NXT_USB is a C++ library used to control a LEGO Mindstorms NXT robot over a USB connection.

This code was modified from:
*NXT++: http://nxtpp.sourceforge.net
*Device::USB: http://search.cpan.org/~gwadej/Device-USB-0.21

= Linux Installation =

== Reqirements ==
# This code can be used only on a Linux distribution with root access. Remember to run any software utilizing this code as root.
# libusb: http://libusb.sourceforge.net/

== Instructions ==
Download libusb from:
http://libusb.sourceforge.net (version 0.1.12)

Then run:
tar zxvf libusb-0.1.12.tar.gz
cd libusb-0.1.12/
./configure CFLAGS=-funsigned-char --prefix=<your libusb directory> --exec-prefix=<your libsub directory>
make
make install

Then add the libusb directory to your $LD_LIBRARY_PATH variable.
Note that the INSTALL.libusb file has information about the installation process.

Another alternative is to use CMake:

SET(CMAKE_CXX_FLAGS
"-funsigned-char"
)

INCLUDE_DIRECTORIES(
...
<your libusb directory (can be a relative path)>
)

ADD_LIBRARY(<your library name>
...
NXT_USB.cxx
NXT_USB_linux.cxx
)

FIND_LIBRARY(LIBUSB_LIB
NAMES libusb-lib
PATHS
<your libusb directory (can be a relative path)>/lib
)

TARGET_LINK_LIBRARIES(Lego
...
<your libusb directory (should be an absolute path)>/lib/libusb.so
)

The simplest way to use this library is to keep the four NXT_USB files (NXT_USB.h, NXT_USB.cxx, NXT_USB_linux.h, and NXT_USB_linux.cxx) in the same directory as your program. Simply #include "NXT_USB.h" and compile as usual.

= Windows Installation =

The Windows installation of the NXT_USB requires the windows port of libusb using libusb-win32 open-source project.

# Download from [http://sourceforge.net/project/showfiles.php?group_id=78138&package_id=79216 SourceForge]
# Install libusb-win32-filter-bin-0.1.12.1.exe by following the instructions
# Download libusb-win32-device-bin-0.1.12.1.tar.gz from [http://sourceforge.net/project/showfiles.php?group_id=78138&package_id=79216 SourceForge]
# Extract libusb-win32-device-bin-0.1.12.1.tar.gz using winrar or cygwin (tar -zxf)
# Plug the USB cable to your computer and start the Lego NXT (it won't be recognized, just wait if you got the windows device wizrd
# Start libusb-win32-device-bin-0.1.12.1/bin/inf-wizard
# Select the device corresponding to the Lego NXT
# Enter some information: name, etc.. (this is arbitrary)
# inf-wizard will create a .cat, .ing, .PNF files
# In the same directory copy the libusb0.dll and libusb0.sys

# Go to 'Start Menu'->'Programs'->'LibUSB-Win32'->'Test Program', you should see the NXT device:

bus-0/\\.\libusb0-0005--0x0694-0x0002 0694/0002
Serial Number: 00165304BDE2
wTotalLength: 32
bNumInterfaces: 1
bConfigurationValue: 1
iConfiguration: 0
bmAttributes: c0h
MaxPower: 0
bInterfaceNumber: 0
bAlternateSetting: 0
bNumEndpoints: 2
bInterfaceClass: 255
bInterfaceSubClass: 255
bInterfaceProtocol: 255
iInterface: 0
bEndpointAddress: 01h
bmAttributes: 02h
wMaxPacketSize: 64
bInterval: 0
bRefresh: 0
bSynchAddress: 0
bEndpointAddress: 82h
bmAttributes: 02h
wMaxPacketSize: 64
bInterval: 0
bRefresh: 0
bSynchAddress: 0

= Contact information =
I would be more than happy to reply to any questions and comments emailed to dpace [at] bwh.harvard.edu.

LEGO IGT Compilation

2008-06-25T14:32:38Z

LEGO IGT Compilation

2008-06-25T13:47:31Z

Jjomier: New page: About NXT_USB: This is a C++ library used to control a LEGO Mindstorms NXT robot over a USB connection. This code was modified from: -NXT++: http://nxtpp.sourceforge.net -Device::...

About NXT_USB:
This is a C++ library used to control a LEGO Mindstorms NXT robot over a USB connection.

This code was modified from:
-NXT++: http://nxtpp.sourceforge.net
-Device::USB: http://search.cpan.org/~gwadej/Device-USB-0.21

Reqirements:
1. This code can be used only on a Linux distribution with root access. Remember to run any software utilizing this code as root.
2. libusb: http://libusb.sourceforge.net/

Instructions:

Download libusb from:
http://libusb.sourceforge.net
(version 0.1.12)

Then run:
tar zxvf libusb-0.1.12.tar.gz
cd libusb-0.1.12/
./configure CFLAGS=-funsigned-char --prefix=<your libusb directory> --exec-prefix=<your libsub directory>
make
make install

Then add the libusb directory to your $LD_LIBRARY_PATH variable.
Note that the INSTALL.libusb file has information about the installation process.

Another alternative is to use CMake:

SET(CMAKE_CXX_FLAGS
"-funsigned-char"
)

INCLUDE_DIRECTORIES(
...
<your libusb directory (can be a relative path)>
)

ADD_LIBRARY(<your library name>
...
NXT_USB.cxx
NXT_USB_linux.cxx
)

FIND_LIBRARY(LIBUSB_LIB
NAMES libusb-lib
PATHS
<your libusb directory (can be a relative path)>/lib
)

TARGET_LINK_LIBRARIES(Lego
...
<your libusb directory (should be an absolute path)>/lib/libusb.so
)

The simplest way to use this library is to keep the four NXT_USB files (NXT_USB.h, NXT_USB.cxx, NXT_USB_linux.h, and NXT_USB_linux.cxx) in the same directory as your program. Simply #include "NXT_USB.h" and compile as usual.

Contact information:
I would be more than happy to reply to any questions and comments emailed to dpace [at] bwh.harvard.edu.

LEGO IGT and Medical Robotics Tutorial

2008-06-25T13:46:50Z

Jjomier:

[[Image:Slicer3-IGT-LEGOTutorial-biopsy.jpg|300px|thumb|The LEGO robot and phantom]]
[[Image:Slicer3-IGT-LEGOTutoral-screenshot.png|300px|thumb|Example tutorial screenshot]]

Back to [[IGT:ToolKit|IGT:ToolKit]]

=LEGO Image Guided Therapy and Medical Robotics Tutorial=

==Overview:==

This tutorial provides a thorough understanding of the main concepts in image-guided therapy and medical robotics, namely imaging, pre-operative planning, targeting by tracking, navigation and registration. The tutorial is open-source and completely free for anyone to use or modify (see http://www.slicer.org for details and for the BSD style open source license).

The tutorial is:
* Hands-on: Using a LEGO robot, a LEGO phantom (anatomical model) and a tutorial module in 3D Slicer v. 3 means that tutorial participants can use real physical equipment and software to learn about IGT and medical robotics.

* Accessible: The tutorial software is open-source, and the cost of the materials is approximately $300 USD + shipping and taxes.

==Tutorial Materials:==

Provided by NA-MIC and the Surgical Planning Lab:
* 3D Slicer v. 3 tutorial module
* CT volume of the phantom
* Tutorial slides
* Assembly instructions for the robot and the phantom
* Phantom placement guide

Provided by tutorial participants:
* 1 LEGO Mindstorms NXT kit
* 1 LEGO Deluxe Brick box
* 2 pom-poms
* Linux computer with root access or Windows with administrator privileges
For purchasing information for user-supplied materials, see the "Tutorial Slides Part 1 - Background and Materials" slides.

'''Getting the Tutorial Materials:'''

Click on the following links to get the tutorial materials:

* Robot assembly instructions: [http://wiki.na-mic.org/Wiki/images/8/81/LEGOIGTAndMedicalRoboticsTutorial_RobotAssemblyInstructions.pdf LEGOIGTAndMedicalRoboticsTutorial_RobotAssemblyInstructions.pdf]

* Phantom assembly instructions: [http://wiki.na-mic.org/Wiki/images/0/0d/LEGOIGTAndMedicalRoboticsTutorial_PhantomAssemblyInstructions.pdf LEGOIGTAndMedicalRoboticsTutorial_PhantomAssemblyInstructions.pdf]

* Phantom placement guide: [http://wiki.na-mic.org/Wiki/images/6/64/LEGOIGTAndMedicalRoboticsTutorial_PhantomPlacementGuide.pdf LEGOIGTAndMedicalRoboticsTutorial_PhantomPlacementGuide.pdf]

* Tutorial Slides Part 1 - Background and Materials: [http://wiki.na-mic.org/Wiki/images/d/d1/LEGOIGTAndMedicalRoboticsTutorial_1_BackgroundAndMaterials.pdf LEGOIGTAndMedicalRoboticsTutorial_1_BackgroundAndMaterials.pdf]

* Tutorial Slides Part 2 - Basic Tutorial: [http://wiki.na-mic.org/Wiki/images/a/ab/LEGOIGTAndMedicalRoboticsTutorial_2_BasicTutorial.pdf LEGOIGTAndMedicalRoboticsTutorial_2_BasicTutorial.pdf]

* Tutorial Slides Part 3 - Advanced Tutorial: [http://wiki.na-mic.org/Wiki/images/f/f4/LEGOIGTAndMedicalRoboticsTutorial_3_AdvancedTutorial.pdf LEGOIGTAndMedicalRoboticsTutorial_3_AdvancedTutorial.pdf]

* CT volume of the LEGO phantom: [http://wiki.na-mic.org/Wiki/images/6/69/000003.SER.zip 000003.SER.zip]

* 3D Slicer LEGO tutorial module (including code to interface between a LEGO robot and a C++ program): Available on the NA-MIC Sandbox - access [http://www.na-mic.org/ViewVC/index.cgi/trunk/LegoTutorial/?root=NAMICSandBox online] or through the [http://wiki.na-mic.org/Wiki/index.php/Engineering:SandBox NA-MIC subversion system]

* MICCAI 2007 "Open Source and Open Data for MICCAI" workshop paper: [[Image:AnAccessibleHandsOnTutorialSystemForIGTAndMedicalRobotics.pdf|Image:AnAccessibleHandsOnTutorialSystemForIGTAndMedicalRobotics.pdf]]

==Software Installation Instructions==
* Installing Slicer: go to the [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Install-Slicer3 Slicer3 Install] site.
* [http://wiki.na-mic.org/Wiki/index.php/LEGO_IGT_Compilation Compiling the LegoTutorial]

==Notes==
* Note that the code supplied above was modified from NXT++ (http://nxtpp.sourceforge.net) and Device::USB (http://search.cpan.org/~gwadej/Device-USB-0.21) and uses libusb (http://libusb.sourceforge.net). See the README file included with the source code for instructions on installation and use.

==People:==

[http://spl.harvard.edu/~dpace Danielle Pace], Surgical Planning Lab and Robarts Research Institute

[http://spl.harvard.edu/~kikinis Ron Kikinis], Surgical Planning Lab

[http://spl.harvard.edu/~noby Nobuhiko Hata], Surgical Planning Lab

'''Questions? Feedback?'''

Contact [http://spl.harvard.edu/~dpace Danielle Pace]

LEGO IGT and Medical Robotics Tutorial

2008-06-25T13:44:33Z

Jjomier:

[[Image:Slicer3-IGT-LEGOTutorial-biopsy.jpg|300px|thumb|The LEGO robot and phantom]]
[[Image:Slicer3-IGT-LEGOTutoral-screenshot.png|300px|thumb|Example tutorial screenshot]]

Back to [[IGT:ToolKit|IGT:ToolKit]]

=LEGO Image Guided Therapy and Medical Robotics Tutorial=

==Overview:==

This tutorial provides a thorough understanding of the main concepts in image-guided therapy and medical robotics, namely imaging, pre-operative planning, targeting by tracking, navigation and registration. The tutorial is open-source and completely free for anyone to use or modify (see http://www.slicer.org for details and for the BSD style open source license).

The tutorial is:
* Hands-on: Using a LEGO robot, a LEGO phantom (anatomical model) and a tutorial module in 3D Slicer v. 3 means that tutorial participants can use real physical equipment and software to learn about IGT and medical robotics.

* Accessible: The tutorial software is open-source, and the cost of the materials is approximately $300 USD + shipping and taxes.

==Tutorial Materials:==

Provided by NA-MIC and the Surgical Planning Lab:
* 3D Slicer v. 3 tutorial module
* CT volume of the phantom
* Tutorial slides
* Assembly instructions for the robot and the phantom
* Phantom placement guide

Provided by tutorial participants:
* 1 LEGO Mindstorms NXT kit
* 1 LEGO Deluxe Brick box
* 2 pom-poms
* Linux computer with root access or Windows with administrator privileges
For purchasing information for user-supplied materials, see the "Tutorial Slides Part 1 - Background and Materials" slides.

'''Getting the Tutorial Materials:'''

Click on the following links to get the tutorial materials:

* Robot assembly instructions: [http://wiki.na-mic.org/Wiki/images/8/81/LEGOIGTAndMedicalRoboticsTutorial_RobotAssemblyInstructions.pdf LEGOIGTAndMedicalRoboticsTutorial_RobotAssemblyInstructions.pdf]

* Phantom assembly instructions: [http://wiki.na-mic.org/Wiki/images/0/0d/LEGOIGTAndMedicalRoboticsTutorial_PhantomAssemblyInstructions.pdf LEGOIGTAndMedicalRoboticsTutorial_PhantomAssemblyInstructions.pdf]

* Phantom placement guide: [http://wiki.na-mic.org/Wiki/images/6/64/LEGOIGTAndMedicalRoboticsTutorial_PhantomPlacementGuide.pdf LEGOIGTAndMedicalRoboticsTutorial_PhantomPlacementGuide.pdf]

* Tutorial Slides Part 1 - Background and Materials: [http://wiki.na-mic.org/Wiki/images/d/d1/LEGOIGTAndMedicalRoboticsTutorial_1_BackgroundAndMaterials.pdf LEGOIGTAndMedicalRoboticsTutorial_1_BackgroundAndMaterials.pdf]

* Tutorial Slides Part 2 - Basic Tutorial: [http://wiki.na-mic.org/Wiki/images/a/ab/LEGOIGTAndMedicalRoboticsTutorial_2_BasicTutorial.pdf LEGOIGTAndMedicalRoboticsTutorial_2_BasicTutorial.pdf]

* Tutorial Slides Part 3 - Advanced Tutorial: [http://wiki.na-mic.org/Wiki/images/f/f4/LEGOIGTAndMedicalRoboticsTutorial_3_AdvancedTutorial.pdf LEGOIGTAndMedicalRoboticsTutorial_3_AdvancedTutorial.pdf]

* CT volume of the LEGO phantom: [http://wiki.na-mic.org/Wiki/images/6/69/000003.SER.zip 000003.SER.zip]

* 3D Slicer LEGO tutorial module (including code to interface between a LEGO robot and a C++ program): Available on the NA-MIC Sandbox - access [http://www.na-mic.org/ViewVC/index.cgi/trunk/LegoTutorial/?root=NAMICSandBox online] or through the [http://wiki.na-mic.org/Wiki/index.php/Engineering:SandBox NA-MIC subversion system]

* MICCAI 2007 "Open Source and Open Data for MICCAI" workshop paper: [[Image:AnAccessibleHandsOnTutorialSystemForIGTAndMedicalRobotics.pdf|Image:AnAccessibleHandsOnTutorialSystemForIGTAndMedicalRobotics.pdf]]

==Software Installation Instructions==
* Installing Slicer: go to the [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Install-Slicer3 Slicer3 Install] site.
* Compiling the LegoTutorial

==Notes==
* Note that the code supplied above was modified from NXT++ (http://nxtpp.sourceforge.net) and Device::USB (http://search.cpan.org/~gwadej/Device-USB-0.21) and uses libusb (http://libusb.sourceforge.net). See the README file included with the source code for instructions on installation and use.

==People:==

[http://spl.harvard.edu/~dpace Danielle Pace], Surgical Planning Lab and Robarts Research Institute

[http://spl.harvard.edu/~kikinis Ron Kikinis], Surgical Planning Lab

[http://spl.harvard.edu/~noby Nobuhiko Hata], Surgical Planning Lab

'''Questions? Feedback?'''

Contact [http://spl.harvard.edu/~dpace Danielle Pace]

Slicer3.2:Training

2008-06-20T22:28:01Z

Jjomier: /* Training Compendium */

__NOTOC__
= Welcome to the 3D Slicer3 Tutorial Page=
This page is under construction
The information on this page applies to '''3D Slicer version 3'''. If you are looking for materials about Slicer version 2, please go to the following [http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 location].
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* Slicer 3 has been designed as
** an easy-to-use application for 3D image analysis and visualization,
** an open-source environment for software development,
** a technology delivery platform for community breakthroughs.
*Slicer3 is distributed under a BSD open source license, and is designed to enable a collaborative development environment.
*This page contains training materials and data sets for self-guided training in the use of Slicer3

*For questions about the materials on this page, please send an e-mail to Sonia Pujol, Ph.D. (spujol at bwh.harvard.edu).
| style="background: #ebeced" colspan="2" align="center"| <b>[http://wiki.na-mic.org/Wiki/index.php/Slicer3:Slicer3Brand Slicer Logo]</b>
|-
| style="background: #ebeced"|[[Image:3DSlicerLogo-H-Color-424x236.png|center|250px|Slicer logo]]
|}

= Software Installation =
The [http://www.slicer.org/pages/Downloads Slicer download page] contains links for downloading the different versions of Slicer 3.

=Training Compendium=
{| border="1" cellpadding="5"
|- style="background:#BBE9E2; color:black" align="left"
| style="width:5%" | '''Level'''
| style="width:35%" | '''Tutorial'''
| style="width:30%" | '''Sample Data'''
| style="width:10%" | '''Image'''
|-
| style="background:#9BF2C5; color:black" align="Center"| '''1'''
| style="background:#D1FFF9; color:black"| [[Media:Slicer3Training_LoadingAndVisualization.ppt| Data Loading and Visualization in Slicer3 ]]
| style="background:#D1FFF9; color:black"| [http://www.na-mic.org/Wiki/index.php/Image:SlicerSampleVisualization.tar.gz SlicerSampleVisualization.tar.gz]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:SceneRestore.png|100px|LoadingandVisualization]]
|-
| style="background:#9BF2C5; color:black" align="Center"| '''1'''
| style="background:#D1FFF9; color:black"| [[Media:AutomaticSegmentation_SoniaPujol_Munich2008.ppt|EM Segmentation Course]]<br>Older materials: [[Media:EMSegTutorial-AHM2008.ppt|1]], [[EMSegmenter| 2]]
| style="background:#D1FFF9; color:black"|[[Media:AutomaticSegmentation.tar.gz|AutomaticSegmentation.tar.gz]]<br>Older Materials: [[Media:EMSegTutorial-AHM2008.zip|1]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:EMSegment.png|100px|EM Segmenter]]
|-
| style="background:#9BF2C5; color:black" align="Center"| '''1'''
| style="background:#D1FFF9; color:black"| Registration in Slicer 3
| style="background:#D1FFF9; color:black"| [[Media:Na-MIC-Slicer-Registration.ppt|Na-MIC-Slicer-Registration.ppt]] [[Media:SlicerSampleRegistration.tgz|SlicerSampleRegistration.tgz]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:SlicerRegistration.png|100px|SlicerRegistration]]
|-
| style="background:#8EDEB5; color:black" align="Center"| '''2'''
| style="background:#D1FFF9; color:black"| [[media:Slicer3CourseForDevelopers SPujol.ppt|Slicer3 Course for Developers]]
This tutorial is intended for engineers and scientists who want to integrate external programs with Slicer3.
| style="background:#D1FFF9; color:black"| [[Media:HelloWorld.zip|HelloWorld.zip]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:HelloWorld.png|100px|Plug-In]]
|-
| style="background:#8EDEB5; color:black" align="Center"| '''2'''
| style="background:#D1FFF9; color:black"| [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning Neurosurgical Planning in Slicer3]
Demonstrate's Slicer3's IGT capabilities by using image registration, model making and DTI to create a preoperative plan for neurosurgery
| style="background:#D1FFF9; color:black"| [[Media:ImageGuidedTherapyPlanning.pdf|ImageGuidedTherapyPlanning.pdf]]
[[Media:NeurosurgicalPlanningTutorialData.zip|NeurosurgicalPlanningTutorialData.zip]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:NeurosurgicalPlanningOverview.png|100px|Neurosurgical Planning Overview]]
|-
| style="background:#72b291; color:black" align="Center"| '''3'''
| style="background:#D1FFF9; color:black"| [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit Slicer3 as a research tool for image guided therapy research (IGT)]
This tutorial is intended for engineers and scientists who want to use Slicer 3 for IGT research.
| style="background:#D1FFF9; color:black"|
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Slicer IGTL NITRobot.jpg|100px|Slicer with robots]]
|}

* Level 1 = Basic functionality
* Level 2 = Advanced functionality
* Level 3 = Specialized application packages

=Additional Materials=
For a variety of data sets for downloading, check the following [http://www.na-mic.org/pages/Special:Publications?collection=13 '''link'''].
<br /> Back to [[Training:Main|Training:Main]]

File:SlicerRegistration.png

2008-06-20T22:27:25Z

Jjomier:

File:SlicerSampleRegistration.tgz

2008-06-20T22:26:12Z

Jjomier:

Slicer3.2:Training

2008-06-20T22:24:05Z

Jjomier: /* Training Compendium */

__NOTOC__
= Welcome to the 3D Slicer3 Tutorial Page=
This page is under construction
The information on this page applies to '''3D Slicer version 3'''. If you are looking for materials about Slicer version 2, please go to the following [http://wiki.na-mic.org/Wiki/index.php/Slicer:Workshops:User_Training_101 location].
{| border="00" cellpadding="5" cellspacing="0"
|-
| rowspan="2"|
* Slicer 3 has been designed as
** an easy-to-use application for 3D image analysis and visualization,
** an open-source environment for software development,
** a technology delivery platform for community breakthroughs.
*Slicer3 is distributed under a BSD open source license, and is designed to enable a collaborative development environment.
*This page contains training materials and data sets for self-guided training in the use of Slicer3

*For questions about the materials on this page, please send an e-mail to Sonia Pujol, Ph.D. (spujol at bwh.harvard.edu).
| style="background: #ebeced" colspan="2" align="center"| <b>[http://wiki.na-mic.org/Wiki/index.php/Slicer3:Slicer3Brand Slicer Logo]</b>
|-
| style="background: #ebeced"|[[Image:3DSlicerLogo-H-Color-424x236.png|center|250px|Slicer logo]]
|}

= Software Installation =
The [http://www.slicer.org/pages/Downloads Slicer download page] contains links for downloading the different versions of Slicer 3.

=Training Compendium=
{| border="1" cellpadding="5"
|- style="background:#BBE9E2; color:black" align="left"
| style="width:5%" | '''Level'''
| style="width:35%" | '''Tutorial'''
| style="width:30%" | '''Sample Data'''
| style="width:10%" | '''Image'''
|-
| style="background:#9BF2C5; color:black" align="Center"| '''1'''
| style="background:#D1FFF9; color:black"| [[Media:Slicer3Training_LoadingAndVisualization.ppt| Data Loading and Visualization in Slicer3 ]]
| style="background:#D1FFF9; color:black"| [http://www.na-mic.org/Wiki/index.php/Image:SlicerSampleVisualization.tar.gz SlicerSampleVisualization.tar.gz]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:SceneRestore.png|100px|LoadingandVisualization]]
|-
| style="background:#9BF2C5; color:black" align="Center"| '''1'''
| style="background:#D1FFF9; color:black"| [[Media:AutomaticSegmentation_SoniaPujol_Munich2008.ppt|EM Segmentation Course]]<br>Older materials: [[Media:EMSegTutorial-AHM2008.ppt|1]], [[EMSegmenter| 2]]
| style="background:#D1FFF9; color:black"|[[Media:AutomaticSegmentation.tar.gz|AutomaticSegmentation.tar.gz]]<br>Older Materials: [[Media:EMSegTutorial-AHM2008.zip|1]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:EMSegment.png|100px|EM Segmenter]]
|-
| style="background:#9BF2C5; color:black" align="Center"| '''1'''
| style="background:#D1FFF9; color:black"| Registration in Slicer 3
| style="background:#D1FFF9; color:black"| [[Media:Na-MIC-Slicer-Registration.ppt|Na-MIC-Slicer-Registration.ppt]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:EMSegment.png|100px|EM Segmenter]]
|-
| style="background:#8EDEB5; color:black" align="Center"| '''2'''
| style="background:#D1FFF9; color:black"| [[media:Slicer3CourseForDevelopers SPujol.ppt|Slicer3 Course for Developers]]
This tutorial is intended for engineers and scientists who want to integrate external programs with Slicer3.
| style="background:#D1FFF9; color:black"| [[Media:HelloWorld.zip|HelloWorld.zip]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:HelloWorld.png|100px|Plug-In]]
|-
| style="background:#8EDEB5; color:black" align="Center"| '''2'''
| style="background:#D1FFF9; color:black"| [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit/Neurosurgical-Planning Neurosurgical Planning in Slicer3]
Demonstrate's Slicer3's IGT capabilities by using image registration, model making and DTI to create a preoperative plan for neurosurgery
| style="background:#D1FFF9; color:black"| [[Media:ImageGuidedTherapyPlanning.pdf|ImageGuidedTherapyPlanning.pdf]]
[[Media:NeurosurgicalPlanningTutorialData.zip|NeurosurgicalPlanningTutorialData.zip]]
| style="background:#C3D1C3; color:black" align="Center"| [[Image:NeurosurgicalPlanningOverview.png|100px|Neurosurgical Planning Overview]]
|-
| style="background:#72b291; color:black" align="Center"| '''3'''
| style="background:#D1FFF9; color:black"| [http://wiki.na-mic.org/Wiki/index.php/IGT:ToolKit Slicer3 as a research tool for image guided therapy research (IGT)]
This tutorial is intended for engineers and scientists who want to use Slicer 3 for IGT research.
| style="background:#D1FFF9; color:black"|
| style="background:#C3D1C3; color:black" align="Center"| [[Image:Slicer IGTL NITRobot.jpg|100px|Slicer with robots]]
|}

* Level 1 = Basic functionality
* Level 2 = Advanced functionality
* Level 3 = Specialized application packages

=Additional Materials=
For a variety of data sets for downloading, check the following [http://www.na-mic.org/pages/Special:Publications?collection=13 '''link'''].
<br /> Back to [[Training:Main|Training:Main]]

Slicer3.2:Training

2007-11-29T03:53:29Z

Jjomier:

Back to [[AHM_2008]], [[Events]]

Owner: Julien Jomier

* Current BatchMake status
** Support for grid computing (Condor)
** Integration with MIDAS
** BatchMake with Slicer
* BatchMake tutorial (depending on time allocated for presentation/ variable length)
* Suggestions for future releases

2008 Winter Project Week Batchmake Update

2007-11-29T03:52:47Z

Jjomier:

User:Barre/ITK Registration Optimization

2007-04-03T18:14:26Z

Jjomier: /* Tests */

==ITK Registration Optimization (BW NAC) Project==

My (Sebastien Barre) notes so far. Once the dust settles, the relevant sections will be moved to the project pages listed below.

===Project===

The ultimate specific goal is B-Spline registration optimization for linux and windows on multi-core and multi-processor, shared memory machines. [...] Also, setup tools and a reporting mechanism for ITK speed to be monitored and reported by us and others. BWH is the driving force behind this work.

* [http://www.na-mic.org/Wiki/index.php/Non_Rigid_Registration Non Rigid Registration] at NA-MIC
* [http://www.na-mic.org/Wiki/index.php/ITK_Registration_Optimization ITK Registration Optimization] at NA-MIC
* [http://www.na-mic.org/Wiki/index.php/Slicer3:Performance_Analysis Slicer3:Performance Analysis] at NA-MIC
* [http://www.na-mic.org/Wiki/index.php/User:Barre/ITK_Registration_Optimization User:Barre/ITK Registration Optimization] at NA-MIC (this page)

===Contacts===

* [mailto:stephen.aylward@gmail.com Stephen Aylward]
* [mailto:julien.jomier@kitware.com Julien Jommier]
* [mailto:brad.davis@kitware.com Brad Davis]
* [mailto:sebastien.barre@kitware.com Sebastien Barre]
* [mailto:LydiaN@alleninstitute.org Lydia Ng]

===Quick Links===
* [http://goog-perftools.sourceforge.net/ Google Performance Tools]
* [http://kcachegrind.sourceforge.net/cgi-bin/show.cgi kcachegrind], [http://docs.kde.org/development/en/kdesdk/kcachegrind/index.html The KCachegrind Handbook], [http://brent.izolo.com/blog/?p=4 Running Kcachegrind on Mac OSX 10.4]
* Also check my [http://www.google.com/notebook/public/14106771154920524977/BDRnWSgoQ_Nq_jY0i BW-NAC Google Notebook] for fresher links.

===Source Code===

cvs -d :pserver:<login>@public.kitware.com:/cvsroot/BWHITKOptimization login

Enter your VTK <login>, and password, then:

cvs -d :pserver:<login>@public.kitware.com:/cvsroot/BWHITKOptimization co BWHITKOptimization

to checkout the code.

You can browse the repository online using [http://public.kitware.com/cgi-bin/viewcvs.cgi/?root=BWHITKOptimization ViewCVS] as well.

===Testing Data===

* [http://insight-journal.org/dspace/handle/1926/459 NAMIC: Deformable registration speed optimization] (DSpace @ Insight-Journal)

===Potential Issues with Timing===
* Repository was updated so that it can compile on Unix.
====__rtdsc()====
CallMonWin includes <tt><intrin.h></tt> to call <tt>__rdtsc()</tt>, a header that does not exist in Microsoft compilers prior to Visual Studio 8/2005. It seems however that one can call <tt>__rdtsc()</tt> directly from assembly:
* [http://www.gamedev.net/community/forums/topic.asp?topic_id=394151&whichpage=1&#2611489 GameDev.net forum, see third comment by Evil Steve (!)]
* [http://www.intel.com/cd/ids/developer/asmo-na/eng/257129.htm CPUID for x64 Platforms and Microsoft Visual Studio* .NET 2005]
* [http://www.codeproject.com/datetime/highreselapsedtimer.asp?df=100&forumid=3030&exp=0&select=88527 High Resolution Elapsed Timer]
A few articles advises against the use of <tt>__rdtsc()</tt>, especially in a multicore/multithread context:
* [http://www.gamedev.net/community/forums/topic.asp?topic_id=394151&whichpage=1&#2611489 GameDev.net forum]
* [http://www.devsource.com/article2/0,1895,2063855,00.asp High Performance Timing under Windows]
The suggested alternative is to use Performance Counters. Hardware counters are actually not an OS feature per se, but a CPU feature that has been around for some time. They provide high-resolution timers that can be used to monitor a wide range of resources:
* [http://www.devx.com/MicrosoftISV/Article/16293 Accessing Nanosecond Timers While Performance Tuning on Windows Servers]
* [http://www.informit.com/guides/content.asp?g=dotnet&seqNum=242&rl=1 High Resolution Timing]
The issue remains on how to access those counters in a cross-platform way:
* [http://icl.cs.utk.edu/papi/overview/index.html PAPI]: "''The Performance API (PAPI) project specifies a standard API for accessing hardware performance counters''".<br>Stephen/Christian reported that Dual Core CPUs were not supported, but it seems from the [http://icl.cs.utk.edu/viewcvs/viewcvs.py/PAPI/papi/RELEASENOTES.txt?view=markup&revision=1.8.10.2.2.2 release notes for PAPI 3.5] (2006-11-09) that both Intel Core2Duo and Pentium D (i.e. dual core) are indeed supported.
===Process Priority===
Whatever our choices, several articles also suggest to bump the application's priority to real-time before performing testing to make sure the wall-clock() results are as realistic as possible. It is however very important to set it back to normal.

* Windows:
See [http://www.devx.com/MicrosoftISV/Article/16293 last paragraph]. Use GetPriorityClass, SetPriorityClass, GetThreadPriority, SetThreadPriority:
<pre>
DWORD dwPriorityClass = GetPriorityClass(GetCurrentProcess());
int nPriority = GetThreadPriority(GetCurrentThread());
SetPriorityClass(GetCurrentProcess(),REALTIME_PRIORITY_CLASS);
SetThreadPriority(GetCurrentThread(),THREAD_PRIORITY_TIME_CRITICAL);
[...]g
SetThreadPriority(GetCurrentThread(),nPriority);
SetPriorityClass(GetCurrentProcess(),dwPriorityClass);
</pre>

* Unix:
The getpriority(), setpriority(), and nice() functions can be used to change the priority of processes. The getpriority() call returns the current nice value for a process, process group, or a user. The returned nice value is in the range of [-NZERO, NZERO-1]. NZERO is defined in /usr/include/limits.h. The default process priority always has the value 0 for UNIX. The setpriority() call sets the current nice value for a process, process group, or a user to the value of value + NZERO.

===Thread Affinity===
We should consider setting the thread affinity to make sure that the starting time is recorded on the same thread as the ending time. Will that constrain the rest of the program to run on a single thread, very good question.

* Windows:
Using [http://msdn2.microsoft.com/en-us/library/ms686247.aspx SetThreadAffinityMask].
Also check Sleep(0), reported in a few discussions, including [http://msdn2.microsoft.com/en-us/library/ms686247.aspx this long one].

* Unix:
Using [http://www.google.com/search?lr=&ie=UTF-8&oe=UTF-8&q=sched_setaffinity sched_setaffinity], but seems to be Linux-only (not POSIX).

===Test Platforms===

The primary target platform at the 8, 16, and 32 processor machines at BWH. However, preliminary tests have been performed on KHQ computers.

====KHQ====
A full software stack was compiled on several machines at Kitware. Each component was build in two flavors, both shared/debug and static/release:
* Tcl/Tk 8.4
* VTK (cvs)
* ITK (cvs)
* ITK Applications (cvs)
* FLTK (1.1 svn)
* BWHItkOptimization (cvs)

All platforms are so far described in the [https://www.kitware.com/scripts/cvsweb/BWHItkOptimization/Results/?cvsroot=Work BWHItkOptimization/Results] directory:

{| border="1" width="90%" align="center" cellspacing="0" cellpadding="3"
|- bgcolor="#abcdef"
! Host !! #CPU !! CPU !! Freq !! RAM !! Arch !! OS !! Login
|-
| [https://www.kitware.com/scripts/cvsweb/BWHItkOptimization/Results/amber2.kitware?cvsroot=Work amber2] || 2 || Pentium Xeon || 2.8 GHz || 4 GB || 64 bits || Linux 2.6 (Red Hat Enterprise 4) || kitware (ssh, vnc; cd ~/barre)
|-
| [https://www.kitware.com/scripts/cvsweb/BWHItkOptimization/Results/fury.kitware?cvsroot=Work fury] || 1 || Pentium 4 (hyperthread) || 2.8 GHz || 1 GB || 32 bits || Linux 2.6 (Fedora Core 4) || [mailto:sebastien.barre@kitware.com barre], jjomier, aylward
|-
| [https://www.kitware.com/scripts/cvsweb/BWHItkOptimization/Results/panzer.kitware?cvsroot=Work panzer] || 1 || Intel Core Duo (dual core) || 1.66 GHz || 1 GB || 32 bits || Mac OS X 10.4.8 || [mailto:sebastien.barre@kitware.com barre], jjomier, aylward
|-
| [https://www.kitware.com/scripts/cvsweb/BWHItkOptimization/Results/sanakhan.kitware?cvsroot=Work sanakhan] || 1 || Pentium M || 1.8 GHz || 1 GB || 32 bits || Windows XP SP2 || [mailto:sebastien.barre@kitware.com barre]
|-
| [https://www.kitware.com/scripts/cvsweb/BWHItkOptimization/Results/tetsuo.kitware?cvsroot=Work tetsuo] || 1 || Pentium D (dual core) || 3.2 GHz || 2 GB || 32 bits || Windows XP SP2 || [mailto:sebastien.barre@kitware.com barre]
|}

====Tests====

* To run tests using the ITK test driver. From the bin directory run:
./OptimizationTests
and select the test you want to run.

* LinearInterp: (to describe)

====BWH====

Systems to be described. We will set up our performancing framework so that it can be run in an automated fashion, using CTest and a dashboard. Running from the spl machine should at that point only require one of us to checkout the code, build and ctest it every night.

===Status===

* kcachegrind and timing are being performed on amber2. Stay tuned.
* valgrind is not supported on x86_64 architecture :( Now using fury instead of amber2.
* <tt>RegTests/RunLinearInterpTest.sh.in</tt> is configured automatically to run and times <tt>LinearInterp</tt> with various combinations of threads, size and factor parameters.
** It was run on fury (release static): <tt>Results/fury.kitware.timings-rel.txt</tt>
** It was run on fury (debug): <tt>Results/fury.kitware.timings-dbg.txt</tt>
** It was run on amber2 (release static): <tt>Results/amber2.kitware.timings-rel.txt</tt>

===Action Items===

* [[User:Barre/ITK Registration Optimization/Action Items|AC1: 03/28/07]]

User:Barre/ITK Registration Optimization

2007-04-03T18:14:10Z

Jjomier: /* Tests */

==ITK Registration Optimization (BW NAC) Project==

My (Sebastien Barre) notes so far. Once the dust settles, the relevant sections will be moved to the project pages listed below.

===Project===

The ultimate specific goal is B-Spline registration optimization for linux and windows on multi-core and multi-processor, shared memory machines. [...] Also, setup tools and a reporting mechanism for ITK speed to be monitored and reported by us and others. BWH is the driving force behind this work.

* [http://www.na-mic.org/Wiki/index.php/Non_Rigid_Registration Non Rigid Registration] at NA-MIC
* [http://www.na-mic.org/Wiki/index.php/ITK_Registration_Optimization ITK Registration Optimization] at NA-MIC
* [http://www.na-mic.org/Wiki/index.php/Slicer3:Performance_Analysis Slicer3:Performance Analysis] at NA-MIC
* [http://www.na-mic.org/Wiki/index.php/User:Barre/ITK_Registration_Optimization User:Barre/ITK Registration Optimization] at NA-MIC (this page)

===Contacts===

* [mailto:stephen.aylward@gmail.com Stephen Aylward]
* [mailto:julien.jomier@kitware.com Julien Jommier]
* [mailto:brad.davis@kitware.com Brad Davis]
* [mailto:sebastien.barre@kitware.com Sebastien Barre]
* [mailto:LydiaN@alleninstitute.org Lydia Ng]

===Quick Links===
* [http://goog-perftools.sourceforge.net/ Google Performance Tools]
* [http://kcachegrind.sourceforge.net/cgi-bin/show.cgi kcachegrind], [http://docs.kde.org/development/en/kdesdk/kcachegrind/index.html The KCachegrind Handbook], [http://brent.izolo.com/blog/?p=4 Running Kcachegrind on Mac OSX 10.4]
* Also check my [http://www.google.com/notebook/public/14106771154920524977/BDRnWSgoQ_Nq_jY0i BW-NAC Google Notebook] for fresher links.

===Source Code===

cvs -d :pserver:<login>@public.kitware.com:/cvsroot/BWHITKOptimization login

Enter your VTK <login>, and password, then:

cvs -d :pserver:<login>@public.kitware.com:/cvsroot/BWHITKOptimization co BWHITKOptimization

to checkout the code.

You can browse the repository online using [http://public.kitware.com/cgi-bin/viewcvs.cgi/?root=BWHITKOptimization ViewCVS] as well.

===Testing Data===

* [http://insight-journal.org/dspace/handle/1926/459 NAMIC: Deformable registration speed optimization] (DSpace @ Insight-Journal)

===Potential Issues with Timing===
* Repository was updated so that it can compile on Unix.
====__rtdsc()====
CallMonWin includes <tt><intrin.h></tt> to call <tt>__rdtsc()</tt>, a header that does not exist in Microsoft compilers prior to Visual Studio 8/2005. It seems however that one can call <tt>__rdtsc()</tt> directly from assembly:
* [http://www.gamedev.net/community/forums/topic.asp?topic_id=394151&whichpage=1&#2611489 GameDev.net forum, see third comment by Evil Steve (!)]
* [http://www.intel.com/cd/ids/developer/asmo-na/eng/257129.htm CPUID for x64 Platforms and Microsoft Visual Studio* .NET 2005]
* [http://www.codeproject.com/datetime/highreselapsedtimer.asp?df=100&forumid=3030&exp=0&select=88527 High Resolution Elapsed Timer]
A few articles advises against the use of <tt>__rdtsc()</tt>, especially in a multicore/multithread context:
* [http://www.gamedev.net/community/forums/topic.asp?topic_id=394151&whichpage=1&#2611489 GameDev.net forum]
* [http://www.devsource.com/article2/0,1895,2063855,00.asp High Performance Timing under Windows]
The suggested alternative is to use Performance Counters. Hardware counters are actually not an OS feature per se, but a CPU feature that has been around for some time. They provide high-resolution timers that can be used to monitor a wide range of resources:
* [http://www.devx.com/MicrosoftISV/Article/16293 Accessing Nanosecond Timers While Performance Tuning on Windows Servers]
* [http://www.informit.com/guides/content.asp?g=dotnet&seqNum=242&rl=1 High Resolution Timing]
The issue remains on how to access those counters in a cross-platform way:
* [http://icl.cs.utk.edu/papi/overview/index.html PAPI]: "''The Performance API (PAPI) project specifies a standard API for accessing hardware performance counters''".<br>Stephen/Christian reported that Dual Core CPUs were not supported, but it seems from the [http://icl.cs.utk.edu/viewcvs/viewcvs.py/PAPI/papi/RELEASENOTES.txt?view=markup&revision=1.8.10.2.2.2 release notes for PAPI 3.5] (2006-11-09) that both Intel Core2Duo and Pentium D (i.e. dual core) are indeed supported.
===Process Priority===
Whatever our choices, several articles also suggest to bump the application's priority to real-time before performing testing to make sure the wall-clock() results are as realistic as possible. It is however very important to set it back to normal.

* Windows:
See [http://www.devx.com/MicrosoftISV/Article/16293 last paragraph]. Use GetPriorityClass, SetPriorityClass, GetThreadPriority, SetThreadPriority:
<pre>
DWORD dwPriorityClass = GetPriorityClass(GetCurrentProcess());
int nPriority = GetThreadPriority(GetCurrentThread());
SetPriorityClass(GetCurrentProcess(),REALTIME_PRIORITY_CLASS);
SetThreadPriority(GetCurrentThread(),THREAD_PRIORITY_TIME_CRITICAL);
[...]g
SetThreadPriority(GetCurrentThread(),nPriority);
SetPriorityClass(GetCurrentProcess(),dwPriorityClass);
</pre>

* Unix:
The getpriority(), setpriority(), and nice() functions can be used to change the priority of processes. The getpriority() call returns the current nice value for a process, process group, or a user. The returned nice value is in the range of [-NZERO, NZERO-1]. NZERO is defined in /usr/include/limits.h. The default process priority always has the value 0 for UNIX. The setpriority() call sets the current nice value for a process, process group, or a user to the value of value + NZERO.

===Thread Affinity===
We should consider setting the thread affinity to make sure that the starting time is recorded on the same thread as the ending time. Will that constrain the rest of the program to run on a single thread, very good question.

* Windows:
Using [http://msdn2.microsoft.com/en-us/library/ms686247.aspx SetThreadAffinityMask].
Also check Sleep(0), reported in a few discussions, including [http://msdn2.microsoft.com/en-us/library/ms686247.aspx this long one].

* Unix:
Using [http://www.google.com/search?lr=&ie=UTF-8&oe=UTF-8&q=sched_setaffinity sched_setaffinity], but seems to be Linux-only (not POSIX).

===Test Platforms===

The primary target platform at the 8, 16, and 32 processor machines at BWH. However, preliminary tests have been performed on KHQ computers.

====KHQ====
A full software stack was compiled on several machines at Kitware. Each component was build in two flavors, both shared/debug and static/release:
* Tcl/Tk 8.4
* VTK (cvs)
* ITK (cvs)
* ITK Applications (cvs)
* FLTK (1.1 svn)
* BWHItkOptimization (cvs)

All platforms are so far described in the [https://www.kitware.com/scripts/cvsweb/BWHItkOptimization/Results/?cvsroot=Work BWHItkOptimization/Results] directory:

{| border="1" width="90%" align="center" cellspacing="0" cellpadding="3"
|- bgcolor="#abcdef"
! Host !! #CPU !! CPU !! Freq !! RAM !! Arch !! OS !! Login
|-
| [https://www.kitware.com/scripts/cvsweb/BWHItkOptimization/Results/amber2.kitware?cvsroot=Work amber2] || 2 || Pentium Xeon || 2.8 GHz || 4 GB || 64 bits || Linux 2.6 (Red Hat Enterprise 4) || kitware (ssh, vnc; cd ~/barre)
|-
| [https://www.kitware.com/scripts/cvsweb/BWHItkOptimization/Results/fury.kitware?cvsroot=Work fury] || 1 || Pentium 4 (hyperthread) || 2.8 GHz || 1 GB || 32 bits || Linux 2.6 (Fedora Core 4) || [mailto:sebastien.barre@kitware.com barre], jjomier, aylward
|-
| [https://www.kitware.com/scripts/cvsweb/BWHItkOptimization/Results/panzer.kitware?cvsroot=Work panzer] || 1 || Intel Core Duo (dual core) || 1.66 GHz || 1 GB || 32 bits || Mac OS X 10.4.8 || [mailto:sebastien.barre@kitware.com barre], jjomier, aylward
|-
| [https://www.kitware.com/scripts/cvsweb/BWHItkOptimization/Results/sanakhan.kitware?cvsroot=Work sanakhan] || 1 || Pentium M || 1.8 GHz || 1 GB || 32 bits || Windows XP SP2 || [mailto:sebastien.barre@kitware.com barre]
|-
| [https://www.kitware.com/scripts/cvsweb/BWHItkOptimization/Results/tetsuo.kitware?cvsroot=Work tetsuo] || 1 || Pentium D (dual core) || 3.2 GHz || 2 GB || 32 bits || Windows XP SP2 || [mailto:sebastien.barre@kitware.com barre]
|}

====Tests====

* To run tests using the ITK test driver. From the bin directory run:
./OptimizationTests

* LinearInterp: (to describe)

====BWH====

Systems to be described. We will set up our performancing framework so that it can be run in an automated fashion, using CTest and a dashboard. Running from the spl machine should at that point only require one of us to checkout the code, build and ctest it every night.

===Status===

* kcachegrind and timing are being performed on amber2. Stay tuned.
* valgrind is not supported on x86_64 architecture :( Now using fury instead of amber2.
* <tt>RegTests/RunLinearInterpTest.sh.in</tt> is configured automatically to run and times <tt>LinearInterp</tt> with various combinations of threads, size and factor parameters.
** It was run on fury (release static): <tt>Results/fury.kitware.timings-rel.txt</tt>
** It was run on fury (debug): <tt>Results/fury.kitware.timings-dbg.txt</tt>
** It was run on amber2 (release static): <tt>Results/amber2.kitware.timings-rel.txt</tt>

===Action Items===

* [[User:Barre/ITK Registration Optimization/Action Items|AC1: 03/28/07]]