Difference between revisions of "4DUSandEndoscope"

From NAMIC Wiki
Jump to: navigation, search
Tag: 2017 source edit
 
(62 intermediate revisions by 3 users not shown)
Line 32: Line 32:
 
The goal of this project is to create a new 3D Slicer Module that can overlay patient registered 4D US volumes with endoscopic images.
 
The goal of this project is to create a new 3D Slicer Module that can overlay patient registered 4D US volumes with endoscopic images.
  
−
The Project is divided into four part: 4D Ultrasound, Patient-Image Registration, Endoscope Overlay, and Endoscope Calibration. All four parts will be accessable through a single 3D Slicer Module.
+
The Project is divided into four part: 4D Ultrasound Volume Reconstruction, Patient-Image Registration, Endoscope Overlay, and Endoscope Calibration. All four parts will be accessable through a single 3D Slicer Module.
 +
 
 +
[[Image:ModuleWorkflow.png | 600px ]]
  
 
=== Overall Progress ===
 
=== Overall Progress ===
Line 73: Line 75:
  
 
|height="10px" |
 
|height="10px" |
 +
|-
 +
 +
| || colspan="2" | New PC set up ||align="center" | x || Thu Jul, 30th
  
 
|-
 
|-
  
−
| || colspan="2" | ||align="center" | ||  
+
| || colspan="2" | New PC arrived ||align="center" | x || Tue Jul, 28th
  
 
|- bgcolor="#E8E8E8"
 
|- bgcolor="#E8E8E8"
Line 92: Line 97:
 
|- bgcolor="#D0D0D0"
 
|- bgcolor="#D0D0D0"
  
−
! Juli !! Week 30 || 20.07.09 - 26.07.09 || ||
+
! July !! Week 30 || 20.07.09 - 26.07.09 || ||
  
 
|-
 
|-
Line 98: Line 103:
 
|}
 
|}
  
−
=== General Tasks ===
+
=== General To Do ===
  
−
{|border="0", cellpadding="5"
+
{|border="0" cellpadding="5"
  
 
|- bgcolor="silver"
 
|- bgcolor="silver"
Line 112: Line 117:
 
|-
 
|-
  
−
| align="center" width="70px" | O || align="left" width="730px"|Order new PC
+
| align="center" width="70px" | O || align="left" width="730px"|Order new Frame Grabber Card
 +
 
 +
|-
 +
 
 +
| align="center" width="70px" bgcolor="#009900" | DONE || align="left" width="730px"|Set Up New Computer
  
 
|-
 
|-
  
−
| align="center" width="70px" | O || align="left" width="730px"|Order new Frame Grabber Card
+
| align="center" width="70px" bgcolor="#009900" | DONE || align="left" width="730px"|Order new PC
  
 
|-
 
|-
  
 
| align="center" bgcolor="#009900" | DONE || align="left" | Create Project Page
 
| align="center" bgcolor="#009900" | DONE || align="left" | Create Project Page
−
|- bgcolor="silver"
 
−
 
−
! colspan="2" | Create 3D volume with Synchrograb
 
  
 
|-
 
|-
  
 
|}
 
|}
 +
 +
=== Details ===
 +
 +
* The following frame grabber card only provides grayscale images: I-O DATA GV-VCP3R/PCI (video decoder chip CX2388x) [http://www.iodata.jp/product/tv/capture/gv-vcp3pci/index.htm]
 +
 +
 +
----
 +
----
  
 
== 3D Slicer Module ==
 
== 3D Slicer Module ==
 +
 +
 +
 
* Responsible: Jan Gumprecht
 
* Responsible: Jan Gumprecht
−
=== Technical Details ===
+
=== Details ===
 +
* The module is available through svn: http://svn.na-mic.org/NAMICSandBox/trunk/IGTLoadableModules/4DUsEndoNav/
  
 
=== Progress ===
 
=== Progress ===
Line 160: Line 178:
  
 
|height="10px" |
 
|height="10px" |
 +
 +
|-
 +
 +
| width="80px"| || colspan="2" width="550px"| Source Code checked in to svn ||align="center" width="50px" |  x || width="120px" |  Thu, Aug 6th
 +
 +
|-
 +
 +
| width="80px"| || colspan="2" width="550px"| Second Window works ||align="center" width="50px" |  x || width="120px" |  Thu, Aug 6th
  
 
|- bgcolor="#D0D0D0"
 
|- bgcolor="#D0D0D0"
Line 168: Line 194:
  
 
|height="10px" |
 
|height="10px" |
 +
 +
|-
 +
 +
| width="80px"| || colspan="2" width="550px"| Created First prototype of module ||align="center" width="50px" |  x || width="120px" |  Fri, Jul 31st
  
 
|- bgcolor="#E8E8E8"
 
|- bgcolor="#E8E8E8"
Line 176: Line 206:
  
 
|height="10px" |
 
|height="10px" |
−
 
−
|-
 
−
 
−
| width="80px"| || colspan="2" width="550px"| Create first prototype of model ||align="center" width="50px" |  x || width="120px" |  Fri, Jul 25th
 
  
 
|- bgcolor="#D0D0D0"
 
|- bgcolor="#D0D0D0"
  
−
! Juli !! Week 30 || 20.07.09 - 26.07.09 || ||
+
! July !! Week 30 || 20.07.09 - 26.07.09 || ||
  
 
|-
 
|-
Line 189: Line 215:
 
|}
 
|}
  
−
=== General Tasks ===
+
=== To Do ===
  
−
{|border="0", cellpadding="5"
+
{|border="0" cellpadding="5"
  
 
|- bgcolor="silver"
 
|- bgcolor="silver"
Line 199: Line 225:
 
|-
 
|-
  
−
| align="center" width="70px" | O || align="left"| Create first prototyp of module
+
| align="center" width="70px" | O || align="left" | Close Second window with OS native commands, i.e. click the "X" in the right upper corner
  
 
|-
 
|-
Line 207: Line 233:
 
|-
 
|-
  
−
| align="center" width="70px" | O || align="left" width="730px"| Read docu of Prostate nav module
+
| align="center" width="70px" bgcolor="#009900" | DONE || align="left" | Check in source to svn
  
−
|- bgcolor="silver"
+
|-
 +
 
 +
| align="center" width="70px" bgcolor="#009900" | DONE || align="left" | Include Second Window source code
 +
 
 +
|-
  
−
! colspan="2" | 3D Slicer module
+
| align="center" width="70px" bgcolor="#009900" | DONE || align="left"| Create first prototyp of module, i.e. adapt IGTWizard Module
  
 
|-
 
|-
Line 217: Line 247:
 
|}
 
|}
  
−
== 4D Ultrasound ==
+
 
 +
----
 +
 
 +
----
 +
 
 +
== 4D Ultrasound Volume Reconstruction==
 
* Responsible: Jan Gumprecht
 
* Responsible: Jan Gumprecht
−
=== Technical Details ===
+
=== Details ===
  
 
The project is described here: [[http://wiki.na-mic.org/Wiki/index.php/User:Gumprecht]]
 
The project is described here: [[http://wiki.na-mic.org/Wiki/index.php/User:Gumprecht]]
Line 262: Line 297:
  
 
| width="80" | || width="550" colspan="2" | Update Calibration and Spacing Handeling  || width="50" align="center" |  || width="120" |
 
| width="80" | || width="550" colspan="2" | Update Calibration and Spacing Handeling  || width="50" align="center" |  || width="120" |
 +
 +
|-
 +
 +
| width="80" | || width="550" colspan="2" | New Commandline parameter added to grab a test image  || width="50" align="center" | x || width="120" | Tue, Jul 30th
 +
 +
|-
 +
 +
| width="80" | || width="550" colspan="2" | All parameters of the calibration file are now used  || width="50" align="center" | x || width="120" | Tue, Jul 28th
 +
 +
|-
 +
 +
| width="80" | || width="550" colspan="2" | OpenIGTLink is now externally, no local copy within the source code is used anymore  || width="50" align="center" | x || width="120" | Mon, Jul 27th
  
 
|- bgcolor="#E8E8E8"
 
|- bgcolor="#E8E8E8"
Line 270: Line 317:
  
 
|height="10px" |
 
|height="10px" |
 +
|-
 +
 +
| width="80" | || width="550" colspan="2" | Show demo of the system  || width="50" align="center" |  || width="120" |
  
 
|- bgcolor="#D0D0D0"
 
|- bgcolor="#D0D0D0"
  
−
! Juli !! Week 30 || 20.07.09 - 26.07.09 || ||
+
! July !! Week 30 || 20.07.09 - 26.07.09 || ||
  
 
|-
 
|-
Line 279: Line 329:
 
|}
 
|}
  
−
=== General Tasks ===
+
=== To Do ===
  
−
{|border="0", cellpadding="5"
+
{|border="0" cellpadding="5"
  
 
|- bgcolor="silver"
 
|- bgcolor="silver"
Line 289: Line 339:
 
|-
 
|-
  
−
| align="center" width="70px" | || align="left" width="730"| Update CalibratioFileReader
+
| align="center" width="70px" s| O || align="left" width="730"| Find Segmentation Fault
  
 
|-
 
|-
  
−
| align="center" width="70px" | || align="left" width="730"| Update Handling of Spacing
+
| align="center" width="70px" | O || align="left" width="730"| Update Handling of Spacing
  
 
|-
 
|-
  
−
| align="center" width="70px" | || align="left" width="730"| Update Calibration Part
+
| align="center" width="70px" | O || align="left" width="730"| Update Calibration Part
  
−
|- bgcolor="silver"
+
|-
 +
 
 +
| align="center" width="70px" bgcolor="#009900" | DONE || align="left" width="730"| Set up existing Hardware for first demo
 +
 
 +
|-
  
−
! colspan="2" | 4D Ultrasound
+
| align="center" width="70px" bgcolor="#009900" | DONE || align="left" width="730"| Update CalibrationFileReader
  
 
|-
 
|-
  
 
|}
 
|}
 +
 +
 +
 +
----
 +
 +
----
  
 
== Patient-Image Registration ==
 
== Patient-Image Registration ==
 
* Responsible: Jae-Sung Hong
 
* Responsible: Jae-Sung Hong
  
−
=== Technical Details ===
+
=== Details ===
  
 
=== Progress ===
 
=== Progress ===
Line 363: Line 423:
 
|- bgcolor="#D0D0D0"
 
|- bgcolor="#D0D0D0"
  
−
! Juli !! Week 30 || 20.07.09 - 26.07.09 || ||
+
! July !! Week 30 || 20.07.09 - 26.07.09 || ||
  
 
|-
 
|-
Line 369: Line 429:
 
|}
 
|}
  
−
=== General Tasks ===
+
=== To Do ===
  
−
{|border="0", cellpadding="5"
+
{|border="0" cellpadding="5"
  
 
|- bgcolor="silver"
 
|- bgcolor="silver"
Line 379: Line 439:
 
|-
 
|-
  
−
| align="center" width="70px" | || align="left" width="730"|Sample Task
+
| align="center" width="70px" | O || align="left" width="730"|Dummy Task
 +
 
 +
|-
 +
 
 +
|}
  
−
|- bgcolor="silver"
 
  
−
! colspan="2" | Patient-Image registration
 
  
−
|-
+
----
  
−
|}
+
----
  
 
== Endoscope Overlay ==
 
== Endoscope Overlay ==
−
* Responsible: Yaamada Atsushi, Haiying Liu
+
* Responsible: Yamada Atsushi, Haiying Liu
−
=== Technical Details ===
+
=== Details ===
 +
* [http://www.na-mic.org/Wiki/index.php/OpenCV_Module_in_Slicer3 OpenCV Module in Slicer3]
 +
* [http://www.na-mic.org/Wiki/index.php/Slicer3_FlexibleLayouts Multiple Camera Support in Slicer3]
 +
* [http://wiki.ncigt.org/index.php/U41:Prostate:BRP:Common_Module_For_Multiple_Robots Transrectal/Transperineal biopsy robot module merge]
 +
* [http://opencv.willowgarage.com/wiki/ Open CV Wiki]
 +
* [http://wiki.intelli-si.org/index.php?title=2009SummerSecondDisplayProject Summer Second Display Project] (Japanese)
 +
 
 +
=== Bug Fixes for the 3D Slicer Module ===
 +
 
 +
* There is a bug in OpenCV related to V4L2 devices:
 +
** Here is the bugtrac with information: [[https://bugs.launchpad.net/ubuntu/+source/linux/+bug/260251]]
 +
*** Somehow this is related to bttv 878 cards. OpenCV seem not to be able to handle all output of the card correctly
 +
** Here is the fix [[http://opencvlibrary.svn.sourceforge.net/viewvc/opencvlibrary/trunk/opencv/src/highgui/cvcap_v4l.cpp?r1=1604&r2=1609]]
 +
*** Apply the changes of revision 1609 to the file # opencv/src/highgui/cvcap_v4l.cpp
  
 
=== Progress ===
 
=== Progress ===
Line 423: Line 498:
 
|-
 
|-
  
−
| width="80" || width="550" colspan="2" |  Endoscopic Overlay shall be finished  ||align="center" width="50" |  || width="120" |
+
| width="80" | || width="550" colspan="2" |  Endoscopic Overlay shall be finished  ||align="center" width="50" |  || width="120" |
  
 
|- bgcolor="#D0D0D0"
 
|- bgcolor="#D0D0D0"
Line 447: Line 522:
 
|- bgcolor="#D0D0D0"
 
|- bgcolor="#D0D0D0"
  
−
! Juli !! Week 30 || 20.07.09 - 26.07.09 || ||
+
! July !! Week 30 || 20.07.09 - 26.07.09 || ||
  
 
|-
 
|-
Line 453: Line 528:
 
|}
 
|}
  
−
=== General Tasks ===
+
=== To Do ===
  
−
{|border="0", cellpadding="5"
+
{|border="0" cellpadding="5"
  
 
|- bgcolor="silver"
 
|- bgcolor="silver"
Line 463: Line 538:
 
|-
 
|-
  
−
| align="center" width="70px" | || align="left" width="730"|Sample Task
+
| align="center" width="70px" | O || align="left" width="730"|Dummy Task
  
 
|- bgcolor="silver"
 
|- bgcolor="silver"
Line 471: Line 546:
  
 
|}
 
|}
 +
 +
 +
 +
----
 +
 +
----
  
 
== Endoscope Calibration ==
 
== Endoscope Calibration ==
 
* Responsible: Dr. Yang
 
* Responsible: Dr. Yang
−
=== Technical Details ===
+
=== Details ===
  
 
=== Progress ===
 
=== Progress ===
Line 530: Line 611:
 
|- bgcolor="#D0D0D0"
 
|- bgcolor="#D0D0D0"
  
−
! Juli !! Week 30 || 20.07.09 - 26.07.09 || ||
+
! July !! Week 30 || 20.07.09 - 26.07.09 || ||
  
 
|-
 
|-
Line 536: Line 617:
 
|}
 
|}
  
−
=== General Tasks ===
+
=== To Do ===
  
−
{|border="0", cellpadding="5"
+
{|border="0" cellpadding="5"
  
 
|- bgcolor="silver"
 
|- bgcolor="silver"
Line 546: Line 627:
 
|-
 
|-
  
−
| align="center" width="70px" | || align="left" width="730"| Sample Task
+
| align="center" width="70px" | O || align="left" width="730"| Dummy Task
−
 
 
−
|-
 
−
 
 
−
|- bgcolor="silver"
 
−
 
 
−
! colspan="2" | Create 3D volume with Synchrograb
 
  
 
|-
 
|-
  
 
|}
 
|}

Latest revision as of 05:23, 11 April 2023

Home < 4DUSandEndoscope

Project Page for 4D Ultrasound with Endoscopic Overlay

Collaborators

Jan Gumprecht

  • E-Mail: jgumprec(at)bwh.harvard.edu
  • Location: Kyushu, Japan
  • Timezone: GMT + 9

Jae-Sung Hung, PhD

  • E-Mail: hong(at)dem.med.kyushu-u.ac.jp
  • Location: Kyushu, Japan
  • Timezone: GMT + 9

Nobuhiko Hata, PhD

  • E-Mail: hata(at)bwh.harvard.edu
  • Location: Boston, USA
  • Timezone: GMT - 5

Haiying Liu

  • E-Mail: hliu(at)bwh.harvard.edu
  • Location: Boston, USA
  • Timezone: GMT - 5

Yamada Atsushi, PhD

  • E-Mail: yamada.atsushi(at)nitech.ac.jp
  • Location: Nagoya, Japan
  • Timezone: GMT + 9

Project Description

The goal of this project is to create a new 3D Slicer Module that can overlay patient registered 4D US volumes with endoscopic images.

The Project is divided into four part: 4D Ultrasound Volume Reconstruction, Patient-Image Registration, Endoscope Overlay, and Endoscope Calibration. All four parts will be accessable through a single 3D Slicer Module.

ModuleWorkflow.png

Overall Progress

Month Week # Start Date - End Date Done Date Done
Week 34 17.08 - 23.08
Week 33 10.08 - 16.08
Endoscopic Overlay and Endoscopic Calibration shall be finished
August Week 32 03.08.09 - 09.08.09
New PC set up x Thu Jul, 30th
New PC arrived x Tue Jul, 28th
Week 31 27.07 - 02.08
Project Page created x Fri Jul, 24th
July Week 30 20.07.09 - 26.07.09

General To Do

Tasks
O Fill Project Page with Information
O Order new Frame Grabber Card
DONE Set Up New Computer
DONE Order new PC
DONE Create Project Page

Details

  • The following frame grabber card only provides grayscale images: I-O DATA GV-VCP3R/PCI (video decoder chip CX2388x) [1]


3D Slicer Module

  • Responsible: Jan Gumprecht

Details

Progress

Month Week # Start Date - End Date Done Date Done
Week 34 17.08 - 23.08
Week 33 10.08 - 16.08
Source Code checked in to svn x Thu, Aug 6th
Second Window works x Thu, Aug 6th
August Week 32 03.08.09 - 09.08.09
Created First prototype of module x Fri, Jul 31st
Week 31 27.07 - 02.08
July Week 30 20.07.09 - 26.07.09

To Do

Tasks
O Close Second window with OS native commands, i.e. click the "X" in the right upper corner
O Comprehend Prostate nav module's source code
DONE Check in source to svn
DONE Include Second Window source code
DONE Create first prototyp of module, i.e. adapt IGTWizard Module


4D Ultrasound Volume Reconstruction

  • Responsible: Jan Gumprecht

Details

The project is described here: [[2]]

Progress

Month Week # Start Date - End Date Done Date Done
Week 34 17.08 - 23.08
Week 33 10.08 - 16.08
August Week 32 03.08.09 - 09.08.09
Update Calibration and Spacing Handeling
New Commandline parameter added to grab a test image x Tue, Jul 30th
All parameters of the calibration file are now used x Tue, Jul 28th
OpenIGTLink is now externally, no local copy within the source code is used anymore x Mon, Jul 27th
Week 31 27.07 - 02.08
Show demo of the system
July Week 30 20.07.09 - 26.07.09

To Do

Tasks
O Find Segmentation Fault
O Update Handling of Spacing
O Update Calibration Part
DONE Set up existing Hardware for first demo
DONE Update CalibrationFileReader


Patient-Image Registration

  • Responsible: Jae-Sung Hong

Details

Progress

Month Week # Start Date - End Date Done Date Done
Week 34 17.08 - 23.08
Week 33 10.08 - 16.08
August Week 32 03.08.09 - 09.08.09
Start integration with 4D Ultrasound
Week 31 27.07 - 02.08


July Week 30 20.07.09 - 26.07.09

To Do

Tasks
O Dummy Task


Endoscope Overlay

  • Responsible: Yamada Atsushi, Haiying Liu

Details

Bug Fixes for the 3D Slicer Module

  • There is a bug in OpenCV related to V4L2 devices:
    • Here is the bugtrac with information: [[3]]
      • Somehow this is related to bttv 878 cards. OpenCV seem not to be able to handle all output of the card correctly
    • Here is the fix [[4]]
      • Apply the changes of revision 1609 to the file # opencv/src/highgui/cvcap_v4l.cpp

Progress

Month Week # Start Date - End Date Done Date Done
Week 34 17.08 - 23.08
Week 33 10.08 - 16.08
Endoscopic Overlay shall be finished
August Week 32 03.08.09 - 09.08.09
Week 31 27.07 - 02.08
July Week 30 20.07.09 - 26.07.09

To Do

Tasks
O Dummy Task
Endoscope overlay


Endoscope Calibration

  • Responsible: Dr. Yang

Details

Progress

Month Week # Start Date - End Date Done Date Done
Week 34 17.08 - 23.08
Week 33 10.08 - 16.08
Endoscopic Calibration shall be finished
August Week 32 03.08.09 - 09.08.09
Week 31 27.07 - 02.08
July Week 30 20.07.09 - 26.07.09

To Do

Tasks
O Dummy Task
Retrieved from "https://www.na-mic.org/w/index.php?title=4DUSandEndoscope&oldid=98832"