/Output Panel'''

The Input/Output panel reflects the required settings for any atlas creation, simple or extended.

[[Image:ACinputoutput.png|360x360px|The '''Input/Output''' panel]]
* ''Original Images'': The folder containing the original images '''Required'''
* ''Segmentations'': The folder containing the segmentations '''Required'''
* ''Output directory'': The output folder - if it does not exist or is not empty, a new output folder with a similar name will be created '''Required'''
* ''Registration Type'': The type of alignment used during registration stage
** ''Pair Fixed'': Register all other cases against a fixed template. By default, the Atlas Creator chooses this template.
** ''Pair Online'': Register all cases against a mean image of all cases which will be generated automatically.
** ''Group Online'': Register all cases using the un-biased groupwise registration provided by the [[Modules:AtlasCreator:CongealingCLI|Congeal]] tool.

'''Parameters Panel'''

[[Image:ACparameters.png|360x360px|The '''Parameters''' panel]]
* ''Toolkit'' for ''Pair Fixed'' and ''Pair Online'': By default ''BRAINSFit'' are used for registration and resampling. If the ''CMTK'' extensions are installed, it be used as an alternative. If ''CMTK'' was chosen but not installed, the Atlas Creator falls back to ''BRAINSFit''.
* ''Deformation'': Choose the deformation model for the registration stage.
** ''Affine'': Use linear transformations (faster, less flexible)
** ''Non-rigid'': Use non-rigid transformations on top of linear transformations (slower, more flexible)
* ''Alignment iterations'', for ''Pair Online'': The number of iterations for generating a mean image and registering against it in ''Pair Online'' mode.
* ''Default case'', for ''Pair Fixed'': The default case to use as the fixed template in ''Pair Fixed'' mode. This gets chosen automatically when selecting ''Original Images'' and ''Segmentations'' but can be modified for convenience.

'''Advanced Panels'''

'''Cluster Configuration Panel'''

The Atlas Creator supports distributing all computations among a Grid Environment. This includes using a scheduler to start all computation jobs (registration, resampling, computing mean images, combine to atlases). All submitted jobs will be monitored for completion and will be re-started up to 4 times on failure. The atlas creation will continue if the failure is not critical but will notify of all failures.

[[Image:ACadvancedCluster.png|360x360px|The advanced '''Cluster Configuration''' panel]]
* ''Use Cluster'': If activated, all computation jobs will be submitted using the ''Scheduler Command''.
* ''Scheduler Command'': This command will be used to submit all jobs. For example, if the ''Scheduler Command'' is ''bsub < '', the computation jobs will be run as ''bsub < script1.sh'' instead of just running ''script1.sh''.

'''Principal Component Analysis Panel'''

Beside generating statistical atlases, the Atlas Creator module supports a Principal Component Analysis (PCA) to incorporate shape information.

[[Image:ACadvancedPCA.png|360x360px|The advanced '''Principal Component Analysis''' panel]]
* ''Activate PCA'': Use Principal Component Analysis instead of statistical atlas generation.
* ''Max. Eigenvectors'': The maximal number of eigenvectors to analyze during the PCA computation. Should be equal to the number of input cases but can be restricted for convenience. The Atlas Creator will detect if the number exceeds the number of cases.
* ''Combine PCAs'': If activated, all structures (labels) will be defined in one PCA model instead of defining a PCA model for each structure.

'''Use Existing Transforms Panel'''

It is possible to skip the registration stage and directly resample segmentations using existing transforms. This can be used to modify existing atlases.

[[Image:ACadvancedUseExisting.png|360x360px|The advanced '''Use Existing Transforms''' panel]]
* ''Skip Registration'': If activated, the registration stage will be skipped and existing transforms are used for resampling the input segmentations.
* ''Transforms directory'': The directory containing existing transformations. In order to be valid, these transformations must have been generated by the same toolkit (CMTK or BRAINSFit) as configured now.
* ''Existing Template:'': The existing template which was used in the previous atlas generation (''template.nrrd'').

'''Misc. Panel'''

Miscellaneous settings can be specified using this panel.

[[Image:ACadvancedMisc.png|360x360px|The advanced '''Misc.''' panel]]
* ''Labels'': The list of structures for which to generate the different atlases. Each structure has to be represented by a label number. By default, the Atlas Creator reads this list from the ''default case'' - if specified - or from the first segmentation automatically.
* ''Save Transforms'': If activated, the generated transforms of the registration stage will be saved. (Default setting)
* ''Normalize Atlases'': The generated statistical atlases can be normalized to a value range from 0..X where X is the ''Normalize to'' value.
* ''Normalize to'': If ''Normalize Atlases'' is activated, this value is the upper boundary of the range to which the atlases are normalized to. By default, this is 1.
* ''Output cast for Atlases'': The output cast for the generated atlases can be specified. Default is short.
* ''Delete aligned Images'': If activated, the aligned images will be deleted after atlas generation. If ''not'' activated, a sub-directory ''registered'' containing the aligned images will be available in the output directory.
* ''Delete aligned Segs.'': If activated, the aligned images will be deleted after atlas generation. If ''not'' activated, a sub-directory ''resampled'' containing the aligned segmentations will be available in the output directory.
* ''Debug Output'': This switch enables extra debug and verbose output during all computations.
* ''Dry-Run (Simulaton)'': If activated, no actual computation is performed and the atlas creation will be simulated. This might be helpful to test a long-run computation before actually performing it.



===='''The Command Line Interface'''====

Beside using the graphical user interface in 3D Slicer, the Atlas Creator can be accessed using the '''commandline interface'''.

<pre>
$ cd Slicer3-release/lib/Slicer3/Modules/AtlasCreator/
$ python atlascreator.py --help
AtlasCreator for 3D Slicer
Version v0.4

Usage:

-h, --help
Show this information.

-i, --images DIR
Directory containing original images.

-s, --segmentations DIR
Directory containing segmentations.

-o, --output DIR
Output directory.

[....]
</pre>

The '''full documentation of the commandline interface''' is available on [[Modules:AtlasCreator:CLI|a separate page]].

== Development ==

===Notes from the Developer(s)===


===='''External invocation using the Atlas Creator MRML Node'''====

It is easy to include the Atlas Creator in third-party 3D Slicer modules (C++, Tcl and Python are supported) or run it via the Tcl or Python consoles. To do so, one has to configure the vtkMRMLAtlasCreatorNode and fire a launch event.

The following example outlines the procedure by configuring a ''Pair fixed'' computation against a defaultCase (Python was chosen for this example):

<pre>
from Slicer import slicer
import os

# we use the testdata which is shipped with the Atlas Creator
dataPath = os.path.normpath(slicer.Application.GetBinDir().. + '/../share/Slicer3/Modules/AtlasCreator/TestData/')

# create a new Atlas Creator MRML Node
n = slicer.vtkMRMLAtlasCreatorNode()

# Initialize with a default configuration
n.InitializeByDefault()

# set the original images by specifying the absolute filepaths for all cases divided by space
n.SetOriginalImagesFilePathList(dataPath + '/originals/case60.nrrd ' + dataPath + '/originals/case61.nrrd ' + dataPath + '/originals/case62.nrrd')
# set the segmentations by specifying the absolute filepaths for all cases divided by space
n.SetSegmentationsFilePathList(dataPath + '/segmentations/case60.nrrd ' + dataPath + '/segmentations/case61.nrrd ' + dataPath + '/segmentations/case62.nrrd')

# configure an output directory
n.SetOutputDirectory('/tmp/acout/')

# set the default case
n.SetFixedTemplateDefaultCaseFilePath(dataPath + '/originals/case62.nrrd')

# add the MRML node to the scene
slicer.MRMLScene.AddNode(n)

# start the computation by firing the launch event
n.Launch()
</pre>

==== Architecture of the Atlas Creator ====

{|
|[[Image:AcFlowNew.png|thumb|280px|The '''computational steps''' of the Atlas Creator]]
|[[Image:AcComponentsNew.png|thumb|360px|'''Different Components''' work together in the Atlas Creator and create a very heterogeneous environment.]]
|[[Image:AtlasCreatorClassDiagramm.png|thumb|360px|The '''class diagram of the Python Scripted Module''' which is the central unit of the Atlas Creator.]]
|}

===Dependencies===
At least BRAINSFit, CMTK or Congeal have to be installed. BRAINSFit is deployed via Slicer, VMTK and Congeal are available as Slicer extensions.

===Tests===

On the [http://www.cdash.org/CDash/index.php?project=Slicer3 Dashboard], these tests verify that the module is working on various platforms:

* vtkMRMLAtlasCreatorNodeTest1 [http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/AtlasCreator/Cxx/Testing/vtkMRMLAtlasCreatorNodeTest1.cxx?view=markup Modules/AtlasCreator/Cxx/Testing/vtkMRMLAtlasCreatorNodeTest1.cxx]
* AtlasCreatorLaunchFixedTest [http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/AtlasCreator/Cxx/Testing/vtkMRMLAtlasCreatorNodeLaunchTest1.py?view=markup Modules/AtlasCreator/Cxx/Testing/vtkMRMLAtlasCreatorNodeLaunchTest1.py]
* AtlasCreatorLaunchFixedFailProofTest [http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/AtlasCreator/Cxx/Testing/vtkMRMLAtlasCreatorNodeLaunchTest2.py?view=markup Modules/AtlasCreator/Cxx/Testing/vtkMRMLAtlasCreatorNodeLaunchTest2.py]
* AtlasCreatorLaunchDynamicTest [http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/AtlasCreator/Cxx/Testing/vtkMRMLAtlasCreatorNodeLaunchTest3.py?view=markup Modules/AtlasCreator/Cxx/Testing/vtkMRMLAtlasCreatorNodeLaunchTest3.py]

===Known bugs===
The AtlasCreator is currently ''not'' supported on Windows machines.

===Usability issues===
* Congeal support is still ''Under Construction''.

===Source code & documentation===

Source code:
*Available in the 3D Slicer Trunk: [http://viewvc.slicer.org/viewvc.cgi/Slicer3/trunk/Modules/AtlasCreator/ Modules/AtlasCreator]

Doxygen documentation:
* [http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classAtlasCreator_1_1AtlasCreatorGUI_1_1AtlasCreatorGUI.html AtlasCreatorGUI]
* [http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classAtlasCreator_1_1AtlasCreatorLogic_1_1AtlasCreatorLogic.html AtlasCreatorLogic]
* [http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classAtlasCreator_1_1AtlasCreatorHelper_1_1AtlasCreatorHelper.html AtlasCreatorHelper]
* [http://www.na-mic.org/Slicer/Documentation/Slicer3-doc/html/classvtkMRMLAtlasCreatorNode.html vtkMRMLAtlasCreatorNode]

== More Information ==

''Please cite this work as:''

L. Zöllei, M. Shenton, W.M. Wells III, K.M. Pohl. The Impact of Atlas Formation Methods on Atlas-Guided Brain Segmentation, Statistical Registration. In ''Pair-wise and Group-wise Alignment and Atlas Formation Workshop at MICCAI 2007: Tenth International Conference on Medical Image Computing and Computer-Assisted Intervention'', pp. 39 - 46, Brisbane, Australia, 2007

===Acknowledgment===
The research was funded by an ARRA supplement to NIH NCRR (P41 RR13218).

The Atlas Creator module benefits from several different Toolkits: Thank you for [[Modules:BRAINSFit|BRAINSTools]] (Hans Johnson et al.), for [[Modules:CMTK|CMTK]] (Torsten Rolfing et al.) and for [[Modules:AtlasCreator:CongealingCLI|Congeal]] (J. De Bonet, L. Zöllei and W.M. Wells III).

Thank you to Dominique Belhachemi and Steve Pieper for their support!

===References===

EMSegmenter-Tasks:EMS Spine

2011-06-23T21:19:40Z

Belhachemi: Created page with 'Return to EMSegmenter Task Overview Page =Description= =Anatomical Tree= * root ** BG ** Bone =Atlas= =Result= =Collaborators= =Acknowledgment= =Ci…'

[[EMSegmenter-Tasks|Return to EMSegmenter Task Overview Page]]

=Description=

=Anatomical Tree=

* root
** BG
** Bone

=Atlas=

=Result=

=Collaborators=

=Acknowledgment=

=Citations=

EMSegmenter-Tasks

2011-06-23T21:17:25Z

Belhachemi: /* Tasks in development */

[[EMSegmenter-Overview|Return to EMSegmenter Overview Page]]

=What is a task?=

Most clinicians are using the EMSegmenter to segment specific parts of the human body. Those segmentations depend heavily on
the used input data. The signal level in the input data varies with the used image modalities (e.g. MRI, CT, ...) and with each anatomical structure.
The EMSegmenter can take advantage of some knowledge about the signal level of those anatomical structures in the different image modalities.
 
Technically, each tasks consist of a .mrml file and a .tcl file.
 
The .mrml file stores the anatomical properties (mean values, covariance values) in a user defined tree structure. 
The .tcl script is used to perform some pre-processing on the input data. 
 
Visit the following web page to create your own [[EMSegmenter-CreateTask| task]] or we can [[ EMSegmenter-UseCaseAdvertisement | help ]] you .

=Segmentation Task Library=
==Existing Tasks in Slicer 3.6.3==
*[[Image:MRI-Human-Brain_BeforeAfter.png|250px]] '''Task 01: [[EMSegmenter-Tasks:MRI-Human-Brain|MRI Human Brain ''' for non-skull stripped T1 scans]]
*[[Image:MRIHumanBrainParcellation.png|250px]] '''Task 02: [[EMSegmenter-Tasks:MRI-Human-Brain-Parcellation|MRI Human Brain Parcellation ''' for skull stripped T1 scans]]
*[[Image:NHP.png|250px]] '''Task 03: [[EMSegmenter-Tasks:Non-Human-Primate|Non-Human Primate ''' for skull stripped T1 scans]]

==Tasks for Slicer 3.6.4==
* [[Image:EMS Result Hand subject2.png|250px]] '''Task 04: [[EMSegmenter-Tasks:CT-Hand-Bone|CT Hand Bone ''']]
* [[Image:MRIHumanBrainFullParcellation_before_after.png|250px]] '''Task 05: [[EMSegmenter-Tasks:MRI-Human-Brain-Full-Parcellation|MRI Human Brain Full Parcellation''' for non-skull stripped T1 scans]]
* [[Image:MRIHumanBrainHIPR beforeafter.png|250px]] '''Task 06: [[EMSegmenter-Tasks:MRI-Human-Brain-HIPR|MRI Human Brain with high in-plane resolution''' for non-skull stripped T1 scans]]
* [[Image:EMS_Hemisphere_before_after.png|250px]]'''Task 07: [[EMSegmenter-Tasks:MRI-Human-Brain-Hemisphere|MRI Human Brain Hemisphere''' for non-skull stripped T1 scans]]

==Tasks in development==
* [[Image:EMS HumanEye Before After.png|250px]]'''Task 08: [[EMSegmenter-Tasks:Human-Eye|Human Eye''']]
* [[Image:EMS MRIHumanBrainExp Before After.png|250px]] '''Task 09: [[EMSegmenter-Tasks:MRI-Human-Brain-Experimental|MRI Human Brain Experimental''' with skull stripping]]
* [[Image:EMSegment-CardioA1-grey-small.jpg|125px]][[Image:EMSegment CardioA1small.jpg|125px]] '''Task 10: [[EMSegmenter-Tasks:cineMARI|cine MRI''' ]]
* [[Image:EMS LesionsExp BeforeAfter.png|250px]] '''Task 11: [[EMSegmenter-Tasks:LesionExp|White matter lesion segmentation''' ]]
* '''Task 12: [[EMSegmenter-Tasks:EMS_Spine|Bone segmentation''' ]]

==External Command Lines (Under Development) ==
* [[Image:GLISTR Flair.png|125px]][[Image:GLISTR Seg.png|125px]]'''Task 12: [https://www.rad.upenn.edu/sbia/projects/glistr.html GLISTR: Automatic Glioma Segmentation'''] The software was developed and is distributed by SBIA. SBIA will soon release an interface for GLISTR to interact with Slicer

=Additional Use Cases=
==Quantitative assessment using MPRAGE and Flair images==
* Collaborator: Tammie Benzinger , Washington University School of Medicine
* Short description: Quantitative assessment using MPRAGE and Flair images
* Image specification: Dimension: 256x256x160 , Spacing 1x1x1, T2 MPRAGE
* Used Task: [[EMSegmenter-Tasks:MRI-Human-Brain-Experimental|'''MRI Human Brain Experimental''' (with skull stripping)]]
<gallery perrow=2: widths=200px : heights=200px>
Image:EMS_Quantitative_assessment_orig.png
Image:EMS_Quantitative_assessment.png
</gallery>

==Brain Atrophy in Aging Patients==
* Collaborator: David Tate, PI (Brigham and Women's Hospital), Daniel McCaffrey (Brigham and Women's Hospital), Alex Zaitsev (Brigham and Women's Hospital/Surgical Planning Laboratory) and Jewish Hospital
* Short description: Evaluate Brain Atrophy in aging subjects (NOTE: the segmentation was done for old scans from 90s. No other tools could segment CSF.)
* Image specification: NA Tesla, Scanner: NA, Psuedo T1, Axial Scans, TR/TI/TE=NA, pixel_xsize = 0.937500, pixel_ysize = 0.937500, fov = 240.000000, aspect = 0.000000, thick = 5.000000
* Used Task: [[EMSegmenter-Tasks:MRI-Human-Brain|'''MRI Human Brain''']]
<gallery perrow=2: widths=200px : heights=200px>
Image:EMS_AgingStudy_DTate_Project_3-6-2.png
Image:EMS_AgingStudy_PseudoT1_OldMIRs_JewishHospEMS_manualTrain_60x.png
</gallery>

==Brain Atrophy in HIV Patients==
* Collaborator: David Tate, PI (Brigham and Women's Hospital), Troy Russel (Brigham and Women's Hospital), Alex Zaitsev (Brigham and Women's Hospital/Surgical Planning Laboratory) and National HIV Consortium
* Short description: Evaluate Brain Atrophy in HIV Patients
* Image specification: 3 Tesla, Scanner: NA, MPRAGE, Sagittal Scans, TR/TI/TE=NA, pixel_xsize = 0.9375, pixel_ysize = 0.9375, fov = NA, aspect = NA, space = 1.5
* Used Task: [[EMSegmenter-Tasks:MRI-Human-Brain|'''MRI Human Brain''']]
<gallery perrow=2: widths=425px : heights=200px>
Image:EMS_HIVStudy_Segmentation.png
Image:EMS_HIVStudy_Segmentation_Auto.png
</gallery>

==Pediatric MS Study==
* Collaborator: Tanuja Chitnis PI (Brigham and Women's Hospital/Multiple Sclerosis Center), Alexander Zaitsev (Brigham and Women's Hospital/Surgical Planning Laboratory) and Massachusetts General Hospital
* Short description: Evaluate brain atrophy for pediatric MS Patients
* Image specification: 3 Tesla, Scanner: SIGNA HDx / GE MEDICAL SYSTEMS, 3D MPRAGE, Sagital Scans, TR/TI/TE=24/0/7 ms, pixel_xsize = 0.976600, pixel_ysize = 0.976600, fov = 250.009598, aspect = 1.535941, thick = 1.500000, space = 0.000000
* Used Task: [[EMSegmenter-Tasks:MRI-Human-Brain|'''MRI Human Brain''']]
<gallery perrow=1: widths=630px : heights=210px>
Image:EMS_PED_MS_Study_Segmentation.png
</gallery>

==Social Cognition Study==
* Collaborator: Collaborator: Andrea Mike, MD (Pecs University, Hungary), Charles Guttmann, MD, Alexander Zaitsev (Brigham and Women's Hospital)
* Short description: Evaluate brain atrophy for elderly MS patients.
* Number of processed cases: 50
* Image specification: 3 Tesla, Scanner: Magnetom TIM Trio, Siemens, 3D MPRAGE, Slice thickness: 1.2mm, Spacing 1.2 1 1 (mm)
* Used Task: [[EMSegmenter-Tasks:MRI-Human-Brain|'''MRI Human Brain''']]
<gallery perrow=1: widths=630px : heights=200px>
Image:EMS_SocialCognitionLESIONS_MANUALLY_SEGMENTED_PECS_S006_Seg.png
</gallery>

==Physiological Brain Activity Longitudinal Study==
* Collaborator: Laura Horky PI (Brigham and Women's Hospital(BWH)), Jon Hainer (BWH), Wendy Plesniak (BWH), Alexander Zaitsev (BWH), Ron Kikinis (BWH) and BWH Division of Nuclear Medicine
* Short description: Evaluate glycolitical brain activity in CSF and White Matter for the patients undergoing chemical therapy courses.
* Image specification: 1.5 Tesla ,Scanner: SIGNA EXCITE / GE MEDICAL SYSTEMS, T1, Axial Scans, TR/TI/TE=500/0/21 ms, pixel_xsize = 0.781251, pixel_ysize = 0.781244, fov = 0.000000, aspect = 7.679990, thick = 5.000000, space = 1.000000
* Used Task: [[EMSegmenter-Tasks:MRI-Human-Brain-Hemisphere|'''MRI Human Brain Hemisphere''']]
<gallery perrow=3: widths=250px : heights=200px>
Image:EmSegment PETCT 1.png
Image:EmSegment PETCT 2.png
Image:EmSegment PETCT 3.png | Result on test data
</gallery>

<gallery perrow=3: widths=250px : heights=200px>
Image:EMSegment PETCT Physiology-1.png
Image:EMSegment PETCT Physiology-2.png
Image:EMSegment PETCT Physiology-3.png | Result on patient data
</gallery>

EMSegmenter-Tasks:LesionExp

2011-06-18T23:23:28Z

Belhachemi: /* Result */

[[EMSegmenter-Tasks|Return to EMSegmenter Task Overview Page]]

=Description=
Two channel automatic segmentation of T1 and FLAIR MRI brain scans into the major tissue classes (gray matter, white matter, csf). The pipeline consist of the following steps:
* Step 1: Perform image inhomogeneity correction of the MRI scan via [http://www.slicer.org/slicerWiki/index.php/Modules:N4ITKBiasFieldCorrection-Documentation-3.6 N4ITKBiasFieldCorrection] (Tustison et al 2010)
* Step 2: Register the atlas to the T1 MRI scan via [[Modules:BRAINSFit| BRAINSFit]] (Johnson et al 2007)
* Step 3: Compute the intensity distributions for each structure 
Compute intensity distribution (mean and variance) for each label by automatically sampling from the MR scan. The sampling for a specific label is constrained to the region that consists of voxels with high probability (top 95%) of being assigned to the label according to the aligned atlas.
* Step 4: Assign T1 GM intensity distribution to T1 Lesion intensity distribution
* Step 5: Automatically segment the MRI scan into the structures of interest using [[Modules:EMSegmenter-3.6|EM Algorithm]] (Pohl et al 2007)

=Anatomical Tree=

* root
** background (BG)
** intracranial cavity (ICC)
*** white matter (WM)
*** grey matter (GM)
*** cerebrospinal fluid (CSF)
*** Lesion

=Atlas=
Atlas was generated based on 82 scans and corresponding segmentations provided by [http://pnl.bwh.harvard.edu/ Psychiatry Neuroimaging Laboratory, BWH]. We registered the scans to a preselected template via Warfield et al. 2001. 
Image Dimension = 256 x 256 x 124 
Image Spacing = 0.9375 x 0.9375 x 1.5 

{| class="wikitable"
|-
| [[Image:EMSegmenter_MRI-Human-Brain_Template_420x420.png|210px]]
| [[Image:EMSegmenter_MRI-Human-Brain_CSF_420x420.png|210px]]
| [[Image:EMSegmenter_MRI-Human-Brain_GM_420x420.png|210px]]
| [[Image:EMSegmenter_MRI-Human-Brain_WM_420x420.png|210px]]
|-
| Template (T1)
| CSF
| GM
| WM
|}

=Result=
<gallery perrow=1: widths=1000px : heights=300px>
Image:EMS LesionExp T1.png
Image:EMS LesionExp FLAIR.png
Image:EMS LesionExp Segmentation.png
</gallery>

=Acknowledgment=
The construction of the pipeline was supported by funding from NIH NCRR 2P41RR013218 Supplement.

=Citations=
* Tustison NJ, Avants BB, Cook PA, Zheng Y, Egan A, Yushkevich PA, Gee JC N4ITK: Improved N3 Bias Correction, IEEE Trans Med Imag, 2010
* 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.
* S. Warfield, J. Rexilius, P. Huppi, T. Inder, E. Miller, W. Wells, G. Zientara, F. Jolesz, and R. Kikinis, “A binary entropy measure to assess nonrigid registration algorithms,” in MICCAI, LNCS, pp. 266–274, Springer, October 2001.
* Johnson H.J., Harris G., Williams K. [http://hdl.handle.net/1926/1291 BRAINSFit: Mutual Information Registrations of Whole-Brain 3D Images, Using the Insight Toolkit], The Insight Journal, July 2007

File:EMS LesionExp FLAIR.png

2011-06-18T23:21:16Z

Belhachemi:

File:EMS LesionExp T1.png

2011-06-18T23:21:07Z

Belhachemi:

EMSegmenter-Tasks:LesionExp

2011-06-18T23:20:50Z

Belhachemi: /* Result */

[[EMSegmenter-Tasks|Return to EMSegmenter Task Overview Page]]

=Description=
Two channel automatic segmentation of T1 and FLAIR MRI brain scans into the major tissue classes (gray matter, white matter, csf). The pipeline consist of the following steps:
* Step 1: Perform image inhomogeneity correction of the MRI scan via [http://www.slicer.org/slicerWiki/index.php/Modules:N4ITKBiasFieldCorrection-Documentation-3.6 N4ITKBiasFieldCorrection] (Tustison et al 2010)
* Step 2: Register the atlas to the T1 MRI scan via [[Modules:BRAINSFit| BRAINSFit]] (Johnson et al 2007)
* Step 3: Compute the intensity distributions for each structure 
Compute intensity distribution (mean and variance) for each label by automatically sampling from the MR scan. The sampling for a specific label is constrained to the region that consists of voxels with high probability (top 95%) of being assigned to the label according to the aligned atlas.
* Step 4: Assign T1 GM intensity distribution to T1 Lesion intensity distribution
* Step 5: Automatically segment the MRI scan into the structures of interest using [[Modules:EMSegmenter-3.6|EM Algorithm]] (Pohl et al 2007)

=Anatomical Tree=

* root
** background (BG)
** intracranial cavity (ICC)
*** white matter (WM)
*** grey matter (GM)
*** cerebrospinal fluid (CSF)
*** Lesion

=Atlas=
Atlas was generated based on 82 scans and corresponding segmentations provided by [http://pnl.bwh.harvard.edu/ Psychiatry Neuroimaging Laboratory, BWH]. We registered the scans to a preselected template via Warfield et al. 2001. 
Image Dimension = 256 x 256 x 124 
Image Spacing = 0.9375 x 0.9375 x 1.5 

{| class="wikitable"
|-
| [[Image:EMSegmenter_MRI-Human-Brain_Template_420x420.png|210px]]
| [[Image:EMSegmenter_MRI-Human-Brain_CSF_420x420.png|210px]]
| [[Image:EMSegmenter_MRI-Human-Brain_GM_420x420.png|210px]]
| [[Image:EMSegmenter_MRI-Human-Brain_WM_420x420.png|210px]]
|-
| Template (T1)
| CSF
| GM
| WM
|}

=Result=
<gallery perrow=1: widths=630px : heights=210px>
Image:EMS LesionExp T1.png
Image:EMS LesionExp FLAIR.png
Image:EMS LesionExp Segmentation.png
</gallery>

=Acknowledgment=
The construction of the pipeline was supported by funding from NIH NCRR 2P41RR013218 Supplement.

=Citations=
* Tustison NJ, Avants BB, Cook PA, Zheng Y, Egan A, Yushkevich PA, Gee JC N4ITK: Improved N3 Bias Correction, IEEE Trans Med Imag, 2010
* 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.
* S. Warfield, J. Rexilius, P. Huppi, T. Inder, E. Miller, W. Wells, G. Zientara, F. Jolesz, and R. Kikinis, “A binary entropy measure to assess nonrigid registration algorithms,” in MICCAI, LNCS, pp. 266–274, Springer, October 2001.
* Johnson H.J., Harris G., Williams K. [http://hdl.handle.net/1926/1291 BRAINSFit: Mutual Information Registrations of Whole-Brain 3D Images, Using the Insight Toolkit], The Insight Journal, July 2007

File:EMS LesionExp Segmentation.png

2011-06-18T23:19:38Z

Belhachemi:

EMSegmenter-Tasks

2011-06-18T23:19:10Z

Belhachemi: /* Tasks in development */

[[EMSegmenter-Overview|Return to EMSegmenter Overview Page]]

=What is a task?=

Most clinicians are using the EMSegmenter to segment specific parts of the human body. Those segmentations depend heavily on
the used input data. The signal level in the input data varies with the used image modalities (e.g. MRI, CT, ...) and with each anatomical structure.
The EMSegmenter can take advantage of some knowledge about the signal level of those anatomical structures in the different image modalities.
 
Technically, each tasks consist of a .mrml file and a .tcl file.
 
The .mrml file stores the anatomical properties (mean values, covariance values) in a user defined tree structure. 
The .tcl script is used to perform some pre-processing on the input data. 
 
Visit the following web page to create your own [[EMSegmenter-CreateTask| task]] or we can [[ EMSegmenter-UseCaseAdvertisement | help ]] you .

=Segmentation Task Library=
==Existing Tasks in Slicer 3.6.3==
*[[Image:MRI-Human-Brain_BeforeAfter.png|250px]] '''Task 01: [[EMSegmenter-Tasks:MRI-Human-Brain|MRI Human Brain ''' for non-skull stripped T1 scans]]
*[[Image:MRIHumanBrainParcellation.png|250px]] '''Task 02: [[EMSegmenter-Tasks:MRI-Human-Brain-Parcellation|MRI Human Brain Parcellation ''' for skull stripped T1 scans]]
*[[Image:NHP.png|250px]] '''Task 03: [[EMSegmenter-Tasks:Non-Human-Primate|Non-Human Primate ''' for skull stripped T1 scans]]

==Tasks for Slicer 3.6.4==
* [[Image:EMS Result Hand subject2.png|250px]] '''Task 04: [[EMSegmenter-Tasks:CT-Hand-Bone|CT Hand Bone ''']]
* [[Image:MRIHumanBrainFullParcellation_before_after.png|250px]] '''Task 05: [[EMSegmenter-Tasks:MRI-Human-Brain-Full-Parcellation|MRI Human Brain Full Parcellation''' for non-skull stripped T1 scans]]
* [[Image:MRIHumanBrainHIPR beforeafter.png|250px]] '''Task 06: [[EMSegmenter-Tasks:MRI-Human-Brain-HIPR|MRI Human Brain with high in-plane resolution''' for non-skull stripped T1 scans]]
* [[Image:EMS_Hemisphere_before_after.png|250px]]'''Task 07: [[EMSegmenter-Tasks:MRI-Human-Brain-Hemisphere|MRI Human Brain Hemisphere''' for non-skull stripped T1 scans]]

==Tasks in development==
* [[Image:EMS HumanEye Before After.png|250px]]'''Task 08: [[EMSegmenter-Tasks:Human-Eye|Human Eye''']]
* [[Image:EMS MRIHumanBrainExp Before After.png|250px]] '''Task 09: [[EMSegmenter-Tasks:MRI-Human-Brain-Experimental|MRI Human Brain Experimental''' with skull stripping]]
* [[Image:EMSegment-CardioA1-grey-small.jpg|125px]][[Image:EMSegment CardioA1small.jpg|125px]] '''Task 10: [[EMSegmenter-Tasks:cineMARI|cine MRI''' ]]
* [[Image:EMS LesionsExp BeforeAfter.png|250px]] '''Task 11: [[EMSegmenter-Tasks:LesionExp|White matter lesion segmentation''' ]]
File:

==External Command Lines (Under Development) ==
* [[Image:GLISTR Flair.png|125px]][[Image:GLISTR Seg.png|125px]]'''Task 12: [https://www.rad.upenn.edu/sbia/projects/glistr.html GLISTR: Automatic Glioma Segmentation''']

=Additional Use Cases=
==Quantitative assessment using MPRAGE and Flair images==
* Collaborator: Tammie Benzinger , Washington University School of Medicine
* Short description: Quantitative assessment using MPRAGE and Flair images
* Image specification: Dimension: 256x256x160 , Spacing 1x1x1, T2 MPRAGE
* Used Task: [[EMSegmenter-Tasks:MRI-Human-Brain-Experimental|'''MRI Human Brain Experimental''' (with skull stripping)]]
<gallery perrow=2: widths=200px : heights=200px>
Image:EMS_Quantitative_assessment_orig.png
Image:EMS_Quantitative_assessment.png
</gallery>

==Brain Atrophy in Aging Patients==
* Collaborator: David Tate, PI (Brigham and Women's Hospital), Daniel McCaffrey (Brigham and Women's Hospital), Alex Zaitsev (Brigham and Women's Hospital/Surgical Planning Laboratory) and Jewish Hospital
* Short description: Evaluate Brain Atrophy in aging subjects (NOTE: the segmentation was done for old scans from 90s. No other tools could segment CSF.)
* Image specification: NA Tesla, Scanner: NA, Psuedo T1, Axial Scans, TR/TI/TE=NA, pixel_xsize = 0.937500, pixel_ysize = 0.937500, fov = 240.000000, aspect = 0.000000, thick = 5.000000
* Used Task: [[EMSegmenter-Tasks:MRI-Human-Brain|'''MRI Human Brain''']]
<gallery perrow=2: widths=200px : heights=200px>
Image:EMS_AgingStudy_DTate_Project_3-6-2.png
Image:EMS_AgingStudy_PseudoT1_OldMIRs_JewishHospEMS_manualTrain_60x.png
</gallery>

==Brain Atrophy in HIV Patients==
* Collaborator: David Tate, PI (Brigham and Women's Hospital), Troy Russel (Brigham and Women's Hospital), Alex Zaitsev (Brigham and Women's Hospital/Surgical Planning Laboratory) and National HIV Consortium
* Short description: Evaluate Brain Atrophy in HIV Patients
* Image specification: 3 Tesla, Scanner: NA, MPRAGE, Sagittal Scans, TR/TI/TE=NA, pixel_xsize = 0.9375, pixel_ysize = 0.9375, fov = NA, aspect = NA, space = 1.5
* Used Task: [[EMSegmenter-Tasks:MRI-Human-Brain|'''MRI Human Brain''']]
<gallery perrow=2: widths=425px : heights=200px>
Image:EMS_HIVStudy_Segmentation.png
Image:EMS_HIVStudy_Segmentation_Auto.png
</gallery>

==Pediatric MS Study==
* Collaborator: Tanuja Chitnis PI (Brigham and Women's Hospital/Multiple Sclerosis Center), Alexander Zaitsev (Brigham and Women's Hospital/Surgical Planning Laboratory) and Massachusetts General Hospital
* Short description: Evaluate brain atrophy for pediatric MS Patients
* Image specification: 3 Tesla, Scanner: SIGNA HDx / GE MEDICAL SYSTEMS, 3D MPRAGE, Sagital Scans, TR/TI/TE=24/0/7 ms, pixel_xsize = 0.976600, pixel_ysize = 0.976600, fov = 250.009598, aspect = 1.535941, thick = 1.500000, space = 0.000000
* Used Task: [[EMSegmenter-Tasks:MRI-Human-Brain|'''MRI Human Brain''']]
<gallery perrow=1: widths=630px : heights=210px>
Image:EMS_PED_MS_Study_Segmentation.png
</gallery>

==Social Cognition Study==
* Collaborator: Collaborator: Andrea Mike, MD (Pecs University, Hungary), Charles Guttmann, MD, Alexander Zaitsev (Brigham and Women's Hospital)
* Short description: Evaluate brain atrophy for elderly MS patients.
* Number of processed cases: 50
* Image specification: 3 Tesla, Scanner: Magnetom TIM Trio, Siemens, 3D MPRAGE, Slice thickness: 1.2mm, Spacing 1.2 1 1 (mm)
* Used Task: [[EMSegmenter-Tasks:MRI-Human-Brain|'''MRI Human Brain''']]
<gallery perrow=1: widths=630px : heights=200px>
Image:EMS_SocialCognitionLESIONS_MANUALLY_SEGMENTED_PECS_S006_Seg.png
</gallery>

==Physiological Brain Activity Longitudinal Study==
* Collaborator: Laura Horky PI (Brigham and Women's Hospital(BWH)), Jon Hainer (BWH), Wendy Plesniak (BWH), Alexander Zaitsev (BWH), Ron Kikinis (BWH) and BWH Division of Nuclear Medicine
* Short description: Evaluate glycolitical brain activity in CSF and White Matter for the patients undergoing chemical therapy courses.
* Image specification: 1.5 Tesla ,Scanner: SIGNA EXCITE / GE MEDICAL SYSTEMS, T1, Axial Scans, TR/TI/TE=500/0/21 ms, pixel_xsize = 0.781251, pixel_ysize = 0.781244, fov = 0.000000, aspect = 7.679990, thick = 5.000000, space = 1.000000
* Used Task: [[EMSegmenter-Tasks:MRI-Human-Brain-Hemisphere|'''MRI Human Brain Hemisphere''']]
<gallery perrow=3: widths=250px : heights=200px>
Image:EmSegment PETCT 1.png
Image:EmSegment PETCT 2.png
Image:EmSegment PETCT 3.png | Result on test data
</gallery>

<gallery perrow=3: widths=250px : heights=200px>
Image:EMSegment PETCT Physiology-1.png
Image:EMSegment PETCT Physiology-2.png
Image:EMSegment PETCT Physiology-3.png | Result on patient data
</gallery>

EMSegmenter-Tasks

2011-06-18T23:18:32Z

Belhachemi: /* Tasks in development */

[[EMSegmenter-Overview|Return to EMSegmenter Overview Page]]

=What is a task?=

Most clinicians are using the EMSegmenter to segment specific parts of the human body. Those segmentations depend heavily on
the used input data. The signal level in the input data varies with the used image modalities (e.g. MRI, CT, ...) and with each anatomical structure.
The EMSegmenter can take advantage of some knowledge about the signal level of those anatomical structures in the different image modalities.
 
Technically, each tasks consist of a .mrml file and a .tcl file.
 
The .mrml file stores the anatomical properties (mean values, covariance values) in a user defined tree structure. 
The .tcl script is used to perform some pre-processing on the input data. 
 
Visit the following web page to create your own [[EMSegmenter-CreateTask| task]] or we can [[ EMSegmenter-UseCaseAdvertisement | help ]] you .

=Segmentation Task Library=
==Existing Tasks in Slicer 3.6.3==
*[[Image:MRI-Human-Brain_BeforeAfter.png|250px]] '''Task 01: [[EMSegmenter-Tasks:MRI-Human-Brain|MRI Human Brain ''' for non-skull stripped T1 scans]]
*[[Image:MRIHumanBrainParcellation.png|250px]] '''Task 02: [[EMSegmenter-Tasks:MRI-Human-Brain-Parcellation|MRI Human Brain Parcellation ''' for skull stripped T1 scans]]
*[[Image:NHP.png|250px]] '''Task 03: [[EMSegmenter-Tasks:Non-Human-Primate|Non-Human Primate ''' for skull stripped T1 scans]]

==Tasks for Slicer 3.6.4==
* [[Image:EMS Result Hand subject2.png|250px]] '''Task 04: [[EMSegmenter-Tasks:CT-Hand-Bone|CT Hand Bone ''']]
* [[Image:MRIHumanBrainFullParcellation_before_after.png|250px]] '''Task 05: [[EMSegmenter-Tasks:MRI-Human-Brain-Full-Parcellation|MRI Human Brain Full Parcellation''' for non-skull stripped T1 scans]]
* [[Image:MRIHumanBrainHIPR beforeafter.png|250px]] '''Task 06: [[EMSegmenter-Tasks:MRI-Human-Brain-HIPR|MRI Human Brain with high in-plane resolution''' for non-skull stripped T1 scans]]
* [[Image:EMS_Hemisphere_before_after.png|250px]]'''Task 07: [[EMSegmenter-Tasks:MRI-Human-Brain-Hemisphere|MRI Human Brain Hemisphere''' for non-skull stripped T1 scans]]

==Tasks in development==
* [[Image:EMS HumanEye Before After.png|250px]]'''Task 08: [[EMSegmenter-Tasks:Human-Eye|Human Eye''']]
* [[Image:EMS MRIHumanBrainExp Before After.png|250px]] '''Task 09: [[EMSegmenter-Tasks:MRI-Human-Brain-Experimental|MRI Human Brain Experimental''' with skull stripping]]
* [[Image:EMSegment-CardioA1-grey-small.jpg|125px]][[Image:EMSegment CardioA1small.jpg|125px]] '''Task 10: [[EMSegmenter-Tasks:cineMARI|cine MRI''' ]]
* [[Image:EMS LesionsExp BeforeAfter.png|125px]] '''Task 11: [[EMSegmenter-Tasks:LesionExp|White matter lesion segmentation''' ]]
File:

==External Command Lines (Under Development) ==
* [[Image:GLISTR Flair.png|125px]][[Image:GLISTR Seg.png|125px]]'''Task 12: [https://www.rad.upenn.edu/sbia/projects/glistr.html GLISTR: Automatic Glioma Segmentation''']

=Additional Use Cases=
==Quantitative assessment using MPRAGE and Flair images==
* Collaborator: Tammie Benzinger , Washington University School of Medicine
* Short description: Quantitative assessment using MPRAGE and Flair images
* Image specification: Dimension: 256x256x160 , Spacing 1x1x1, T2 MPRAGE
* Used Task: [[EMSegmenter-Tasks:MRI-Human-Brain-Experimental|'''MRI Human Brain Experimental''' (with skull stripping)]]
<gallery perrow=2: widths=200px : heights=200px>
Image:EMS_Quantitative_assessment_orig.png
Image:EMS_Quantitative_assessment.png
</gallery>

==Brain Atrophy in Aging Patients==
* Collaborator: David Tate, PI (Brigham and Women's Hospital), Daniel McCaffrey (Brigham and Women's Hospital), Alex Zaitsev (Brigham and Women's Hospital/Surgical Planning Laboratory) and Jewish Hospital
* Short description: Evaluate Brain Atrophy in aging subjects (NOTE: the segmentation was done for old scans from 90s. No other tools could segment CSF.)
* Image specification: NA Tesla, Scanner: NA, Psuedo T1, Axial Scans, TR/TI/TE=NA, pixel_xsize = 0.937500, pixel_ysize = 0.937500, fov = 240.000000, aspect = 0.000000, thick = 5.000000
* Used Task: [[EMSegmenter-Tasks:MRI-Human-Brain|'''MRI Human Brain''']]
<gallery perrow=2: widths=200px : heights=200px>
Image:EMS_AgingStudy_DTate_Project_3-6-2.png
Image:EMS_AgingStudy_PseudoT1_OldMIRs_JewishHospEMS_manualTrain_60x.png
</gallery>

==Brain Atrophy in HIV Patients==
* Collaborator: David Tate, PI (Brigham and Women's Hospital), Troy Russel (Brigham and Women's Hospital), Alex Zaitsev (Brigham and Women's Hospital/Surgical Planning Laboratory) and National HIV Consortium
* Short description: Evaluate Brain Atrophy in HIV Patients
* Image specification: 3 Tesla, Scanner: NA, MPRAGE, Sagittal Scans, TR/TI/TE=NA, pixel_xsize = 0.9375, pixel_ysize = 0.9375, fov = NA, aspect = NA, space = 1.5
* Used Task: [[EMSegmenter-Tasks:MRI-Human-Brain|'''MRI Human Brain''']]
<gallery perrow=2: widths=425px : heights=200px>
Image:EMS_HIVStudy_Segmentation.png
Image:EMS_HIVStudy_Segmentation_Auto.png
</gallery>

==Pediatric MS Study==
* Collaborator: Tanuja Chitnis PI (Brigham and Women's Hospital/Multiple Sclerosis Center), Alexander Zaitsev (Brigham and Women's Hospital/Surgical Planning Laboratory) and Massachusetts General Hospital
* Short description: Evaluate brain atrophy for pediatric MS Patients
* Image specification: 3 Tesla, Scanner: SIGNA HDx / GE MEDICAL SYSTEMS, 3D MPRAGE, Sagital Scans, TR/TI/TE=24/0/7 ms, pixel_xsize = 0.976600, pixel_ysize = 0.976600, fov = 250.009598, aspect = 1.535941, thick = 1.500000, space = 0.000000
* Used Task: [[EMSegmenter-Tasks:MRI-Human-Brain|'''MRI Human Brain''']]
<gallery perrow=1: widths=630px : heights=210px>
Image:EMS_PED_MS_Study_Segmentation.png
</gallery>

==Social Cognition Study==
* Collaborator: Collaborator: Andrea Mike, MD (Pecs University, Hungary), Charles Guttmann, MD, Alexander Zaitsev (Brigham and Women's Hospital)
* Short description: Evaluate brain atrophy for elderly MS patients.
* Number of processed cases: 50
* Image specification: 3 Tesla, Scanner: Magnetom TIM Trio, Siemens, 3D MPRAGE, Slice thickness: 1.2mm, Spacing 1.2 1 1 (mm)
* Used Task: [[EMSegmenter-Tasks:MRI-Human-Brain|'''MRI Human Brain''']]
<gallery perrow=1: widths=630px : heights=200px>
Image:EMS_SocialCognitionLESIONS_MANUALLY_SEGMENTED_PECS_S006_Seg.png
</gallery>

==Physiological Brain Activity Longitudinal Study==
* Collaborator: Laura Horky PI (Brigham and Women's Hospital(BWH)), Jon Hainer (BWH), Wendy Plesniak (BWH), Alexander Zaitsev (BWH), Ron Kikinis (BWH) and BWH Division of Nuclear Medicine
* Short description: Evaluate glycolitical brain activity in CSF and White Matter for the patients undergoing chemical therapy courses.
* Image specification: 1.5 Tesla ,Scanner: SIGNA EXCITE / GE MEDICAL SYSTEMS, T1, Axial Scans, TR/TI/TE=500/0/21 ms, pixel_xsize = 0.781251, pixel_ysize = 0.781244, fov = 0.000000, aspect = 7.679990, thick = 5.000000, space = 1.000000
* Used Task: [[EMSegmenter-Tasks:MRI-Human-Brain-Hemisphere|'''MRI Human Brain Hemisphere''']]
<gallery perrow=3: widths=250px : heights=200px>
Image:EmSegment PETCT 1.png
Image:EmSegment PETCT 2.png
Image:EmSegment PETCT 3.png | Result on test data
</gallery>

<gallery perrow=3: widths=250px : heights=200px>
Image:EMSegment PETCT Physiology-1.png
Image:EMSegment PETCT Physiology-2.png
Image:EMSegment PETCT Physiology-3.png | Result on patient data
</gallery>

File:EMS LesionsExp BeforeAfter.png

2011-06-18T23:17:40Z

Belhachemi:

EMSegmenter-Tasks:LesionExp

2011-06-18T22:49:51Z

Belhachemi: /* Anatomical Tree */

[[EMSegmenter-Tasks|Return to EMSegmenter Task Overview Page]]

=Description=
Two channel automatic segmentation of T1 and FLAIR MRI brain scans into the major tissue classes (gray matter, white matter, csf). The pipeline consist of the following steps:
* Step 1: Perform image inhomogeneity correction of the MRI scan via [http://www.slicer.org/slicerWiki/index.php/Modules:N4ITKBiasFieldCorrection-Documentation-3.6 N4ITKBiasFieldCorrection] (Tustison et al 2010)
* Step 2: Register the atlas to the T1 MRI scan via [[Modules:BRAINSFit| BRAINSFit]] (Johnson et al 2007)
* Step 3: Compute the intensity distributions for each structure 
Compute intensity distribution (mean and variance) for each label by automatically sampling from the MR scan. The sampling for a specific label is constrained to the region that consists of voxels with high probability (top 95%) of being assigned to the label according to the aligned atlas.
* Step 4: Assign T1 GM intensity distribution to T1 Lesion intensity distribution
* Step 5: Automatically segment the MRI scan into the structures of interest using [[Modules:EMSegmenter-3.6|EM Algorithm]] (Pohl et al 2007)

=Anatomical Tree=

* root
** background (BG)
** intracranial cavity (ICC)
*** white matter (WM)
*** grey matter (GM)
*** cerebrospinal fluid (CSF)
*** Lesion

=Atlas=
Atlas was generated based on 82 scans and corresponding segmentations provided by [http://pnl.bwh.harvard.edu/ Psychiatry Neuroimaging Laboratory, BWH]. We registered the scans to a preselected template via Warfield et al. 2001. 
Image Dimension = 256 x 256 x 124 
Image Spacing = 0.9375 x 0.9375 x 1.5 

{| class="wikitable"
|-
| [[Image:EMSegmenter_MRI-Human-Brain_Template_420x420.png|210px]]
| [[Image:EMSegmenter_MRI-Human-Brain_CSF_420x420.png|210px]]
| [[Image:EMSegmenter_MRI-Human-Brain_GM_420x420.png|210px]]
| [[Image:EMSegmenter_MRI-Human-Brain_WM_420x420.png|210px]]
|-
| Template (T1)
| CSF
| GM
| WM
|}

=Result=
<gallery perrow=1: widths=630px : heights=210px>
Image:MRI-Human-Brain-T1.png
Image:MRI-Human-Brain-Labelmap.png
</gallery>

=Acknowledgment=
The construction of the pipeline was supported by funding from NIH NCRR 2P41RR013218 Supplement.

=Citations=
* Tustison NJ, Avants BB, Cook PA, Zheng Y, Egan A, Yushkevich PA, Gee JC N4ITK: Improved N3 Bias Correction, IEEE Trans Med Imag, 2010
* 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.
* S. Warfield, J. Rexilius, P. Huppi, T. Inder, E. Miller, W. Wells, G. Zientara, F. Jolesz, and R. Kikinis, “A binary entropy measure to assess nonrigid registration algorithms,” in MICCAI, LNCS, pp. 266–274, Springer, October 2001.
* Johnson H.J., Harris G., Williams K. [http://hdl.handle.net/1926/1291 BRAINSFit: Mutual Information Registrations of Whole-Brain 3D Images, Using the Insight Toolkit], The Insight Journal, July 2007

EMSegmenter-Tasks:LesionExp

2011-06-18T22:49:33Z

Belhachemi: Created page with 'Return to EMSegmenter Task Overview Page =Description= Two channel automatic segmentation of T1 and FLAIR MRI brain scans into the major tissue classes (gr…'

[[EMSegmenter-Tasks|Return to EMSegmenter Task Overview Page]]

=Description=
Two channel automatic segmentation of T1 and FLAIR MRI brain scans into the major tissue classes (gray matter, white matter, csf). The pipeline consist of the following steps:
* Step 1: Perform image inhomogeneity correction of the MRI scan via [http://www.slicer.org/slicerWiki/index.php/Modules:N4ITKBiasFieldCorrection-Documentation-3.6 N4ITKBiasFieldCorrection] (Tustison et al 2010)
* Step 2: Register the atlas to the T1 MRI scan via [[Modules:BRAINSFit| BRAINSFit]] (Johnson et al 2007)
* Step 3: Compute the intensity distributions for each structure 
Compute intensity distribution (mean and variance) for each label by automatically sampling from the MR scan. The sampling for a specific label is constrained to the region that consists of voxels with high probability (top 95%) of being assigned to the label according to the aligned atlas.
* Step 4: Assign T1 GM intensity distribution to T1 Lesion intensity distribution
* Step 5: Automatically segment the MRI scan into the structures of interest using [[Modules:EMSegmenter-3.6|EM Algorithm]] (Pohl et al 2007)

=Anatomical Tree=

* root
** background (BG)
** intracranial cavity (ICC)
*** white matter (WM)
*** grey matter (GM)
*** cerebrospinal fluid (CSF)

=Atlas=
Atlas was generated based on 82 scans and corresponding segmentations provided by [http://pnl.bwh.harvard.edu/ Psychiatry Neuroimaging Laboratory, BWH]. We registered the scans to a preselected template via Warfield et al. 2001. 
Image Dimension = 256 x 256 x 124 
Image Spacing = 0.9375 x 0.9375 x 1.5 

{| class="wikitable"
|-
| [[Image:EMSegmenter_MRI-Human-Brain_Template_420x420.png|210px]]
| [[Image:EMSegmenter_MRI-Human-Brain_CSF_420x420.png|210px]]
| [[Image:EMSegmenter_MRI-Human-Brain_GM_420x420.png|210px]]
| [[Image:EMSegmenter_MRI-Human-Brain_WM_420x420.png|210px]]
|-
| Template (T1)
| CSF
| GM
| WM
|}

=Result=
<gallery perrow=1: widths=630px : heights=210px>
Image:MRI-Human-Brain-T1.png
Image:MRI-Human-Brain-Labelmap.png
</gallery>

=Acknowledgment=
The construction of the pipeline was supported by funding from NIH NCRR 2P41RR013218 Supplement.

=Citations=
* Tustison NJ, Avants BB, Cook PA, Zheng Y, Egan A, Yushkevich PA, Gee JC N4ITK: Improved N3 Bias Correction, IEEE Trans Med Imag, 2010
* 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.
* S. Warfield, J. Rexilius, P. Huppi, T. Inder, E. Miller, W. Wells, G. Zientara, F. Jolesz, and R. Kikinis, “A binary entropy measure to assess nonrigid registration algorithms,” in MICCAI, LNCS, pp. 266–274, Springer, October 2001.
* Johnson H.J., Harris G., Williams K. [http://hdl.handle.net/1926/1291 BRAINSFit: Mutual Information Registrations of Whole-Brain 3D Images, Using the Insight Toolkit], The Insight Journal, July 2007

EMSegmenter-Tasks

2011-06-18T22:45:56Z

Belhachemi: /* Segmentation Task Library */

[[EMSegmenter-Overview|Return to EMSegmenter Overview Page]]

=What is a task?=

Most clinicians are using the EMSegmenter to segment specific parts of the human body. Those segmentations depend heavily on
the used input data. The signal level in the input data varies with the used image modalities (e.g. MRI, CT, ...) and with each anatomical structure.
The EMSegmenter can take advantage of some knowledge about the signal level of those anatomical structures in the different image modalities.
 
Technically, each tasks consist of a .mrml file and a .tcl file.
 
The .mrml file stores the anatomical properties (mean values, covariance values) in a user defined tree structure. 
The .tcl script is used to perform some pre-processing on the input data. 
 
Visit the following web page to create your own [[EMSegmenter-CreateTask| task]] or we can [[ EMSegmenter-UseCaseAdvertisement | help ]] you .

=Segmentation Task Library=
==Existing Tasks in Slicer 3.6.3==
*[[Image:MRI-Human-Brain_BeforeAfter.png|250px]] '''Task 01: [[EMSegmenter-Tasks:MRI-Human-Brain|MRI Human Brain ''' for non-skull stripped T1 scans]]
*[[Image:MRIHumanBrainParcellation.png|250px]] '''Task 02: [[EMSegmenter-Tasks:MRI-Human-Brain-Parcellation|MRI Human Brain Parcellation ''' for skull stripped T1 scans]]
*[[Image:NHP.png|250px]] '''Task 03: [[EMSegmenter-Tasks:Non-Human-Primate|Non-Human Primate ''' for skull stripped T1 scans]]

==Tasks for Slicer 3.6.4==
* [[Image:EMS Result Hand subject2.png|250px]] '''Task 04: [[EMSegmenter-Tasks:CT-Hand-Bone|CT Hand Bone ''']]
* [[Image:MRIHumanBrainFullParcellation_before_after.png|250px]] '''Task 05: [[EMSegmenter-Tasks:MRI-Human-Brain-Full-Parcellation|MRI Human Brain Full Parcellation''' for non-skull stripped T1 scans]]
* [[Image:MRIHumanBrainHIPR beforeafter.png|250px]] '''Task 06: [[EMSegmenter-Tasks:MRI-Human-Brain-HIPR|MRI Human Brain with high in-plane resolution''' for non-skull stripped T1 scans]]
* [[Image:EMS_Hemisphere_before_after.png|250px]]'''Task 07: [[EMSegmenter-Tasks:MRI-Human-Brain-Hemisphere|MRI Human Brain Hemisphere''' for non-skull stripped T1 scans]]

==Tasks in development==
* [[Image:EMS HumanEye Before After.png|250px]]'''Task 08: [[EMSegmenter-Tasks:Human-Eye|Human Eye''']]
* [[Image:EMS MRIHumanBrainExp Before After.png|250px]] '''Task 09: [[EMSegmenter-Tasks:MRI-Human-Brain-Experimental|MRI Human Brain Experimental''' with skull stripping]]
* [[Image:EMSegment-CardioA1-grey-small.jpg|125px]][[Image:EMSegment CardioA1small.jpg|125px]] '''Task 10: [[EMSegmenter-Tasks:cineMARI|cine MRI''' ]]
* [[Image:EMSegment-CardioA1-grey-small.jpg|125px]][[Image:EMSegment CardioA1small.jpg|125px]] '''Task 11: [[EMSegmenter-Tasks:LesionExp|White matter lesion segmentation''' ]]

==External Command Lines (Under Development) ==
* [[Image:GLISTR Flair.png|125px]][[Image:GLISTR Seg.png|125px]]'''Task 12: [https://www.rad.upenn.edu/sbia/projects/glistr.html GLISTR: Automatic Glioma Segmentation''']

=Additional Use Cases=
==Quantitative assessment using MPRAGE and Flair images==
* Collaborator: Tammie Benzinger , Washington University School of Medicine
* Short description: Quantitative assessment using MPRAGE and Flair images
* Image specification: Dimension: 256x256x160 , Spacing 1x1x1, T2 MPRAGE
* Used Task: [[EMSegmenter-Tasks:MRI-Human-Brain-Experimental|'''MRI Human Brain Experimental''' (with skull stripping)]]
<gallery perrow=2: widths=200px : heights=200px>
Image:EMS_Quantitative_assessment_orig.png
Image:EMS_Quantitative_assessment.png
</gallery>

==Brain Atrophy in Aging Patients==
* Collaborator: David Tate, PI (Brigham and Women's Hospital), Daniel McCaffrey (Brigham and Women's Hospital), Alex Zaitsev (Brigham and Women's Hospital/Surgical Planning Laboratory) and Jewish Hospital
* Short description: Evaluate Brain Atrophy in aging subjects (NOTE: the segmentation was done for old scans from 90s. No other tools could segment CSF.)
* Image specification: NA Tesla, Scanner: NA, Psuedo T1, Axial Scans, TR/TI/TE=NA, pixel_xsize = 0.937500, pixel_ysize = 0.937500, fov = 240.000000, aspect = 0.000000, thick = 5.000000
* Used Task: [[EMSegmenter-Tasks:MRI-Human-Brain|'''MRI Human Brain''']]
<gallery perrow=2: widths=200px : heights=200px>
Image:EMS_AgingStudy_DTate_Project_3-6-2.png
Image:EMS_AgingStudy_PseudoT1_OldMIRs_JewishHospEMS_manualTrain_60x.png
</gallery>

==Brain Atrophy in HIV Patients==
* Collaborator: David Tate, PI (Brigham and Women's Hospital), Troy Russel (Brigham and Women's Hospital), Alex Zaitsev (Brigham and Women's Hospital/Surgical Planning Laboratory) and National HIV Consortium
* Short description: Evaluate Brain Atrophy in HIV Patients
* Image specification: 3 Tesla, Scanner: NA, MPRAGE, Sagittal Scans, TR/TI/TE=NA, pixel_xsize = 0.9375, pixel_ysize = 0.9375, fov = NA, aspect = NA, space = 1.5
* Used Task: [[EMSegmenter-Tasks:MRI-Human-Brain|'''MRI Human Brain''']]
<gallery perrow=2: widths=425px : heights=200px>
Image:EMS_HIVStudy_Segmentation.png
Image:EMS_HIVStudy_Segmentation_Auto.png
</gallery>

==Pediatric MS Study==
* Collaborator: Tanuja Chitnis PI (Brigham and Women's Hospital/Multiple Sclerosis Center), Alexander Zaitsev (Brigham and Women's Hospital/Surgical Planning Laboratory) and Massachusetts General Hospital
* Short description: Evaluate brain atrophy for pediatric MS Patients
* Image specification: 3 Tesla, Scanner: SIGNA HDx / GE MEDICAL SYSTEMS, 3D MPRAGE, Sagital Scans, TR/TI/TE=24/0/7 ms, pixel_xsize = 0.976600, pixel_ysize = 0.976600, fov = 250.009598, aspect = 1.535941, thick = 1.500000, space = 0.000000
* Used Task: [[EMSegmenter-Tasks:MRI-Human-Brain|'''MRI Human Brain''']]
<gallery perrow=1: widths=630px : heights=210px>
Image:EMS_PED_MS_Study_Segmentation.png
</gallery>

==Social Cognition Study==
* Collaborator: Collaborator: Andrea Mike, MD (Pecs University, Hungary), Charles Guttmann, MD, Alexander Zaitsev (Brigham and Women's Hospital)
* Short description: Evaluate brain atrophy for elderly MS patients.
* Number of processed cases: 50
* Image specification: 3 Tesla, Scanner: Magnetom TIM Trio, Siemens, 3D MPRAGE, Slice thickness: 1.2mm, Spacing 1.2 1 1 (mm)
* Used Task: [[EMSegmenter-Tasks:MRI-Human-Brain|'''MRI Human Brain''']]
<gallery perrow=1: widths=630px : heights=200px>
Image:EMS_SocialCognitionLESIONS_MANUALLY_SEGMENTED_PECS_S006_Seg.png
</gallery>

==Physiological Brain Activity Longitudinal Study==
* Collaborator: Laura Horky PI (Brigham and Women's Hospital(BWH)), Jon Hainer (BWH), Wendy Plesniak (BWH), Alexander Zaitsev (BWH), Ron Kikinis (BWH) and BWH Division of Nuclear Medicine
* Short description: Evaluate glycolitical brain activity in CSF and White Matter for the patients undergoing chemical therapy courses.
* Image specification: 1.5 Tesla ,Scanner: SIGNA EXCITE / GE MEDICAL SYSTEMS, T1, Axial Scans, TR/TI/TE=500/0/21 ms, pixel_xsize = 0.781251, pixel_ysize = 0.781244, fov = 0.000000, aspect = 7.679990, thick = 5.000000, space = 1.000000
* Used Task: [[EMSegmenter-Tasks:MRI-Human-Brain-Hemisphere|'''MRI Human Brain Hemisphere''']]
<gallery perrow=3: widths=250px : heights=200px>
Image:EmSegment PETCT 1.png
Image:EmSegment PETCT 2.png
Image:EmSegment PETCT 3.png | Result on test data
</gallery>

<gallery perrow=3: widths=250px : heights=200px>
Image:EMSegment PETCT Physiology-1.png
Image:EMSegment PETCT Physiology-2.png
Image:EMSegment PETCT Physiology-3.png | Result on patient data
</gallery>

Slicer3:Debian

2011-06-13T00:10:39Z

Belhachemi: /* Cloud computing */

Slicer3:Debian

2011-06-13T00:09:54Z

Belhachemi: /* Cloud computing */