Documentation/4.2/Extensions/iGyne - Revision history

UpdateBot: Prepend documentation/versioncheck template. See http://na-mic.org/Mantis/view.php?id=2887

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Prepend documentation/versioncheck template. See http://na-mic.org/Mantis/view.php?id=2887

Gpernelle at 19:49, 21 November 2012

2012-11-21T19:49:46Z

Gpernelle at 19:45, 21 November 2012

2012-11-21T19:45:10Z

Gpernelle at 17:07, 21 November 2012

2012-11-21T17:07:33Z

Gpernelle at 17:05, 21 November 2012

2012-11-21T17:05:15Z

Gpernelle at 17:03, 21 November 2012

2012-11-21T17:03:40Z

Gpernelle at 16:21, 21 November 2012

2012-11-21T16:21:27Z

Gpernelle at 15:56, 21 November 2012

2012-11-21T15:56:32Z

UpdateBot: Nightly -> 4.2

2012-10-31T21:57:59Z

Nightly -> 4.2

New page

{{documentation/{{documentation/version}}/module-header}}



{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
Author: Xiaojun Chen<br>
Contributors: iGyne Team (url coming)<br>
Contact: Xiaojun Chen, <email>xiaojun@bwh.harvard.edu</email><br>
Website: https://github.com/xjchen/igyne<br>
License: [http://www.slicer.org/pages/LicenseText Slicer license]


{{documentation/{{documentation/version}}/extension-section|Extension Description}}
iGyne is an open source software for MR-Guided Interstitial Gynecologic Brachytherapy. It enables on-time processing of the intra-operative MRI data via a DICOM connection to the scanner followed by a multi-stage registration of CAD models of the template and the obturator to the patient images. This allows the virtual placement of interstitial needles during the intervention. Software features include:

*Loading of Applicator CAD models and MR images
*Initial registration of CAD model of the Template to MR images
*Registration Refinement
*Visualization of Registration
*Needle Selection and Display of Virtual Needles relative to Applicator CAD models and Tumor Segmentation


{{documentation/{{documentation/version}}/extension-section|Modules}}


{{documentation/{{documentation/version}}/extension-section|Use Cases}}
[https://github.com/xjchen/igyne/tree/master/Sample%20data Sample data] and
[https://github.com/xjchen/igyne/tree/master/scene%20for%20template%20and%20obturator CAD models] to use with modules.
<gallery widths="200px" perrow="4">
Image:IGyne 1.0-registration.png|Screenshot of Registration
Image:IGyne 1.0 needle visualization.png|Screenshot of Needle Visualization
Image:Igyne 1.0-Tumor and Needle Visualization.png|Screenshot of Tumor and Needle Visualization
</gallery>


{{documentation/{{documentation/version}}/extension-section|Tutorials}}
[[media:IGyne1.0_Tutorial.ppt | Igyne Tutorial]] (a .PPT file with 18 pages) will guide you step-by-step through the process of loading of applicator CAD models, performing registration, selecting virtual needle and viewing the results within Slicer4. It will take about 10 minutes to finish this tutorial.



{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}
N/A


{{documentation/{{documentation/version}}/extension-section|References}}
* http://www.na-mic.org/Wiki/index.php/2012_Summer_Project_Week:iGyne
* Xiaojun Chen, Jan Egger, Akila Viswanathan, Neha Agrawal, William Wells, Ron Kikinis, Clare Tempany, Ferenc Jolesz and Tina Kapur. "Image Processing for MR-guided Gynecologic Interstitial Brachytherapy in AMIGO", The 9th Interventional MRI Symposium. September 22-23, 2012.


{{documentation/{{documentation/version}}/extension-section|Information for Developers}}
{{documentation/{{documentation/version}}/extension-developerinfo}}


{{documentation/{{documentation/version}}/extension-footer}}

← Older revision		Revision as of 07:44, 14 June 2013
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 {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
-Authors: Guillaume Pernelle, Xiaojun Chen<br>
+Authors: Guillaume Pernelle, Xiaojun Chen, Yi Gao<br>
 Contributors: iGyne Team<br>
 Contact: Guillaume Pernelle, <email>gpernelle@gmail.com</email><br>

@@ Line 58: / Line 58: @@
 * Xiaojun Chen, Jan Egger, Akila Viswanathan, Neha Agrawal, William Wells, Ron Kikinis, Clare Tempany, Ferenc Jolesz and Tina Kapur.  "Image Processing for MR-guided Gynecologic Interstitial Brachytherapy in AMIGO", The 9th Interventional MRI Symposium. September 22-23, 2012.
 * Gao, Farhat, Pernelle et al. "Needle Labeling for Interstitial Gynecological Brachytherapy". Fifth National Image Guided Therapy Workshop, Sept 21, 2012
 * Pernelle. "Needle labeling for Image-Guided Brachytherapy", Masters thesis (in preparation). Technical University Munich and Ecole Centrale Marseille, Dec 14, 2012

@@ Line 10: / Line 10: @@
 Website: https://github.com/gpernelle/iGynePy<br>
 License: [http://www.slicer.org/pages/LicenseText Slicer license]
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/extension-section|Extension Description}}
-iGyne is an open source software for MR-Guided Interstitial Gynecologic Brachytherapy. It enables on-time processing of the intra-operative MRI data via a DICOM connection to the scanner followed by a multi-stage registration of CAD models of the template and the obturator to the patient images. This allows the virtual placement of interstitial needles during the intervention. Software features include:
+iGyne is an open source software for MR-Guided Interstitial Gynecologic Brachytherapy. It enables on-time processing of the intra-operative MRI data via a DICOM connection to the scanner followed by a multi-stage registration of CAD models of the template and the obturator to the patient images. This allows the virtual placement of interstitial needles during the intervention, as well as needle detection and needle labeling.
-*Loading of Applicator CAD models and MR images
+iGyne is currently articulated in seven steps:
-*Initial registration of CAD model of the Template to MR images
+) procedure selection
-*Registration Refinement
+) applicator selection
-*Visualization of Registration
+) data importation
-*Needle Selection and Display of Virtual Needles relative to Applicator CAD models and Tumor Segmentation
+) initial applicator registration
 <!-- ---------------------------- -->
@@ Line 56: / Line 57: @@
 * http://www.na-mic.org/Wiki/index.php/2012_Summer_Project_Week:iGyne
 * Xiaojun Chen, Jan Egger, Akila Viswanathan, Neha Agrawal, William Wells, Ron Kikinis, Clare Tempany, Ferenc Jolesz and Tina Kapur.  "Image Processing for MR-guided Gynecologic Interstitial Brachytherapy in AMIGO", The 9th Interventional MRI Symposium. September 22-23, 2012.
+* Gao, Farhat, Pernelle et al. "Needle Labeling for Interstitial Gynecological Brachytherapy". Fifth National Image Guided Therapy Workshop, Sept 21, 2012
 <!-- ---------------------------- -->
@@ Line 85: / Line 87: @@
 - iGyneNeedleSegmentationStep.py (7) is the "keystone" of iGyne. Start by clicking on "Start Giving Needle Tips" and at each click in the 2D axial viewer, a needle will be segmented. You can display, delete the needles individually or all together. You can also differentiate the different insertion steps and separate each group of needles. A table shows some parameters of the caculated needles. If a registration has been done previously, it will assign to each needle the most probable label. It is also possible to tweak the needle segmentation parameters.
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/extension-footer}}
 <!-- ---------------------------- -->

@@ Line 33: / Line 33: @@
 <gallery widths="200px" perrow="4">
 Image:IGyne-beforeFirstRegsitration.png|Data loaded
-Image:IGyne 1.0 needle visualization.png|Screenshot of Needle Visualization
+Image:IGyne-BeforeRefinedRegistration.png|After the initial registration
-Image:Igyne 1.0-Tumor and Needle Visualization.png|Screenshot of Tumor and Needle Visualization
+Image:IGyne-applicatorSegmentation.png|Applicator Segmentation
 </gallery>
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/extension-section|Tutorials}}
-[[media:IGyne1.0_Tutorial.ppt | Igyne Tutorial]] (a .PPT file with 18 pages) will guide you step-by-step through the process of loading of applicator CAD models, performing registration, selecting virtual needle and viewing the results within Slicer4. It will take about 10 minutes to finish this tutorial.
+A video tutorial should be soon available
 <!--<gallery widths="200px" perrow="4">
 </gallery>-->
@@ Line 51: / Line 56: @@
 * http://www.na-mic.org/Wiki/index.php/2012_Summer_Project_Week:iGyne
 * Xiaojun Chen, Jan Egger, Akila Viswanathan, Neha Agrawal, William Wells, Ron Kikinis, Clare Tempany, Ferenc Jolesz and Tina Kapur.  "Image Processing for MR-guided Gynecologic Interstitial Brachytherapy in AMIGO", The 9th Interventional MRI Symposium. September 22-23, 2012.
-* Gao, Farhat, Pernelle et al. "Needle Labeling for Interstitial Gynecological Brachytherapy". Fifth National Image Guided Therapy Workshop, Sept 21, 2012
 <!-- ---------------------------- -->
@@ Line 81: / Line 85: @@
 - iGyneNeedleSegmentationStep.py (7) is the "keystone" of iGyne. Start by clicking on "Start Giving Needle Tips" and at each click in the 2D axial viewer, a needle will be segmented. You can display, delete the needles individually or all together. You can also differentiate the different insertion steps and separate each group of needles. A table shows some parameters of the caculated needles. If a registration has been done previously, it will assign to each needle the most probable label. It is also possible to tweak the needle segmentation parameters.
+{{documentation/{{documentation/version}}/extension-developerinfo}}
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/extension-footer}}
 <!-- ---------------------------- -->

@@ Line 5: / Line 5: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
-Author: Xiaojun Chen<br>
+Authors: Guillaume Pernelle, Xiaojun Chen<br>
-Contributors: iGyne Team (url coming)<br>
+Contributors: iGyne Team<br>
-Contact: Xiaojun Chen, <email>xiaojun@bwh.harvard.edu</email><br>
+Contact: Guillaume Pernelle, <email>gpernelle@gmail.com</email><br>
-Website: https://github.com/xjchen/igyne<br>
+Website: https://github.com/gpernelle/iGynePy<br>
 License: [http://www.slicer.org/pages/LicenseText Slicer license]
@@ Line 28: / Line 28: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/extension-section|Use Cases}}
-[https://github.com/xjchen/igyne/tree/master/Sample%20data Sample data] and
+[http://slicer.kitware.com/midas3/folder/876 Phantom Study] and
-[https://github.com/xjchen/igyne/tree/master/scene%20for%20template%20and%20obturator CAD models] to use with modules.
+[https://github.com/xjchen/igyne/tree/master/Sample%20data Sample data]
 <gallery widths="200px" perrow="4">
 Image:IGyne 1.0-registration.png|Screenshot of Registration
@@ Line 54: / Line 55: @@
 <!-- ---------------------------- -->
 {{documentation/{{documentation/version}}/extension-section|Information for Developers}}
 {{documentation/{{documentation/version}}/extension-developerinfo}}