Difference between revisions of "3D Ultrasound Module in Slicer 3"

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(New page: Back to IGT-Tool-Kit ==='''Disclaimer'''===<br> Slicer and Slicer for IGT have been designed for research purposes only and have not been reviewed or approved by the Food...)
 
m (Text replacement - "http://www.slicer.org/slicerWiki/index.php/" to "https://www.slicer.org/wiki/")
 
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Back to [[IGT-Tool-Kit|IGT-Tool-Kit]]
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Back to [[IGT:ToolKit|IGT:ToolKit]]
  
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==='''Disclaimer'''===<br>
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==='''Disclaimer'''===
−
Slicer and Slicer for IGT have been designed for research purposes only and have not been reviewed or approved by the Food and Drug Administration or by any
+
<br>
−
other agency. YOU ACKNOWLEDGE AND AGREE THAT CLINICAL APPLICATIONS ARE NEITHER RECOMMENDED NOR ADVISED. Read the [[http://wiki.na-mic.org/Wiki/index.php/Slicer License for Slicer]] for details. One may use '''Slicer for Image Guided Therapy (IGT)''' in clinical studies at his/her own risk after approval from his/her institution through its own IRB certification procedure. The example clinical cases listed in this website are either from mock-up or clinical validation study approved by IRB that weighed the merit against the risk of using Slicer for IGT, which is not recommended for clinical use. For more information about the human clinical trials, visit NIH-NCI web site [http://www.cancer.gov/clinicaltrials/learning/page3].
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*Slicer and Slicer for IGT have been designed for research purposes only. The packages have not been reviewed or approved by the Food and Drug Administration or by any other agency.  
 +
*YOU ACKNOWLEDGE AND AGREE THAT CLINICAL APPLICATIONS ARE NEITHER RECOMMENDED NOR ADVISED. Read the [[http://wiki.na-mic.org/Wiki/index.php/Slicer License for Slicer]] for details.  
 +
*The example clinical cases listed in this website are either from mock-up procedures or obtained in clinical validation studies approved by the local internal review board (IRB). For more information about human clinical trials, visit NIH-NCI web site [http://www.cancer.gov/clinicaltrials/learning/page3].
 +
*If you want to do research with this software, it is your responsibility to ensure compliance with all relevant rules and regulations.
  
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==='''People'''===<br>
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==='''People'''===
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Sandy Wells (U41 Computational Core PI)<br>
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<br>
 +
'''Harvard Medical School, Boston, USA:'''<br><br>
 
Nobuhiko Hata, PhD (Slicer IGT Project Director)<br>
 
Nobuhiko Hata, PhD (Slicer IGT Project Director)<br>
−
Alex Golby, MD (Neurosurgery)<br>
+
Haiying Liu<br>
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Haiying Liu, MS (Senior Engineer)<br>
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Junichi Tokuda, PhD<br>
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Clare Tempany, MD (Prostate Therapy)<br>
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Benjamin Grauer<br><br>
  
−
==='''Summary of IGT Functions in Slicer'''===<br>
+
'''SJTU, Shanghai, China'''<br><br>
−
3D Slicer [http://wiki.na-mic.org/Wiki/index.php/Slicer] (simply Slicer) is a multi-platform, free open source software (FOSS) for visualization and image computing. The Slicer IGT project is aimed at extending Slicer for Image Guided Therapy. Currently, we supports the following IGT functions:
+
Lixu Gu, PhD (Director of IGST)<br>
 +
Yan Sun, PhD
  
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* Free open-source software for Image Guided Therapy research
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*Developers:
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* Provides software foundation (GUI, Image I/O, 3D viewer, tracker support), and you can focus on developping your original clinical application
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Tingting Xi<br>
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* Available for Windows, Mac, Linux
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Shuqin Ding<br>
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* Access to state-of-art scientific medical image processing algorithms as well as most of commercial tracking devices
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Ziying Jiang<br>
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* [http://wiki.na-mic.org/Wiki/index.php/Slicer-IGT#Events Affiliated scientific workshops and seminars] to discuss and exchange ideas
+
Qingfeng Jin<br>
−
* Increasing visibility of your research in IGT community using popular software platform
+
* supporters:
−
* Available for commercialization by concealing proprietary codes*
+
Size Lv<br>
 +
Jun Ye <br>
 +
Ze Luo<br>
 +
Pengyan Hou<br>
 +
Guangchao Zheng<br>
 +
* Clinical Members:
 +
Weiwei Zhan (Director of Ultrasound department, Ruijin Hospital, Shanghai)<br>
 +
Jianqiao Zhou (Ultrasound Radiologist, Ruijin Hospital, Shanghai)
  
−
(*) Acknowledgment needed
+
'''Robarts Research Institute and University of Western Ontario, Canada:'''<br><br>
 +
Terry Peters, PhD (Director of VASST Lab)<br>
 +
Danielle Pace <br>
  
−
==='''Using Slicer for IGT'''===<br>
+
'''Queen's University, Canada:'''<br><br>
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* [http://wiki.na-mic.org/Wiki/index.php/Slicer-IGT/For_Clinicians '''Guidelines for Clinicians''']
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David Gobbi, PhD<br>
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* [http://wiki.na-mic.org/Wiki/index.php/Slicer-IGT/For_Developers '''Develop your IGT projects with Slicer''']
+
 
−
* [http://wiki.na-mic.org/Wiki/index.php/Slicer-IGT/Screenshots '''Slicer 2 Screenshots''']
+
==='''Summary of Project'''===
−
* [http://www.na-mic.org/Wiki/index.php/Slicer3:VisualBlog '''Slicer 3 VisualBlog''']
+
<br>
 +
This project is aimed to develop a comprehensive plug-in module for slicer 3, which is used for 3D ultrasound(US) image acquisition by using a traditional 2D US scanner. The module should be functioned with 3D US scanning, reconstruction and visualization, and could be used for clinical applications in Liver CAD, Prostate IGT and Cardiac Surgery Navigation.<br>
 +
The project is a joint research activity between SPL of Harvard University and IGST Lab in Shanghai Jiaotong University, China.
 +
 
 +
==='''Project Schedule'''===
 +
<br>
 +
* 03/01/2008 - 03/31/2008
 +
** Slicer IGT Training
 +
* 04/01/2008 - 04/30/2008
 +
** Set up hardware for ultrasound probe tracking
 +
** 3D ultrasound image acquisition and reconstruction
 +
** 3D ultrasound image visualization
 +
** Developing 3D Ultrasound module in Slicer 3
 +
* 05/01/2008 - 05/31/2008
 +
** Phantom experiment
 +
** Assessment of accuracy
 +
** Animal trials
 +
* 06/01/2008 - 06/31/2008
 +
** Clinical trials
 +
** Liver application
 +
 
 +
 
 +
==='''Slicer IGT Training'''===
 +
'''Week of 03/03:'''<br>
 +
* Agenda:
 +
** Time: March 6, Thursday, 9:30 am - 12:00 noon
 +
** Instructors: Haiying Liu and Lixu Gu
 +
** Audience: Graduate students at SJTU, Shanghai, China
 +
** Topic: Slicer 3 architecture, download, build, doxygen, data loading, volume visualization, data saving
 +
** Communication: Long distance phone between Boston, USA and Shanghai, China; Skype
 +
* Materials: [http://wiki.na-mic.org/Wiki/index.php/Slicer_Training_Basic  '''Slicer basics''']<br>
 +
* Issues: Accessing to Slicer code is extremely slow. We fedexed a CD with latest Slicer code to Shanghai.
 +
'''Week of 03/10:''' <br>
 +
* Agenda:
 +
** Time: March 13, Thursday, 10:00 am - 12:00 noon
 +
** Instructors: Haiying Liu and Lixu Gu
 +
** Audience: Graduate students at SJTU, Shanghai, China
 +
** Topic: Command line module, how to add one into Slicer 3, how to write a filter inside Slicer 3.
 +
** Communication: Long distance phone between Boston, USA and Shanghai, China; Skype
 +
* Materials: [http://wiki.na-mic.org/Wiki/index.php/Slicer_Training_CommandLine_Module '''How to create a command line module''']<br>
 +
'''Week of 03/24:''' <br>
 +
* Agenda:
 +
** Time: March 27, Thursday, 10:00 am - 12:00 noon
 +
** Instructors: Haiying Liu and Lixu Gu
 +
** Audience: Graduate students at SJTU, Shanghai, China
 +
** Topic: Aurora connection to computer, compiling IGSTK and IGSTKSandbox, acquiring tracking data from Aurora, sending tracking data to Slicer 3, Slicer 3 display update as new data coming in.
 +
** Communication: Long distance phone between Boston, USA and Shanghai, China; Skype
 +
* Materials: [http://wiki.na-mic.org/Wiki/index.php/Slicer_Training_Navigation_With_Aurora '''Navigation with Aurora''']<br>
 +
'''Week of 03/31:''' <br>
 +
* Agenda:
 +
** Time: April 3, Thursday, 10:00 am - 12:00 noon
 +
** Instructors: Benjamin Grauer and Haiying Liu
 +
** Audience: Graduate students at SJTU, Shanghai, China
 +
** Topic: Application of OpenIGTLink and volume rendering in Slicer 3.
 +
** Communication: Long distance phone between Boston, USA and Shanghai, China; Skype
 +
* Materials:
 +
** [http://wiki.na-mic.org/Wiki/index.php/OpenIGTLink '''OpenIGTLink: A network protocol]
 +
** [http://www.na-mic.org/Wiki/index.php/Slicer3:4DUltrasound_4D_US '''OpenIGTLink & 4D Ultrasound 1''']<br>
 +
** [http://www.na-mic.org/Wiki/index.php/Slicer3:openIGT_Tutorial_For_4D_Volume_Rendering_Data '''OpenIGTLink & 4D Ultrasound 2''']<br>
 +
** [http://wiki.na-mic.org/Wiki/index.php/Slicer_Training_Volume_Rendering  '''Volume rendering''']<br>
 +
 
 +
==='''Progress Report'''===
 +
<br>
 +
 
 +
==='''Events'''===
 +
<br>
 +
'''04/17/2008 10am'''
 +
* TCOM
 +
* Topic: Ultrasound module for Slicer 3
 +
** 1) requirements
 +
** 2) components
 +
** 3) task breaks
 +
** 4) time frame
 +
** 5) experiments
 +
** 6) clinical trials
 +
** 7) packaging and distributions
 +
* People: Noby, Haiying, Benjamin, Lixu, Terry, Danielle, David
  
−
==='''Events'''===<br>
+
==='''Work in progress datasets'''===
−
* '''[[AHM_2008|January 6-11, 2008, AHM, EAB, Project Half Week]]
+
See the link [http://wiki.na-mic.org/Wiki/index.php/3D_Ultrasound_Module_in_Slicer_3_datasets here]
−
* [[Slicer3:Spring-2008-User-Training|Spring 2008]] (Wednesday February 20th, 9 AM to 11 AM) Slicer3 user Training Workshop at the SPL 1249 Boylston St, Boston
 
−
* March 24-27 2008: [[2008_Engineering_review_at_Utah|2008 Engineering review at Utah]]
 
−
* April 14, 2008: Full day Slicer 3 Users and Plug-in Workshop hosted by UNC-Chapel Hill faculty
 
−
* '''[[2008_Summer_Project_Week|June 23-27, 2008, Summer Project Week]]'''
 
−
* September 6-9, 2008 [http://miccai2008.rutgers.edu/ MICCAI] Submitted for consideration a full day Slicer 3 Users and Plug-in Workshop
 
−
* November 30 through December 5, 2008 [http://rsna2008.rsna.org/ RSNA] Proposal for a daily 2 hour 3D Slicer as DICOM viewer training Workshop submitted.
 
  
−
==='''Useful Links'''===<br>
+
==='''Useful Links'''===
−
* [http://wiki.na-mic.org/Wiki/index.php/Slicer-IGT/Collaborators_and_Sponsors Collaborators and Sponsors]
+
<br>
−
* [http://wiki.ncigt.org/index.php/U41:cc:SA_Slicer_Engineering Internal Developers Page (authorization required)]
 
 
* [http://wiki.na-mic.org/Wiki/index.php/Slicer-IGT/GPU-IGT GPU accelerated medical image processing for IGT]
 
* [http://wiki.na-mic.org/Wiki/index.php/Slicer-IGT/GPU-IGT GPU accelerated medical image processing for IGT]
−
* [[Slicer-IGT/VTK-MIST|VTK-Mist integration for fast volume rendering]]
+
* [https://www.slicer.org/wiki/Slicer-IGT/VTK-MIST VTK-Mist integration for fast volume rendering]
 +
* [http://www.na-mic.org/Wiki/index.php/Slicer3:VisualBlog '''Slicer 3 VisualBlog''']
 +
* [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Style '''Slicer 3 Coding Style''']

Latest revision as of 18:07, 10 July 2017

Home < 3D Ultrasound Module in Slicer 3

Back to IGT:ToolKit

Disclaimer


  • Slicer and Slicer for IGT have been designed for research purposes only. The packages have not been reviewed or approved by the Food and Drug Administration or by any other agency.
  • YOU ACKNOWLEDGE AND AGREE THAT CLINICAL APPLICATIONS ARE NEITHER RECOMMENDED NOR ADVISED. Read the [License for Slicer] for details.
  • The example clinical cases listed in this website are either from mock-up procedures or obtained in clinical validation studies approved by the local internal review board (IRB). For more information about human clinical trials, visit NIH-NCI web site [1].
  • If you want to do research with this software, it is your responsibility to ensure compliance with all relevant rules and regulations.

People


Harvard Medical School, Boston, USA:

Nobuhiko Hata, PhD (Slicer IGT Project Director)
Haiying Liu
Junichi Tokuda, PhD
Benjamin Grauer

SJTU, Shanghai, China

Lixu Gu, PhD (Director of IGST)
Yan Sun, PhD

  • Developers:

Tingting Xi
Shuqin Ding
Ziying Jiang
Qingfeng Jin

  • supporters:

Size Lv
Jun Ye
Ze Luo
Pengyan Hou
Guangchao Zheng

  • Clinical Members:

Weiwei Zhan (Director of Ultrasound department, Ruijin Hospital, Shanghai)
Jianqiao Zhou (Ultrasound Radiologist, Ruijin Hospital, Shanghai)

Robarts Research Institute and University of Western Ontario, Canada:

Terry Peters, PhD (Director of VASST Lab)
Danielle Pace

Queen's University, Canada:

David Gobbi, PhD

Summary of Project


This project is aimed to develop a comprehensive plug-in module for slicer 3, which is used for 3D ultrasound(US) image acquisition by using a traditional 2D US scanner. The module should be functioned with 3D US scanning, reconstruction and visualization, and could be used for clinical applications in Liver CAD, Prostate IGT and Cardiac Surgery Navigation.
The project is a joint research activity between SPL of Harvard University and IGST Lab in Shanghai Jiaotong University, China.

Project Schedule


  • 03/01/2008 - 03/31/2008
    • Slicer IGT Training
  • 04/01/2008 - 04/30/2008
    • Set up hardware for ultrasound probe tracking
    • 3D ultrasound image acquisition and reconstruction
    • 3D ultrasound image visualization
    • Developing 3D Ultrasound module in Slicer 3
  • 05/01/2008 - 05/31/2008
    • Phantom experiment
    • Assessment of accuracy
    • Animal trials
  • 06/01/2008 - 06/31/2008
    • Clinical trials
    • Liver application


Slicer IGT Training

Week of 03/03:

  • Agenda:
    • Time: March 6, Thursday, 9:30 am - 12:00 noon
    • Instructors: Haiying Liu and Lixu Gu
    • Audience: Graduate students at SJTU, Shanghai, China
    • Topic: Slicer 3 architecture, download, build, doxygen, data loading, volume visualization, data saving
    • Communication: Long distance phone between Boston, USA and Shanghai, China; Skype
  • Materials: Slicer basics
  • Issues: Accessing to Slicer code is extremely slow. We fedexed a CD with latest Slicer code to Shanghai.

Week of 03/10:

  • Agenda:
    • Time: March 13, Thursday, 10:00 am - 12:00 noon
    • Instructors: Haiying Liu and Lixu Gu
    • Audience: Graduate students at SJTU, Shanghai, China
    • Topic: Command line module, how to add one into Slicer 3, how to write a filter inside Slicer 3.
    • Communication: Long distance phone between Boston, USA and Shanghai, China; Skype
  • Materials: How to create a command line module

Week of 03/24:

  • Agenda:
    • Time: March 27, Thursday, 10:00 am - 12:00 noon
    • Instructors: Haiying Liu and Lixu Gu
    • Audience: Graduate students at SJTU, Shanghai, China
    • Topic: Aurora connection to computer, compiling IGSTK and IGSTKSandbox, acquiring tracking data from Aurora, sending tracking data to Slicer 3, Slicer 3 display update as new data coming in.
    • Communication: Long distance phone between Boston, USA and Shanghai, China; Skype
  • Materials: Navigation with Aurora

Week of 03/31:

Progress Report


Events


04/17/2008 10am

  • TCOM
  • Topic: Ultrasound module for Slicer 3
    • 1) requirements
    • 2) components
    • 3) task breaks
    • 4) time frame
    • 5) experiments
    • 6) clinical trials
    • 7) packaging and distributions
  • People: Noby, Haiying, Benjamin, Lixu, Terry, Danielle, David

Work in progress datasets

See the link here

Useful Links


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