https://www.slicer.org/w/api.php?action=feedcontributions&user=Gpernelle&feedformat=atomSlicer Wiki - User contributions [en]2024-03-29T09:35:10ZUser contributionsMediaWiki 1.33.0https://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/NeedleFinder&diff=37724Documentation/Nightly/Extensions/NeedleFinder2014-04-28T18:33:15Z<p>Gpernelle: </p>
<hr />
<div>NeedleFinder documentation TBD<br />
<br />
<noinclude>{{documentation/versioncheck}}</noinclude><br />
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{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
NeedleFinder: fast interactive needle detection.It provides interactive tools to segment needles in MR/CT images. It has been mostly tested on MRI from gynelogical brachytherapy cases. [6]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
Authors: Guillaume Pernelle<br><br />
Contact: Guillaume Pernelle, <email>gpernelle@gmail.com</email><br><br />
Website: https://github.com/gpernelle/NeedleFinder<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
NeedleFinder: fast interactive needle detection.It provides interactive tools to segment needles in MR/CT images. It has been mostly tested on MRI from gynelogical brachytherapy cases. <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<br />
[http://slicer.kitware.com/midas3/folder/876 Phantom Study] and<br />
[https://github.com/xjchen/igyne/tree/master/Sample%20data Sample data]<br />
<br />
<gallery widths="200px" perrow="4"><br />
Image:IGyne-needleSegmentation.png|Real needles segmentation<br />
<br />
</gallery><br />
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{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
N/A<br />
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{{documentation/{{documentation/version}}/extension-section|References}}<br />
[1] http://www.na-mic.org/Wiki/index.php/2012_Summer_Project_Week:iGyne <br />
<br />
[2] 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.<br />
<br />
[3] Gao, Farhat, Pernelle et al. "Needle Labeling for Interstitial Gynecological Brachytherapy". Fifth National Image Guided Therapy Workshop, Sept 21, 2012<br />
<br />
[4] Pernelle, Egger, Vale, Chen, Irlinger, Lueth, Wells, Kikinis, Viswanathan and Kapur. Robust Applicator Registration for Interstitial Gynecologic Brachytherapy. ABS 2013 Annual Meeting<br />
<br />
[5] Pernelle. "Needle labeling for Image-Guided Brachytherapy", Masters thesis (in preparation). Technical University Munich and Ecole Centrale Marseille, Dec 14, 2012<br />
<br />
[6] Pernelle, Guillaume, et al. "Validation of Catheter Segmentation for MR-Guided Gynecologic Cancer Brachytherapy." Medical Image Computing and Computer-Assisted Intervention–MICCAI 2013. Springer Berlin Heidelberg, 2013. 380-387.<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
<br />
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.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Gpernellehttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/NeedleFinder&diff=37723Documentation/Nightly/Extensions/NeedleFinder2014-04-28T18:32:33Z<p>Gpernelle: Created page with 'NeedleFinder documentation TBD <noinclude>{{documentation/versioncheck}}</noinclude> <!-- ---------------------------- --> {{documentation/{{documentation/version}}/module-heade…'</p>
<hr />
<div>NeedleFinder documentation TBD<br />
<br />
<noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
NeedleFinder: fast interactive needle detection.It provides interactive tools to segment needles in MR/CT images. It has been mostly tested on MRI from gynelogical brachytherapy cases. [6]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
Authors: Guillaume Pernelle<br><br />
Contact: Guillaume Pernelle, <email>gpernelle@gmail.com</email><br><br />
Website: https://github.com/gpernelle/NeedleFinder<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
NeedleFinder: fast interactive needle detection.It provides interactive tools to segment needles in MR/CT images. It has been mostly tested on MRI from gynelogical brachytherapy cases. <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<br />
[http://slicer.kitware.com/midas3/folder/876 Phantom Study] and<br />
[https://github.com/xjchen/igyne/tree/master/Sample%20data Sample data]<br />
<br />
<gallery widths="200px" perrow="4"><br />
Image:IGyne-needleSegmentation.png|Real needles segmentation<br />
<br />
</gallery><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|References}}<br />
[1] http://www.na-mic.org/Wiki/index.php/2012_Summer_Project_Week:iGyne <br />
[2] 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.<br />
[3] Gao, Farhat, Pernelle et al. "Needle Labeling for Interstitial Gynecological Brachytherapy". Fifth National Image Guided Therapy Workshop, Sept 21, 2012<br />
[4] Pernelle, Egger, Vale, Chen, Irlinger, Lueth, Wells, Kikinis, Viswanathan and Kapur. Robust Applicator Registration for Interstitial Gynecologic Brachytherapy. ABS 2013 Annual Meeting<br />
[5] Pernelle. "Needle labeling for Image-Guided Brachytherapy", Masters thesis (in preparation). Technical University Munich and Ecole Centrale Marseille, Dec 14, 2012<br />
[6] Pernelle, Guillaume, et al. "Validation of Catheter Segmentation for MR-Guided Gynecologic Cancer Brachytherapy." Medical Image Computing and Computer-Assisted Intervention–MICCAI 2013. Springer Berlin Heidelberg, 2013. 380-387.<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
<br />
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.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Gpernellehttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/iGyne&diff=37722Documentation/Nightly/Extensions/iGyne2014-04-28T18:32:09Z<p>Gpernelle: </p>
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<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
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{{documentation/{{documentation/version}}/module-header}}<br />
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<br />
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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
Authors: Guillaume Pernelle, Xiaojun Chen, Yi Gao, Jan Egger<br><br />
Contributors: iGyne Team<br><br />
Contact: Guillaume Pernelle, <email>gpernelle@gmail.com</email><br><br />
Website: https://github.com/gpernelle/iGyne<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br><br />
Related Master's Thesis: [http://www.ncigt.org/publications/item/view/2316 Labeled Needle Rendering Solution for Image Guided Brachytherapy]<br />
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{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
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. <br />
<br />
iGyne is currently articulated in seven steps: <br />
1) procedure selection<br />
2) applicator selection<br />
3) data importation<br />
4) initial applicator registration<br />
5) refined applicator registration<br />
6) needle position planning<br />
7) needle detection<br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<br />
[http://slicer.kitware.com/midas3/folder/876 Phantom Study] and<br />
[https://github.com/xjchen/igyne/tree/master/Sample%20data Sample data]<br />
<br />
<gallery widths="200px" perrow="4"><br />
Image:IGyne-beforeFirstRegsitration.png|Data loaded<br />
Image:IGyne-BeforeRefinedRegistration.png|After the initial registration<br />
Image:IGyne-applicatorSegmentation.png|Applicator Segmentation<br />
Image:IGyne-registrationResult.png|Registration results<br />
Image:IGyne-needlePlanning.png|Planning with virtual needles<br />
Image:IGyne-needleSegmentation.png|Real needles segmentation<br />
Image:IGyne-labelingResult.png|Labeling result on the planning sheet<br />
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</gallery><br />
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<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|References}}<br />
* http://www.na-mic.org/Wiki/index.php/2012_Summer_Project_Week:iGyne <br />
* 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.<br />
* Gao, Farhat, Pernelle et al. "Needle Labeling for Interstitial Gynecological Brachytherapy". Fifth National Image Guided Therapy Workshop, Sept 21, 2012<br />
* Pernelle, Egger, Vale, Chen, Irlinger, Lueth, Wells, Kikinis, Viswanathan and Kapur. Robust Applicator Registration for Interstitial Gynecologic Brachytherapy. ABS 2013 Annual Meeting<br />
* Pernelle. "Needle labeling for Image-Guided Brachytherapy", Masters thesis (in preparation). Technical University Munich and Ecole Centrale Marseille, Dec 14, 2012<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
iGyne is currently articulated in seven steps: <br />
1) procedure selection<br />
2) applicator selection<br />
3) data importation<br />
4) initial applicator registration<br />
5) refined applicator registration<br />
6) needle position planning<br />
7) needle detection<br />
It offers also a way to go directly from 1) to 7), skipping the registration/planning steps<br />
<br />
- iGyneSelectProcedureStep.py (1) and iGyneSelectApplicatorStep.py (2) let you choose to use or not an applicator, and to select the most convenient one. There are different configurations for the fiducial markers: <br />
* 4 landmarks, ordered from the top left corner and counting counter-clockwise (new cases)<br />
* 3 landmarks, positioned at the corners of the template, ordered as above<br />
* 3 landmarks, starting from the one in the middle of the template and counting counter-clockwise<br />
This step offers an automatic registration option if the CLI module Hough Transformed has been previously enabled<br />
<br />
- iGyneLoadModelStep.py (3) let you load the data while the scene is loaded depending on the made in step 2.<br />
<br />
- iGyneFirstRegistrationStep.py (4) is the initial registration step. Depending on the choice you made on the previous step, you can click on the bright markers in the image or let the automatic registration find them for you (requires the CLI module called Hough Transform). <br />
<br />
- iGyneSecondRegistrationStep.py (5) is the refined applicator registration step. It offers fully automated computation to complete manual parameterization if needed. Thus, several segmentation methods are available to segment the obturator, and the registration parameters can be tweaked. By default, the most efficient parameters are chosen and all steps of the refined registration are computed successively. Evaluation functions have also been integrated to allow developers to measure time and accuracy of the chosen methods and parameters. Beside the control interface, 2D views display cross sections of the applicator in axial, sagital and coronal planes giving the user a visual characterization of the registration state.<br />
<br />
- iGyneNeedlePlanningStep.py (6) let you insert "virtual needles" and visualize their trajectory in the 2D/3D viewer. You can tweak the color and the length of the needles.<br />
<br />
- 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.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Gpernellehttps://www.slicer.org/w/index.php?title=Documentation/4.3/Extensions/NeedleFinder&diff=37721Documentation/4.3/Extensions/NeedleFinder2014-04-28T18:23:52Z<p>Gpernelle: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
NeedleFinder: fast interactive needle detection.It provides interactive tools to segment needles in MR/CT images. It has been mostly tested on MRI from gynelogical brachytherapy cases. [6]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
Authors: Guillaume Pernelle<br><br />
Contact: Guillaume Pernelle, <email>gpernelle@gmail.com</email><br><br />
Website: https://github.com/gpernelle/NeedleFinder<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
NeedleFinder: fast interactive needle detection.It provides interactive tools to segment needles in MR/CT images. It has been mostly tested on MRI from gynelogical brachytherapy cases. <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<br />
[http://slicer.kitware.com/midas3/folder/876 Phantom Study] and<br />
[https://github.com/xjchen/igyne/tree/master/Sample%20data Sample data]<br />
<br />
<gallery widths="200px" perrow="4"><br />
Image:IGyne-needleSegmentation.png|Real needles segmentation<br />
<br />
</gallery><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|References}}<br />
[1] http://www.na-mic.org/Wiki/index.php/2012_Summer_Project_Week:iGyne<br />
<br />
[2] 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.<br />
<br />
[3] Gao, Farhat, Pernelle et al. "Needle Labeling for Interstitial Gynecological Brachytherapy". Fifth National Image Guided Therapy Workshop, Sept 21, 2012<br />
<br />
[4] Pernelle, Egger, Vale, Chen, Irlinger, Lueth, Wells, Kikinis, Viswanathan and Kapur. Robust Applicator Registration for Interstitial Gynecologic Brachytherapy. ABS 2013 Annual Meeting<br />
<br />
[5] Pernelle. "Needle labeling for Image-Guided Brachytherapy", Masters thesis (in preparation). Technical University Munich and Ecole Centrale Marseille, Dec 14, 2012<br />
<br />
[6] Pernelle, Guillaume, et al. "Validation of Catheter Segmentation for MR-Guided Gynecologic Cancer Brachytherapy." Medical Image Computing and Computer-Assisted Intervention–MICCAI 2013. Springer Berlin Heidelberg, 2013. 380-387.<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
<br />
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.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Gpernellehttps://www.slicer.org/w/index.php?title=Documentation/4.3/Extensions/NeedleFinder&diff=37720Documentation/4.3/Extensions/NeedleFinder2014-04-28T18:23:07Z<p>Gpernelle: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
NeedleFinder: fast interactive needle detection.It provides interactive tools to segment needles in MR/CT images. It has been mostly tested on MRI from gynelogical brachytherapy cases. [6]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
Authors: Guillaume Pernelle<br><br />
Contact: Guillaume Pernelle, <email>gpernelle@gmail.com</email><br><br />
Website: https://github.com/gpernelle/NeedleFinder<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
NeedleFinder: fast interactive needle detection.It provides interactive tools to segment needles in MR/CT images. It has been mostly tested on MRI from gynelogical brachytherapy cases. <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<br />
[http://slicer.kitware.com/midas3/folder/876 Phantom Study] and<br />
[https://github.com/xjchen/igyne/tree/master/Sample%20data Sample data]<br />
<br />
<gallery widths="200px" perrow="4"><br />
Image:IGyne-needleSegmentation.png|Real needles segmentation<br />
<br />
</gallery><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|References}}<br />
[1] http://www.na-mic.org/Wiki/index.php/2012_Summer_Project_Week:iGyne<br />
<br />
[2] 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.<br />
<br />
[3] Gao, Farhat, Pernelle et al. "Needle Labeling for Interstitial Gynecological Brachytherapy". Fifth National Image Guided Therapy Workshop, Sept 21, 2012<br />
<br />
[4] Pernelle, Egger, Vale, Chen, Irlinger, Lueth, Wells, Kikinis, Viswanathan and Kapur. Robust Applicator Registration for Interstitial Gynecologic Brachytherapy. ABS 2013 Annual Meeting<br />
<br />
[5] Pernelle. "Needle labeling for Image-Guided Brachytherapy", Masters thesis (in preparation). Technical University Munich and Ecole Centrale Marseille, Dec 14, 2012<br />
<br />
[6] Pernelle, Guillaume, et al. "Validation of Catheter Segmentation for MR-Guided Gynecologic Cancer Brachytherapy." Medical Image Computing and Computer-Assisted Intervention–MICCAI 2013. Springer Berlin Heidelberg, 2013. 380-387.<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
<br />
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.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Gpernellehttps://www.slicer.org/w/index.php?title=Documentation/4.3/Extensions/NeedleFinder&diff=37719Documentation/4.3/Extensions/NeedleFinder2014-04-28T18:22:07Z<p>Gpernelle: </p>
<hr />
<div><noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
NeedleFinder: fast interactive needle detection.It provides interactive tools to segment needles in MR/CT images. It has been mostly tested on MRI from gynelogical brachytherapy cases. [6]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
Authors: Guillaume Pernelle<br><br />
Contact: Guillaume Pernelle, <email>gpernelle@gmail.com</email><br><br />
Website: https://github.com/gpernelle/NeedleFinder<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
NeedleFinder: fast interactive needle detection.It provides interactive tools to segment needles in MR/CT images. It has been mostly tested on MRI from gynelogical brachytherapy cases. <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<br />
[http://slicer.kitware.com/midas3/folder/876 Phantom Study] and<br />
[https://github.com/xjchen/igyne/tree/master/Sample%20data Sample data]<br />
<br />
<gallery widths="200px" perrow="4"><br />
Image:IGyne-needleSegmentation.png|Real needles segmentation<br />
<br />
</gallery><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|References}}<br />
[1] http://www.na-mic.org/Wiki/index.php/2012_Summer_Project_Week:iGyne <br />
[2] 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.<br />
[3] Gao, Farhat, Pernelle et al. "Needle Labeling for Interstitial Gynecological Brachytherapy". Fifth National Image Guided Therapy Workshop, Sept 21, 2012<br />
[4] Pernelle, Egger, Vale, Chen, Irlinger, Lueth, Wells, Kikinis, Viswanathan and Kapur. Robust Applicator Registration for Interstitial Gynecologic Brachytherapy. ABS 2013 Annual Meeting<br />
[5] Pernelle. "Needle labeling for Image-Guided Brachytherapy", Masters thesis (in preparation). Technical University Munich and Ecole Centrale Marseille, Dec 14, 2012<br />
[6] Pernelle, Guillaume, et al. "Validation of Catheter Segmentation for MR-Guided Gynecologic Cancer Brachytherapy." Medical Image Computing and Computer-Assisted Intervention–MICCAI 2013. Springer Berlin Heidelberg, 2013. 380-387.<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
<br />
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.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Gpernellehttps://www.slicer.org/w/index.php?title=Documentation/4.3/Extensions/NeedleFinder&diff=37718Documentation/4.3/Extensions/NeedleFinder2014-04-28T18:21:41Z<p>Gpernelle: </p>
<hr />
<div>NeedleFinder documentation TBD<br />
<br />
<noinclude>{{documentation/versioncheck}}</noinclude><br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
NeedleFinder: fast interactive needle detection.It provides interactive tools to segment needles in MR/CT images. It has been mostly tested on MRI from gynelogical brachytherapy cases. [6]<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
Authors: Guillaume Pernelle<br><br />
Contact: Guillaume Pernelle, <email>gpernelle@gmail.com</email><br><br />
Website: https://github.com/gpernelle/NeedleFinder<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
NeedleFinder: fast interactive needle detection.It provides interactive tools to segment needles in MR/CT images. It has been mostly tested on MRI from gynelogical brachytherapy cases. <br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<br />
[http://slicer.kitware.com/midas3/folder/876 Phantom Study] and<br />
[https://github.com/xjchen/igyne/tree/master/Sample%20data Sample data]<br />
<br />
<gallery widths="200px" perrow="4"><br />
Image:IGyne-needleSegmentation.png|Real needles segmentation<br />
<br />
</gallery><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|References}}<br />
[1] http://www.na-mic.org/Wiki/index.php/2012_Summer_Project_Week:iGyne <br />
[2] 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.<br />
[3] Gao, Farhat, Pernelle et al. "Needle Labeling for Interstitial Gynecological Brachytherapy". Fifth National Image Guided Therapy Workshop, Sept 21, 2012<br />
[4] Pernelle, Egger, Vale, Chen, Irlinger, Lueth, Wells, Kikinis, Viswanathan and Kapur. Robust Applicator Registration for Interstitial Gynecologic Brachytherapy. ABS 2013 Annual Meeting<br />
[5] Pernelle. "Needle labeling for Image-Guided Brachytherapy", Masters thesis (in preparation). Technical University Munich and Ecole Centrale Marseille, Dec 14, 2012<br />
[6] Pernelle, Guillaume, et al. "Validation of Catheter Segmentation for MR-Guided Gynecologic Cancer Brachytherapy." Medical Image Computing and Computer-Assisted Intervention–MICCAI 2013. Springer Berlin Heidelberg, 2013. 380-387.<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
<br />
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.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Gpernellehttps://www.slicer.org/w/index.php?title=Documentation/4.3/Extensions/NeedleFinder&diff=37717Documentation/4.3/Extensions/NeedleFinder2014-04-28T18:12:44Z<p>Gpernelle: Created page with 'NeedleFinder documentation TBD'</p>
<hr />
<div>NeedleFinder documentation TBD</div>Gpernellehttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/iGyne&diff=31003Documentation/Nightly/Extensions/iGyne2013-03-26T16:06:15Z<p>Gpernelle: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
Authors: Guillaume Pernelle, Xiaojun Chen, Yi Gao, Jan Egger<br><br />
Contributors: iGyne Team<br><br />
Contact: Guillaume Pernelle, <email>gpernelle@gmail.com</email><br><br />
Website: https://github.com/gpernelle/iGynePy<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br><br />
Related Master's Thesis: [http://www.ncigt.org/publications/item/view/2316 Labeled Needle Rendering Solution for Image Guided Brachytherapy]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
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. <br />
<br />
iGyne is currently articulated in seven steps: <br />
1) procedure selection<br />
2) applicator selection<br />
3) data importation<br />
4) initial applicator registration<br />
5) refined applicator registration<br />
6) needle position planning<br />
7) needle detection<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<br />
[http://slicer.kitware.com/midas3/folder/876 Phantom Study] and<br />
[https://github.com/xjchen/igyne/tree/master/Sample%20data Sample data]<br />
<br />
<gallery widths="200px" perrow="4"><br />
Image:IGyne-beforeFirstRegsitration.png|Data loaded<br />
Image:IGyne-BeforeRefinedRegistration.png|After the initial registration<br />
Image:IGyne-applicatorSegmentation.png|Applicator Segmentation<br />
Image:IGyne-registrationResult.png|Registration results<br />
Image:IGyne-needlePlanning.png|Planning with virtual needles<br />
Image:IGyne-needleSegmentation.png|Real needles segmentation<br />
Image:IGyne-labelingResult.png|Labeling result on the planning sheet<br />
<br />
</gallery><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|References}}<br />
* http://www.na-mic.org/Wiki/index.php/2012_Summer_Project_Week:iGyne <br />
* 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.<br />
* Gao, Farhat, Pernelle et al. "Needle Labeling for Interstitial Gynecological Brachytherapy". Fifth National Image Guided Therapy Workshop, Sept 21, 2012<br />
* Pernelle, Egger, Vale, Chen, Irlinger, Lueth, Wells, Kikinis, Viswanathan and Kapur. Robust Applicator Registration for Interstitial Gynecologic Brachytherapy. ABS 2013 Annual Meeting<br />
* Pernelle. "Needle labeling for Image-Guided Brachytherapy", Masters thesis (in preparation). Technical University Munich and Ecole Centrale Marseille, Dec 14, 2012<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
iGyne is currently articulated in seven steps: <br />
1) procedure selection<br />
2) applicator selection<br />
3) data importation<br />
4) initial applicator registration<br />
5) refined applicator registration<br />
6) needle position planning<br />
7) needle detection<br />
It offers also a way to go directly from 1) to 7), skipping the registration/planning steps<br />
<br />
- iGyneSelectProcedureStep.py (1) and iGyneSelectApplicatorStep.py (2) let you choose to use or not an applicator, and to select the most convenient one. There are different configurations for the fiducial markers: <br />
* 4 landmarks, ordered from the top left corner and counting counter-clockwise (new cases)<br />
* 3 landmarks, positioned at the corners of the template, ordered as above<br />
* 3 landmarks, starting from the one in the middle of the template and counting counter-clockwise<br />
This step offers an automatic registration option if the CLI module Hough Transformed has been previously enabled<br />
<br />
- iGyneLoadModelStep.py (3) let you load the data while the scene is loaded depending on the made in step 2.<br />
<br />
- iGyneFirstRegistrationStep.py (4) is the initial registration step. Depending on the choice you made on the previous step, you can click on the bright markers in the image or let the automatic registration find them for you (requires the CLI module called Hough Transform). <br />
<br />
- iGyneSecondRegistrationStep.py (5) is the refined applicator registration step. It offers fully automated computation to complete manual parameterization if needed. Thus, several segmentation methods are available to segment the obturator, and the registration parameters can be tweaked. By default, the most efficient parameters are chosen and all steps of the refined registration are computed successively. Evaluation functions have also been integrated to allow developers to measure time and accuracy of the chosen methods and parameters. Beside the control interface, 2D views display cross sections of the applicator in axial, sagital and coronal planes giving the user a visual characterization of the registration state.<br />
<br />
- iGyneNeedlePlanningStep.py (6) let you insert "virtual needles" and visualize their trajectory in the 2D/3D viewer. You can tweak the color and the length of the needles.<br />
<br />
- 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.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Gpernellehttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/iGyne&diff=30452Documentation/Nightly/Extensions/iGyne2013-02-13T17:26:29Z<p>Gpernelle: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
Authors: Guillaume Pernelle, Xiaojun Chen, Yi Gao, Jan Egger<br><br />
Contributors: iGyne Team<br><br />
Contact: Guillaume Pernelle, <email>gpernelle@gmail.com</email><br><br />
Website: https://github.com/gpernelle/iGynePy<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br><br />
Related Master's Thesis: [http://www.ncigt.org/publications/item/view/2316 Labeled Needle Rendering Solution for Image Guided Brachytherapy]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
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. <br />
<br />
iGyne is currently articulated in seven steps: <br />
1) procedure selection<br />
2) applicator selection<br />
3) data importation<br />
4) initial applicator registration<br />
5) refined applicator registration<br />
6) needle position planning<br />
7) needle detection<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<br />
[http://slicer.kitware.com/midas3/folder/876 Phantom Study] and<br />
[https://github.com/xjchen/igyne/tree/master/Sample%20data Sample data]<br />
<br />
<gallery widths="200px" perrow="4"><br />
Image:IGyne-beforeFirstRegsitration.png|Data loaded<br />
Image:IGyne-BeforeRefinedRegistration.png|After the initial registration<br />
Image:IGyne-applicatorSegmentation.png|Applicator Segmentation<br />
Image:IGyne-registrationResult.png|Registration results<br />
Image:IGyne-needlePlanning.png|Planning with virtual needles<br />
Image:IGyne-needleSegmentation.png|Real needles segmentation<br />
Image:IGyne-labelingResult.png|Labeling result on the planning sheet<br />
<br />
</gallery><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
A video tutorial should be soon available<br />
<!--<gallery widths="200px" perrow="4"><br />
</gallery>--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|References}}<br />
* http://www.na-mic.org/Wiki/index.php/2012_Summer_Project_Week:iGyne <br />
* 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.<br />
* Gao, Farhat, Pernelle et al. "Needle Labeling for Interstitial Gynecological Brachytherapy". Fifth National Image Guided Therapy Workshop, Sept 21, 2012<br />
* Pernelle, Egger, Vale, Chen, Irlinger, Lueth, Wells, Kikinis, Viswanathan and Kapur. Robust Applicator Registration for Interstitial Gynecologic Brachytherapy. ABS 2013 Annual Meeting (submitted)<br />
* Pernelle. "Needle labeling for Image-Guided Brachytherapy", Masters thesis (in preparation). Technical University Munich and Ecole Centrale Marseille, Dec 14, 2012<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
iGyne is currently articulated in seven steps: <br />
1) procedure selection<br />
2) applicator selection<br />
3) data importation<br />
4) initial applicator registration<br />
5) refined applicator registration<br />
6) needle position planning<br />
7) needle detection<br />
It offers also a way to go directly from 1) to 7), skipping the registration/planning steps<br />
<br />
- iGyneSelectProcedureStep.py (1) and iGyneSelectApplicatorStep.py (2) let you choose to use or not an applicator, and to select the most convenient one. There are different configurations for the fiducial markers: <br />
* 4 landmarks, ordered from the top left corner and counting counter-clockwise (new cases)<br />
* 3 landmarks, positioned at the corners of the template, ordered as above<br />
* 3 landmarks, starting from the one in the middle of the template and counting counter-clockwise<br />
This step offers an automatic registration option if the CLI module Hough Transformed has been previously enabled<br />
<br />
- iGyneLoadModelStep.py (3) let you load the data while the scene is loaded depending on the made in step 2.<br />
<br />
- iGyneFirstRegistrationStep.py (4) is the initial registration step. Depending on the choice you made on the previous step, you can click on the bright markers in the image or let the automatic registration find them for you (requires the CLI module called Hough Transform). <br />
<br />
- iGyneSecondRegistrationStep.py (5) is the refined applicator registration step. It offers fully automated computation to complete manual parameterization if needed. Thus, several segmentation methods are available to segment the obturator, and the registration parameters can be tweaked. By default, the most efficient parameters are chosen and all steps of the refined registration are computed successively. Evaluation functions have also been integrated to allow developers to measure time and accuracy of the chosen methods and parameters. Beside the control interface, 2D views display cross sections of the applicator in axial, sagital and coronal planes giving the user a visual characterization of the registration state.<br />
<br />
- iGyneNeedlePlanningStep.py (6) let you insert "virtual needles" and visualize their trajectory in the 2D/3D viewer. You can tweak the color and the length of the needles.<br />
<br />
- 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.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Gpernellehttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/iGyne&diff=30451Documentation/Nightly/Extensions/iGyne2013-02-13T17:25:33Z<p>Gpernelle: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
Authors: Guillaume Pernelle, Xiaojun Chen, Yi Gao, Jan Egger<br><br />
Contributors: iGyne Team<br><br />
Contact: Guillaume Pernelle, <email>gpernelle@gmail.com</email><br><br />
Website: https://github.com/gpernelle/iGynePy<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br />
Related Master's Thesis: [http://www.ncigt.org/publications/item/view/2316]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
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. <br />
<br />
iGyne is currently articulated in seven steps: <br />
1) procedure selection<br />
2) applicator selection<br />
3) data importation<br />
4) initial applicator registration<br />
5) refined applicator registration<br />
6) needle position planning<br />
7) needle detection<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<br />
[http://slicer.kitware.com/midas3/folder/876 Phantom Study] and<br />
[https://github.com/xjchen/igyne/tree/master/Sample%20data Sample data]<br />
<br />
<gallery widths="200px" perrow="4"><br />
Image:IGyne-beforeFirstRegsitration.png|Data loaded<br />
Image:IGyne-BeforeRefinedRegistration.png|After the initial registration<br />
Image:IGyne-applicatorSegmentation.png|Applicator Segmentation<br />
Image:IGyne-registrationResult.png|Registration results<br />
Image:IGyne-needlePlanning.png|Planning with virtual needles<br />
Image:IGyne-needleSegmentation.png|Real needles segmentation<br />
Image:IGyne-labelingResult.png|Labeling result on the planning sheet<br />
<br />
</gallery><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
A video tutorial should be soon available<br />
<!--<gallery widths="200px" perrow="4"><br />
</gallery>--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|References}}<br />
* http://www.na-mic.org/Wiki/index.php/2012_Summer_Project_Week:iGyne <br />
* 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.<br />
* Gao, Farhat, Pernelle et al. "Needle Labeling for Interstitial Gynecological Brachytherapy". Fifth National Image Guided Therapy Workshop, Sept 21, 2012<br />
* Pernelle, Egger, Vale, Chen, Irlinger, Lueth, Wells, Kikinis, Viswanathan and Kapur. Robust Applicator Registration for Interstitial Gynecologic Brachytherapy. ABS 2013 Annual Meeting (submitted)<br />
* Pernelle. "Needle labeling for Image-Guided Brachytherapy", Masters thesis (in preparation). Technical University Munich and Ecole Centrale Marseille, Dec 14, 2012<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
iGyne is currently articulated in seven steps: <br />
1) procedure selection<br />
2) applicator selection<br />
3) data importation<br />
4) initial applicator registration<br />
5) refined applicator registration<br />
6) needle position planning<br />
7) needle detection<br />
It offers also a way to go directly from 1) to 7), skipping the registration/planning steps<br />
<br />
- iGyneSelectProcedureStep.py (1) and iGyneSelectApplicatorStep.py (2) let you choose to use or not an applicator, and to select the most convenient one. There are different configurations for the fiducial markers: <br />
* 4 landmarks, ordered from the top left corner and counting counter-clockwise (new cases)<br />
* 3 landmarks, positioned at the corners of the template, ordered as above<br />
* 3 landmarks, starting from the one in the middle of the template and counting counter-clockwise<br />
This step offers an automatic registration option if the CLI module Hough Transformed has been previously enabled<br />
<br />
- iGyneLoadModelStep.py (3) let you load the data while the scene is loaded depending on the made in step 2.<br />
<br />
- iGyneFirstRegistrationStep.py (4) is the initial registration step. Depending on the choice you made on the previous step, you can click on the bright markers in the image or let the automatic registration find them for you (requires the CLI module called Hough Transform). <br />
<br />
- iGyneSecondRegistrationStep.py (5) is the refined applicator registration step. It offers fully automated computation to complete manual parameterization if needed. Thus, several segmentation methods are available to segment the obturator, and the registration parameters can be tweaked. By default, the most efficient parameters are chosen and all steps of the refined registration are computed successively. Evaluation functions have also been integrated to allow developers to measure time and accuracy of the chosen methods and parameters. Beside the control interface, 2D views display cross sections of the applicator in axial, sagital and coronal planes giving the user a visual characterization of the registration state.<br />
<br />
- iGyneNeedlePlanningStep.py (6) let you insert "virtual needles" and visualize their trajectory in the 2D/3D viewer. You can tweak the color and the length of the needles.<br />
<br />
- 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.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Gpernellehttps://www.slicer.org/w/index.php?title=File:IGynePyIcon.png&diff=29358File:IGynePyIcon.png2012-11-21T21:56:30Z<p>Gpernelle: </p>
<hr />
<div></div>Gpernellehttps://www.slicer.org/w/index.php?title=File:HtIcon.png&diff=29357File:HtIcon.png2012-11-21T20:23:51Z<p>Gpernelle: </p>
<hr />
<div></div>Gpernellehttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/circlesDetectionHoughTransform&diff=29356Documentation/Nightly/Extensions/circlesDetectionHoughTransform2012-11-21T19:52:06Z<p>Gpernelle: Created page with '<!-- ---------------------------- --> {{documentation/{{documentation/version}}/module-header}} <!-- ---------------------------- --> <!-- ---------------------------- --> {{doc…'</p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
Authors: Guillaume Pernelle<br><br />
Contributors: Guillaume Pernelle<br />
Contact: Guillaume Pernelle, <email>gpernelle@gmail.com</email><br><br />
Website: https://github.com/gpernelle/houghTransform<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
This modules performs a circles detection by implementing the itk class developed by The GoFigure Dev. Team. at Megason Lab, Systems biology, Harvard Medical school, 2009<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<br />
[http://slicer.kitware.com/midas3/folder/876 Phantom Study]<br />
<br />
<gallery widths="200px" perrow="4"><br />
Image:circlesDetectionHoughTransform-result.png<br />
<br />
</gallery><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
No tutorial<br />
<!--<gallery widths="200px" perrow="4"><br />
</gallery>--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|References}}<br />
* Mosaliganti K., Gelas A., Cowgill P., Megason S. An Optimized N-Dimensional Hough Filter for Detecting Spherical Image Objects. 2009 Sep. [http://hdl.handle.net/10380/3129]<br />
* Pernelle, Egger, Vale, Chen, Irlinger, Lueth, Wells, Kikinis, Viswanathan and Kapur. Robust Applicator Registration for Interstitial Gynecologic Brachytherapy. ABS 2013 Annual Meeting (submitted)<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
This is a CLI module. The output is written into a file situated in the same place as where the module is executed. <br />
This file can be read back into slicer, see an example of a python script here: <br />
[https://github.com/gpernelle/iGynePy/blob/master/iGyneWizard/iGyneFirstRegistrationStep.py#L209 python script using json]<br />
A radius information is also available, please uncomment this part of the code to access it: [https://github.com/gpernelle/houghTransform/blob/master/houghTransformCLI.cxx#L152 Radius output]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Gpernellehttps://www.slicer.org/w/index.php?title=Documentation/Nightly/Extensions/iGyne&diff=29355Documentation/Nightly/Extensions/iGyne2012-11-21T19:51:12Z<p>Gpernelle: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
Authors: Guillaume Pernelle, Xiaojun Chen, Yi Gao<br><br />
Contributors: iGyne Team<br><br />
Contact: Guillaume Pernelle, <email>gpernelle@gmail.com</email><br><br />
Website: https://github.com/gpernelle/iGynePy<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
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. <br />
<br />
iGyne is currently articulated in seven steps: <br />
1) procedure selection<br />
2) applicator selection<br />
3) data importation<br />
4) initial applicator registration<br />
5) refined applicator registration<br />
6) needle position planning<br />
7) needle detection<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<br />
[http://slicer.kitware.com/midas3/folder/876 Phantom Study] and<br />
[https://github.com/xjchen/igyne/tree/master/Sample%20data Sample data]<br />
<br />
<gallery widths="200px" perrow="4"><br />
Image:IGyne-beforeFirstRegsitration.png|Data loaded<br />
Image:IGyne-BeforeRefinedRegistration.png|After the initial registration<br />
Image:IGyne-applicatorSegmentation.png|Applicator Segmentation<br />
Image:IGyne-registrationResult.png|Registration results<br />
Image:IGyne-needlePlanning.png|Planning with virtual needles<br />
Image:IGyne-needleSegmentation.png|Real needles segmentation<br />
Image:IGyne-labelingResult.png|Labeling result on the planning sheet<br />
<br />
</gallery><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
A video tutorial should be soon available<br />
<!--<gallery widths="200px" perrow="4"><br />
</gallery>--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|References}}<br />
* http://www.na-mic.org/Wiki/index.php/2012_Summer_Project_Week:iGyne <br />
* 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.<br />
* Gao, Farhat, Pernelle et al. "Needle Labeling for Interstitial Gynecological Brachytherapy". Fifth National Image Guided Therapy Workshop, Sept 21, 2012<br />
* Pernelle, Egger, Vale, Chen, Irlinger, Lueth, Wells, Kikinis, Viswanathan and Kapur. Robust Applicator Registration for Interstitial Gynecologic Brachytherapy. ABS 2013 Annual Meeting (submitted)<br />
* Pernelle. "Needle labeling for Image-Guided Brachytherapy", Masters thesis (in preparation). Technical University Munich and Ecole Centrale Marseille, Dec 14, 2012<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
iGyne is currently articulated in seven steps: <br />
1) procedure selection<br />
2) applicator selection<br />
3) data importation<br />
4) initial applicator registration<br />
5) refined applicator registration<br />
6) needle position planning<br />
7) needle detection<br />
It offers also a way to go directly from 1) to 7), skipping the registration/planning steps<br />
<br />
- iGyneSelectProcedureStep.py (1) and iGyneSelectApplicatorStep.py (2) let you choose to use or not an applicator, and to select the most convenient one. There are different configurations for the fiducial markers: <br />
* 4 landmarks, ordered from the top left corner and counting counter-clockwise (new cases)<br />
* 3 landmarks, positioned at the corners of the template, ordered as above<br />
* 3 landmarks, starting from the one in the middle of the template and counting counter-clockwise<br />
This step offers an automatic registration option if the CLI module Hough Transformed has been previously enabled<br />
<br />
- iGyneLoadModelStep.py (3) let you load the data while the scene is loaded depending on the made in step 2.<br />
<br />
- iGyneFirstRegistrationStep.py (4) is the initial registration step. Depending on the choice you made on the previous step, you can click on the bright markers in the image or let the automatic registration find them for you (requires the CLI module called Hough Transform). <br />
<br />
- iGyneSecondRegistrationStep.py (5) is the refined applicator registration step. It offers fully automated computation to complete manual parameterization if needed. Thus, several segmentation methods are available to segment the obturator, and the registration parameters can be tweaked. By default, the most efficient parameters are chosen and all steps of the refined registration are computed successively. Evaluation functions have also been integrated to allow developers to measure time and accuracy of the chosen methods and parameters. Beside the control interface, 2D views display cross sections of the applicator in axial, sagital and coronal planes giving the user a visual characterization of the registration state.<br />
<br />
- iGyneNeedlePlanningStep.py (6) let you insert "virtual needles" and visualize their trajectory in the 2D/3D viewer. You can tweak the color and the length of the needles.<br />
<br />
- 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.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Gpernellehttps://www.slicer.org/w/index.php?title=Documentation/4.2/Extensions/iGyne&diff=29354Documentation/4.2/Extensions/iGyne2012-11-21T19:49:46Z<p>Gpernelle: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
Authors: Guillaume Pernelle, Xiaojun Chen, Yi Gao<br><br />
Contributors: iGyne Team<br><br />
Contact: Guillaume Pernelle, <email>gpernelle@gmail.com</email><br><br />
Website: https://github.com/gpernelle/iGynePy<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
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. <br />
<br />
iGyne is currently articulated in seven steps: <br />
1) procedure selection<br />
2) applicator selection<br />
3) data importation<br />
4) initial applicator registration<br />
5) refined applicator registration<br />
6) needle position planning<br />
7) needle detection<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<br />
[http://slicer.kitware.com/midas3/folder/876 Phantom Study] and<br />
[https://github.com/xjchen/igyne/tree/master/Sample%20data Sample data]<br />
<br />
<gallery widths="200px" perrow="4"><br />
Image:IGyne-beforeFirstRegsitration.png|Data loaded<br />
Image:IGyne-BeforeRefinedRegistration.png|After the initial registration<br />
Image:IGyne-applicatorSegmentation.png|Applicator Segmentation<br />
Image:IGyne-registrationResult.png|Registration results<br />
Image:IGyne-needlePlanning.png|Planning with virtual needles<br />
Image:IGyne-needleSegmentation.png|Real needles segmentation<br />
Image:IGyne-labelingResult.png|Labeling result on the planning sheet<br />
<br />
</gallery><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
A video tutorial should be soon available<br />
<!--<gallery widths="200px" perrow="4"><br />
</gallery>--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|References}}<br />
* http://www.na-mic.org/Wiki/index.php/2012_Summer_Project_Week:iGyne <br />
* 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.<br />
* Gao, Farhat, Pernelle et al. "Needle Labeling for Interstitial Gynecological Brachytherapy". Fifth National Image Guided Therapy Workshop, Sept 21, 2012<br />
* Pernelle, Egger, Vale, Chen, Irlinger, Lueth, Wells, Kikinis, Viswanathan and Kapur. Robust Applicator Registration for Interstitial Gynecologic Brachytherapy. ABS 2013 Annual Meeting (submitted)<br />
* Pernelle. "Needle labeling for Image-Guided Brachytherapy", Masters thesis (in preparation). Technical University Munich and Ecole Centrale Marseille, Dec 14, 2012<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
iGyne is currently articulated in seven steps: <br />
1) procedure selection<br />
2) applicator selection<br />
3) data importation<br />
4) initial applicator registration<br />
5) refined applicator registration<br />
6) needle position planning<br />
7) needle detection<br />
It offers also a way to go directly from 1) to 7), skipping the registration/planning steps<br />
<br />
- iGyneSelectProcedureStep.py (1) and iGyneSelectApplicatorStep.py (2) let you choose to use or not an applicator, and to select the most convenient one. There are different configurations for the fiducial markers: <br />
* 4 landmarks, ordered from the top left corner and counting counter-clockwise (new cases)<br />
* 3 landmarks, positioned at the corners of the template, ordered as above<br />
* 3 landmarks, starting from the one in the middle of the template and counting counter-clockwise<br />
This step offers an automatic registration option if the CLI module Hough Transformed has been previously enabled<br />
<br />
- iGyneLoadModelStep.py (3) let you load the data while the scene is loaded depending on the made in step 2.<br />
<br />
- iGyneFirstRegistrationStep.py (4) is the initial registration step. Depending on the choice you made on the previous step, you can click on the bright markers in the image or let the automatic registration find them for you (requires the CLI module called Hough Transform). <br />
<br />
- iGyneSecondRegistrationStep.py (5) is the refined applicator registration step. It offers fully automated computation to complete manual parameterization if needed. Thus, several segmentation methods are available to segment the obturator, and the registration parameters can be tweaked. By default, the most efficient parameters are chosen and all steps of the refined registration are computed successively. Evaluation functions have also been integrated to allow developers to measure time and accuracy of the chosen methods and parameters. Beside the control interface, 2D views display cross sections of the applicator in axial, sagital and coronal planes giving the user a visual characterization of the registration state.<br />
<br />
- iGyneNeedlePlanningStep.py (6) let you insert "virtual needles" and visualize their trajectory in the 2D/3D viewer. You can tweak the color and the length of the needles.<br />
<br />
- 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.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Gpernellehttps://www.slicer.org/w/index.php?title=Documentation/4.2/Extensions/circlesDetectionHoughTransform&diff=29353Documentation/4.2/Extensions/circlesDetectionHoughTransform2012-11-21T19:47:00Z<p>Gpernelle: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
Authors: Guillaume Pernelle<br><br />
Contributors: Guillaume Pernelle<br />
Contact: Guillaume Pernelle, <email>gpernelle@gmail.com</email><br><br />
Website: https://github.com/gpernelle/houghTransform<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
This modules performs a circles detection by implementing the itk class developed by The GoFigure Dev. Team. at Megason Lab, Systems biology, Harvard Medical school, 2009<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<br />
[http://slicer.kitware.com/midas3/folder/876 Phantom Study]<br />
<br />
<gallery widths="200px" perrow="4"><br />
Image:circlesDetectionHoughTransform-result.png<br />
<br />
</gallery><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
No tutorial<br />
<!--<gallery widths="200px" perrow="4"><br />
</gallery>--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|References}}<br />
* Mosaliganti K., Gelas A., Cowgill P., Megason S. An Optimized N-Dimensional Hough Filter for Detecting Spherical Image Objects. 2009 Sep. [http://hdl.handle.net/10380/3129]<br />
* Pernelle, Egger, Vale, Chen, Irlinger, Lueth, Wells, Kikinis, Viswanathan and Kapur. Robust Applicator Registration for Interstitial Gynecologic Brachytherapy. ABS 2013 Annual Meeting (submitted)<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
This is a CLI module. The output is written into a file situated in the same place as where the module is executed. <br />
This file can be read back into slicer, see an example of a python script here: <br />
[https://github.com/gpernelle/iGynePy/blob/master/iGyneWizard/iGyneFirstRegistrationStep.py#L209 python script using json]<br />
A radius information is also available, please uncomment this part of the code to access it: [https://github.com/gpernelle/houghTransform/blob/master/houghTransformCLI.cxx#L152 Radius output]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Gpernellehttps://www.slicer.org/w/index.php?title=Documentation/4.2/Extensions/circlesDetectionHoughTransform&diff=29352Documentation/4.2/Extensions/circlesDetectionHoughTransform2012-11-21T19:46:36Z<p>Gpernelle: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
Authors: Guillaume Pernelle<br><br />
Contributors: Guillaume Pernelle<br />
Contact: Guillaume Pernelle, <email>gpernelle@gmail.com</email><br><br />
Website: https://github.com/gpernelle/houghTransform<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
This modules performs a circles detection by implementing the itk class developed by The GoFigure Dev. Team. at Megason Lab, Systems biology, Harvard Medical school, 2009<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<br />
[http://slicer.kitware.com/midas3/folder/876 Phantom Study]<br />
<br />
<gallery widths="200px" perrow="4"><br />
Image:circlesDetectionHoughTransform-result.png<br />
<br />
</gallery><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
No tutorial<br />
<!--<gallery widths="200px" perrow="4"><br />
</gallery>--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|References}}<br />
* Mosaliganti K., Gelas A., Cowgill P., Megason S. An Optimized N-Dimensional Hough Filter for Detecting Spherical Image Objects. 2009 Sep. <br />
[http://hdl.handle.net/10380/3129]<br />
* Pernelle, Egger, Vale, Chen, Irlinger, Lueth, Wells, Kikinis, Viswanathan and Kapur. Robust Applicator Registration for Interstitial Gynecologic Brachytherapy. ABS 2013 Annual Meeting (submitted)<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
This is a CLI module. The output is written into a file situated in the same place as where the module is executed. <br />
This file can be read back into slicer, see an example of a python script here: <br />
[https://github.com/gpernelle/iGynePy/blob/master/iGyneWizard/iGyneFirstRegistrationStep.py#L209 python script using json]<br />
A radius information is also available, please uncomment this part of the code to access it: [https://github.com/gpernelle/houghTransform/blob/master/houghTransformCLI.cxx#L152 Radius output]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Gpernellehttps://www.slicer.org/w/index.php?title=Documentation/4.2/Extensions/iGyne&diff=29351Documentation/4.2/Extensions/iGyne2012-11-21T19:45:10Z<p>Gpernelle: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
Authors: Guillaume Pernelle, Xiaojun Chen<br><br />
Contributors: iGyne Team<br><br />
Contact: Guillaume Pernelle, <email>gpernelle@gmail.com</email><br><br />
Website: https://github.com/gpernelle/iGynePy<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
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. <br />
<br />
iGyne is currently articulated in seven steps: <br />
1) procedure selection<br />
2) applicator selection<br />
3) data importation<br />
4) initial applicator registration<br />
5) refined applicator registration<br />
6) needle position planning<br />
7) needle detection<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<br />
[http://slicer.kitware.com/midas3/folder/876 Phantom Study] and<br />
[https://github.com/xjchen/igyne/tree/master/Sample%20data Sample data]<br />
<br />
<gallery widths="200px" perrow="4"><br />
Image:IGyne-beforeFirstRegsitration.png|Data loaded<br />
Image:IGyne-BeforeRefinedRegistration.png|After the initial registration<br />
Image:IGyne-applicatorSegmentation.png|Applicator Segmentation<br />
Image:IGyne-registrationResult.png|Registration results<br />
Image:IGyne-needlePlanning.png|Planning with virtual needles<br />
Image:IGyne-needleSegmentation.png|Real needles segmentation<br />
Image:IGyne-labelingResult.png|Labeling result on the planning sheet<br />
<br />
</gallery><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
A video tutorial should be soon available<br />
<!--<gallery widths="200px" perrow="4"><br />
</gallery>--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|References}}<br />
* http://www.na-mic.org/Wiki/index.php/2012_Summer_Project_Week:iGyne <br />
* 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.<br />
* Gao, Farhat, Pernelle et al. "Needle Labeling for Interstitial Gynecological Brachytherapy". Fifth National Image Guided Therapy Workshop, Sept 21, 2012<br />
* Pernelle, Egger, Vale, Chen, Irlinger, Lueth, Wells, Kikinis, Viswanathan and Kapur. Robust Applicator Registration for Interstitial Gynecologic Brachytherapy. ABS 2013 Annual Meeting (submitted)<br />
* Pernelle. "Needle labeling for Image-Guided Brachytherapy", Masters thesis (in preparation). Technical University Munich and Ecole Centrale Marseille, Dec 14, 2012<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
iGyne is currently articulated in seven steps: <br />
1) procedure selection<br />
2) applicator selection<br />
3) data importation<br />
4) initial applicator registration<br />
5) refined applicator registration<br />
6) needle position planning<br />
7) needle detection<br />
It offers also a way to go directly from 1) to 7), skipping the registration/planning steps<br />
<br />
- iGyneSelectProcedureStep.py (1) and iGyneSelectApplicatorStep.py (2) let you choose to use or not an applicator, and to select the most convenient one. There are different configurations for the fiducial markers: <br />
* 4 landmarks, ordered from the top left corner and counting counter-clockwise (new cases)<br />
* 3 landmarks, positioned at the corners of the template, ordered as above<br />
* 3 landmarks, starting from the one in the middle of the template and counting counter-clockwise<br />
This step offers an automatic registration option if the CLI module Hough Transformed has been previously enabled<br />
<br />
- iGyneLoadModelStep.py (3) let you load the data while the scene is loaded depending on the made in step 2.<br />
<br />
- iGyneFirstRegistrationStep.py (4) is the initial registration step. Depending on the choice you made on the previous step, you can click on the bright markers in the image or let the automatic registration find them for you (requires the CLI module called Hough Transform). <br />
<br />
- iGyneSecondRegistrationStep.py (5) is the refined applicator registration step. It offers fully automated computation to complete manual parameterization if needed. Thus, several segmentation methods are available to segment the obturator, and the registration parameters can be tweaked. By default, the most efficient parameters are chosen and all steps of the refined registration are computed successively. Evaluation functions have also been integrated to allow developers to measure time and accuracy of the chosen methods and parameters. Beside the control interface, 2D views display cross sections of the applicator in axial, sagital and coronal planes giving the user a visual characterization of the registration state.<br />
<br />
- iGyneNeedlePlanningStep.py (6) let you insert "virtual needles" and visualize their trajectory in the 2D/3D viewer. You can tweak the color and the length of the needles.<br />
<br />
- 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.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Gpernellehttps://www.slicer.org/w/index.php?title=File:CirclesDetectionHoughTransform-result.png&diff=29349File:CirclesDetectionHoughTransform-result.png2012-11-21T17:40:26Z<p>Gpernelle: </p>
<hr />
<div></div>Gpernellehttps://www.slicer.org/w/index.php?title=Documentation/4.2/Extensions/circlesDetectionHoughTransform&diff=29348Documentation/4.2/Extensions/circlesDetectionHoughTransform2012-11-21T17:39:38Z<p>Gpernelle: Created page with '<!-- ---------------------------- --> {{documentation/{{documentation/version}}/module-header}} <!-- ---------------------------- --> <!-- ---------------------------- --> {{doc…'</p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
Authors: Guillaume Pernelle<br><br />
Contributors: Guillaume Pernelle<br />
Contact: Guillaume Pernelle, <email>gpernelle@gmail.com</email><br><br />
Website: https://github.com/gpernelle/houghTransform<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
This modules performs a circles detection by implementing the itk class developed by The GoFigure Dev. Team. at Megason Lab, Systems biology, Harvard Medical school, 2009<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<br />
[http://slicer.kitware.com/midas3/folder/876 Phantom Study]<br />
<br />
<gallery widths="200px" perrow="4"><br />
Image:circlesDetectionHoughTransform-result.png<br />
<br />
</gallery><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
No tutorial<br />
<!--<gallery widths="200px" perrow="4"><br />
</gallery>--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|References}}<br />
* Mosaliganti K., Gelas A., Cowgill P., Megason S. An Optimized N-Dimensional Hough Filter for Detecting Spherical Image Objects. 2009 Sep. <br />
[http://hdl.handle.net/10380/3129]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
This is a CLI module. The output is written into a file situated in the same place as where the module is executed. <br />
This file can be read back into slicer, see an example of a python script here: <br />
[https://github.com/gpernelle/iGynePy/blob/master/iGyneWizard/iGyneFirstRegistrationStep.py#L209 python script using json]<br />
A radius information is also available, please uncomment this part of the code to access it: [https://github.com/gpernelle/houghTransform/blob/master/houghTransformCLI.cxx#L152 Radius output]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Gpernellehttps://www.slicer.org/w/index.php?title=Documentation/4.2/Extensions/iGyne&diff=29347Documentation/4.2/Extensions/iGyne2012-11-21T17:07:33Z<p>Gpernelle: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
Authors: Guillaume Pernelle, Xiaojun Chen<br><br />
Contributors: iGyne Team<br><br />
Contact: Guillaume Pernelle, <email>gpernelle@gmail.com</email><br><br />
Website: https://github.com/gpernelle/iGynePy<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
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. <br />
<br />
iGyne is currently articulated in seven steps: <br />
1) procedure selection<br />
2) applicator selection<br />
3) data importation<br />
4) initial applicator registration<br />
5) refined applicator registration<br />
6) needle position planning<br />
7) needle detection<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<br />
[http://slicer.kitware.com/midas3/folder/876 Phantom Study] and<br />
[https://github.com/xjchen/igyne/tree/master/Sample%20data Sample data]<br />
<br />
<gallery widths="200px" perrow="4"><br />
Image:IGyne-beforeFirstRegsitration.png|Data loaded<br />
Image:IGyne-BeforeRefinedRegistration.png|After the initial registration<br />
Image:IGyne-applicatorSegmentation.png|Applicator Segmentation<br />
Image:IGyne-registrationResult.png|Registration results<br />
Image:IGyne-needlePlanning.png|Planning with virtual needles<br />
Image:IGyne-needleSegmentation.png|Real needles segmentation<br />
Image:IGyne-labelingResult.png|Labeling result on the planning sheet<br />
<br />
</gallery><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
A video tutorial should be soon available<br />
<!--<gallery widths="200px" perrow="4"><br />
</gallery>--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|References}}<br />
* http://www.na-mic.org/Wiki/index.php/2012_Summer_Project_Week:iGyne <br />
* 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.<br />
* Gao, Farhat, Pernelle et al. "Needle Labeling for Interstitial Gynecological Brachytherapy". Fifth National Image Guided Therapy Workshop, Sept 21, 2012<br />
* Pernelle. "Needle labeling for Image-Guided Brachytherapy", Masters thesis (in preparation). Technical University Munich and Ecole Centrale Marseille, Dec 14, 2012<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
iGyne is currently articulated in seven steps: <br />
1) procedure selection<br />
2) applicator selection<br />
3) data importation<br />
4) initial applicator registration<br />
5) refined applicator registration<br />
6) needle position planning<br />
7) needle detection<br />
It offers also a way to go directly from 1) to 7), skipping the registration/planning steps<br />
<br />
- iGyneSelectProcedureStep.py (1) and iGyneSelectApplicatorStep.py (2) let you choose to use or not an applicator, and to select the most convenient one. There are different configurations for the fiducial markers: <br />
* 4 landmarks, ordered from the top left corner and counting counter-clockwise (new cases)<br />
* 3 landmarks, positioned at the corners of the template, ordered as above<br />
* 3 landmarks, starting from the one in the middle of the template and counting counter-clockwise<br />
This step offers an automatic registration option if the CLI module Hough Transformed has been previously enabled<br />
<br />
- iGyneLoadModelStep.py (3) let you load the data while the scene is loaded depending on the made in step 2.<br />
<br />
- iGyneFirstRegistrationStep.py (4) is the initial registration step. Depending on the choice you made on the previous step, you can click on the bright markers in the image or let the automatic registration find them for you (requires the CLI module called Hough Transform). <br />
<br />
- iGyneSecondRegistrationStep.py (5) is the refined applicator registration step. It offers fully automated computation to complete manual parameterization if needed. Thus, several segmentation methods are available to segment the obturator, and the registration parameters can be tweaked. By default, the most efficient parameters are chosen and all steps of the refined registration are computed successively. Evaluation functions have also been integrated to allow developers to measure time and accuracy of the chosen methods and parameters. Beside the control interface, 2D views display cross sections of the applicator in axial, sagital and coronal planes giving the user a visual characterization of the registration state.<br />
<br />
- iGyneNeedlePlanningStep.py (6) let you insert "virtual needles" and visualize their trajectory in the 2D/3D viewer. You can tweak the color and the length of the needles.<br />
<br />
- 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.<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Gpernellehttps://www.slicer.org/w/index.php?title=Documentation/4.2/Extensions/iGyne&diff=29346Documentation/4.2/Extensions/iGyne2012-11-21T17:05:15Z<p>Gpernelle: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
Authors: Guillaume Pernelle, Xiaojun Chen<br><br />
Contributors: iGyne Team<br><br />
Contact: Guillaume Pernelle, <email>gpernelle@gmail.com</email><br><br />
Website: https://github.com/gpernelle/iGynePy<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br />
<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
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:<br />
<br />
*Loading of Applicator CAD models and MR images<br />
*Initial registration of CAD model of the Template to MR images<br />
*Registration Refinement<br />
*Visualization of Registration<br />
*Needle Selection and Display of Virtual Needles relative to Applicator CAD models and Tumor Segmentation<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<br />
[http://slicer.kitware.com/midas3/folder/876 Phantom Study] and<br />
[https://github.com/xjchen/igyne/tree/master/Sample%20data Sample data]<br />
<br />
<gallery widths="200px" perrow="4"><br />
Image:IGyne-beforeFirstRegsitration.png|Data loaded<br />
Image:IGyne-BeforeRefinedRegistration.png|After the initial registration<br />
Image:IGyne-applicatorSegmentation.png|Applicator Segmentation<br />
Image:IGyne-registrationResult.png|Registration results<br />
Image:IGyne-needlePlanning.png|Planning with virtual needles<br />
Image:IGyne-needleSegmentation.png|Real needles segmentation<br />
Image:IGyne-labelingResult.png|Labeling result on the planning sheet<br />
<br />
</gallery><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
A video tutorial should be soon available<br />
<!--<gallery widths="200px" perrow="4"><br />
</gallery>--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|References}}<br />
* http://www.na-mic.org/Wiki/index.php/2012_Summer_Project_Week:iGyne <br />
* 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.<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
iGyne is currently articulated in seven steps: <br />
1) procedure selection<br />
2) applicator selection<br />
3) data importation<br />
4) initial applicator registration<br />
5) refined applicator registration<br />
6) needle position planning<br />
7) needle detection<br />
It offers also a way to go directly from 1) to 7), skipping the registration/planning steps<br />
<br />
- iGyneSelectProcedureStep.py (1) and iGyneSelectApplicatorStep.py (2) let you choose to use or not an applicator, and to select the most convenient one. There are different configurations for the fiducial markers: <br />
* 4 landmarks, ordered from the top left corner and counting counter-clockwise (new cases)<br />
* 3 landmarks, positioned at the corners of the template, ordered as above<br />
* 3 landmarks, starting from the one in the middle of the template and counting counter-clockwise<br />
This step offers an automatic registration option if the CLI module Hough Transformed has been previously enabled<br />
<br />
- iGyneLoadModelStep.py (3) let you load the data while the scene is loaded depending on the made in step 2.<br />
<br />
- iGyneFirstRegistrationStep.py (4) is the initial registration step. Depending on the choice you made on the previous step, you can click on the bright markers in the image or let the automatic registration find them for you (requires the CLI module called Hough Transform). <br />
<br />
- iGyneSecondRegistrationStep.py (5) is the refined applicator registration step. It offers fully automated computation to complete manual parameterization if needed. Thus, several segmentation methods are available to segment the obturator, and the registration parameters can be tweaked. By default, the most efficient parameters are chosen and all steps of the refined registration are computed successively. Evaluation functions have also been integrated to allow developers to measure time and accuracy of the chosen methods and parameters. Beside the control interface, 2D views display cross sections of the applicator in axial, sagital and coronal planes giving the user a visual characterization of the registration state.<br />
<br />
- iGyneNeedlePlanningStep.py (6) let you insert "virtual needles" and visualize their trajectory in the 2D/3D viewer. You can tweak the color and the length of the needles.<br />
<br />
- 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.<br />
{{documentation/{{documentation/version}}/extension-developerinfo}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Gpernellehttps://www.slicer.org/w/index.php?title=Documentation/4.2/Extensions/iGyne&diff=29345Documentation/4.2/Extensions/iGyne2012-11-21T17:03:40Z<p>Gpernelle: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
Authors: Guillaume Pernelle, Xiaojun Chen<br><br />
Contributors: iGyne Team<br><br />
Contact: Guillaume Pernelle, <email>gpernelle@gmail.com</email><br><br />
Website: https://github.com/gpernelle/iGynePy<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br />
<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
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:<br />
<br />
*Loading of Applicator CAD models and MR images<br />
*Initial registration of CAD model of the Template to MR images<br />
*Registration Refinement<br />
*Visualization of Registration<br />
*Needle Selection and Display of Virtual Needles relative to Applicator CAD models and Tumor Segmentation<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<br />
[http://slicer.kitware.com/midas3/folder/876 Phantom Study] and<br />
[https://github.com/xjchen/igyne/tree/master/Sample%20data Sample data]<br />
<br />
<gallery widths="200px" perrow="4"><br />
Image:IGyne-beforeFirstRegsitration.png|Data loaded<br />
Image:IGyne 1.0 needle visualization.png|Screenshot of Needle Visualization<br />
Image:Igyne 1.0-Tumor and Needle Visualization.png|Screenshot of Tumor and Needle Visualization<br />
</gallery><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
[[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.<br />
<!--<gallery widths="200px" perrow="4"><br />
</gallery>--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|References}}<br />
* http://www.na-mic.org/Wiki/index.php/2012_Summer_Project_Week:iGyne <br />
* 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.<br />
* Gao, Farhat, Pernelle et al. "Needle Labeling for Interstitial Gynecological Brachytherapy". Fifth National Image Guided Therapy Workshop, Sept 21, 2012<br />
* Pernelle. "Needle labeling for Image-Guided Brachytherapy", Masters thesis (in preparation). Technical University Munich and Ecole Centrale Marseille, Dec 14, 2012<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
iGyne is currently articulated in seven steps: <br />
1) procedure selection<br />
2) applicator selection<br />
3) data importation<br />
4) initial applicator registration<br />
5) refined applicator registration<br />
6) needle position planning<br />
7) needle detection<br />
It offers also a way to go directly from 1) to 7), skipping the registration/planning steps<br />
<br />
- iGyneSelectProcedureStep.py (1) and iGyneSelectApplicatorStep.py (2) let you choose to use or not an applicator, and to select the most convenient one. There are different configurations for the fiducial markers: <br />
* 4 landmarks, ordered from the top left corner and counting counter-clockwise (new cases)<br />
* 3 landmarks, positioned at the corners of the template, ordered as above<br />
* 3 landmarks, starting from the one in the middle of the template and counting counter-clockwise<br />
This step offers an automatic registration option if the CLI module Hough Transformed has been previously enabled<br />
<br />
- iGyneLoadModelStep.py (3) let you load the data while the scene is loaded depending on the made in step 2.<br />
<br />
- iGyneFirstRegistrationStep.py (4) is the initial registration step. Depending on the choice you made on the previous step, you can click on the bright markers in the image or let the automatic registration find them for you (requires the CLI module called Hough Transform). <br />
<br />
- iGyneSecondRegistrationStep.py (5) is the refined applicator registration step. It offers fully automated computation to complete manual parameterization if needed. Thus, several segmentation methods are available to segment the obturator, and the registration parameters can be tweaked. By default, the most efficient parameters are chosen and all steps of the refined registration are computed successively. Evaluation functions have also been integrated to allow developers to measure time and accuracy of the chosen methods and parameters. Beside the control interface, 2D views display cross sections of the applicator in axial, sagital and coronal planes giving the user a visual characterization of the registration state.<br />
<br />
- iGyneNeedlePlanningStep.py (6) let you insert "virtual needles" and visualize their trajectory in the 2D/3D viewer. You can tweak the color and the length of the needles.<br />
<br />
- 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.<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-footer}}<br />
<!-- ---------------------------- --></div>Gpernellehttps://www.slicer.org/w/index.php?title=Documentation/4.2/Extensions/iGyne&diff=29344Documentation/4.2/Extensions/iGyne2012-11-21T16:21:27Z<p>Gpernelle: </p>
<hr />
<div><!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-header}}<br />
<!-- ---------------------------- --><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
Authors: Guillaume Pernelle, Xiaojun Chen<br><br />
Contributors: iGyne Team<br><br />
Contact: Guillaume Pernelle, <email>gpernelle@gmail.com</email><br><br />
Website: https://github.com/gpernelle/iGynePy<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br />
<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
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:<br />
<br />
*Loading of Applicator CAD models and MR images<br />
*Initial registration of CAD model of the Template to MR images<br />
*Registration Refinement<br />
*Visualization of Registration<br />
*Needle Selection and Display of Virtual Needles relative to Applicator CAD models and Tumor Segmentation<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Modules}}<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Use Cases}}<br />
[http://slicer.kitware.com/midas3/folder/876 Phantom Study] and<br />
[https://github.com/xjchen/igyne/tree/master/Sample%20data Sample data]<br />
<br />
<gallery widths="200px" perrow="4"><br />
Image:IGyne-beforeFirstRegsitration.png|Data loaded<br />
Image:IGyne 1.0 needle visualization.png|Screenshot of Needle Visualization<br />
Image:Igyne 1.0-Tumor and Needle Visualization.png|Screenshot of Tumor and Needle Visualization<br />
</gallery><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Tutorials}}<br />
[[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.<br />
<!--<gallery widths="200px" perrow="4"><br />
</gallery>--><br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Similar Extensions}}<br />
N/A<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|References}}<br />
* http://www.na-mic.org/Wiki/index.php/2012_Summer_Project_Week:iGyne <br />
* 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.<br />
<br />
<br />
<!-- ---------------------------- --><br />
{{documentation/{{documentation/version}}/extension-section|Information for Developers}}<br />
iGyne is currently articulated in seven steps: <br />
1) procedure selection<br />
2) applicator selection<br />
3) data importation<br />
4) initial applicator registration<br />
5) refined applicator registration<br />
6) needle position planning<br />
7) needle detection<br />
It offers also a way to go directly from 1) to 7), skipping the registration/planning steps<br />
<br />
- iGyneSelectProcedureStep.py (1) and iGyneSelectApplicatorStep.py (2) let you choose to use or not an applicator, and to select the most convenient one. There are different configurations for the fiducial markers: <br />
* 4 landmarks, ordered from the top left corner and counting counter-clockwise (new cases)<br />
* 3 landmarks, positioned at the corners of the template, ordered as above<br />
* 3 landmarks, starting from the one in the middle of the template and counting counter-clockwise<br />
This step offers an automatic registration option if the CLI module Hough Transformed has been previously enabled<br />
<br />
- iGyneLoadModelStep.py (3) let you load the data while the scene is loaded depending on the made in step 2.<br />
<br />
- iGyneFirstRegistrationStep.py (4) is the initial registration step. Depending on the choice you made on the previous step, you can click on the bright markers in the image or let the automatic registration find them for you (requires the CLI module called Hough Transform). <br />
<br />
- iGyneSecondRegistrationStep.py (5) is the refined applicator registration step. It offers fully automated computation to complete manual parameterization if needed. Thus, several segmentation methods are available to segment the obturator, and the registration parameters can be tweaked. By default, the most efficient parameters are chosen and all steps of the refined registration are computed successively. Evaluation functions have also been integrated to allow developers to measure time and accuracy of the chosen methods and parameters. Beside the control interface, 2D views display cross sections of the applicator in axial, sagital and coronal planes giving the user a visual characterization of the registration state.<br />
<br />
- iGyneNeedlePlanningStep.py (6) let you insert "virtual needles" and visualize their trajectory in the 2D/3D viewer. You can tweak the color and the length of the needles.<br />
<br />
- 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.<br />
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{{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}<br />
Authors: Guillaume Pernelle, Xiaojun Chen<br><br />
Contributors: iGyne Team<br><br />
Contact: Guillaume Pernelle, <email>gpernelle@gmail.com</email><br><br />
Website: https://github.com/gpernelle/iGynePy<br><br />
License: [http://www.slicer.org/pages/LicenseText Slicer license]<br />
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{{documentation/{{documentation/version}}/extension-section|Extension Description}}<br />
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:<br />
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*Loading of Applicator CAD models and MR images<br />
*Initial registration of CAD model of the Template to MR images<br />
*Registration Refinement<br />
*Visualization of Registration<br />
*Needle Selection and Display of Virtual Needles relative to Applicator CAD models and Tumor Segmentation<br />
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[http://slicer.kitware.com/midas3/folder/876 Phantom Study] and<br />
[https://github.com/xjchen/igyne/tree/master/Sample%20data Sample data]<br />
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Image:IGyne 1.0-registration.png|Screenshot of Registration<br />
Image:IGyne 1.0 needle visualization.png|Screenshot of Needle Visualization<br />
Image:Igyne 1.0-Tumor and Needle Visualization.png|Screenshot of Tumor and Needle Visualization<br />
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[[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.<br />
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* http://www.na-mic.org/Wiki/index.php/2012_Summer_Project_Week:iGyne <br />
* 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.<br />
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iGyne is currently articulated in seven steps: <br />
1) procedure selection<br />
2) applicator selection<br />
3) data importation<br />
4) initial applicator registration<br />
5) refined applicator registration<br />
6) needle position planning<br />
7) needle detection<br />
It offers also a way to go directly from 1) to 7), skipping the registration/planning steps<br />
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- iGyneSelectProcedureStep.py (1) and iGyneSelectApplicatorStep.py (2) let you choose to use or not an applicator, and to select the most convenient one. There are different configurations for the fiducial markers: <br />
* 4 landmarks, ordered from the top left corner and counting counter-clockwise (new cases)<br />
* 3 landmarks, positioned at the corners of the template, ordered as above<br />
* 3 landmarks, starting from the one in the middle of the template and counting counter-clockwise<br />
This step offers an automatic registration option if the CLI module Hough Transformed has been previously enabled<br />
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- iGyneLoadModelStep.py (3) let you load the data while the scene is loaded depending on the made in step 2.<br />
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- iGyneFirstRegistrationStep.py (4) is the initial registration step. Depending on the choice you made on the previous step, you can click on the bright markers in the image or let the automatic registration find them for you (requires the CLI module called Hough Transform). <br />
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- iGyneSecondRegistrationStep.py (5) is the refined applicator registration step. It offers fully automated computation to complete manual parameterization if needed. Thus, several segmentation methods are available to segment the obturator, and the registration parameters can be tweaked. By default, the most efficient parameters are chosen and all steps of the refined registration are computed successively. Evaluation functions have also been integrated to allow developers to measure time and accuracy of the chosen methods and parameters. Beside the control interface, 2D views display cross sections of the applicator in axial, sagital and coronal planes giving the user a visual characterization of the registration state.<br />
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- iGyneNeedlePlanningStep.py (6) let you insert "virtual needles" and visualize their trajectory in the 2D/3D viewer. You can tweak the color and the length of the needles.<br />
<br />
- 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.<br />
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