Documentation/Nightly/Extensions/VirtualFractureReconstruction - Revision history

Kfritscher76 at 22:28, 20 June 2013

2013-06-20T22:28:39Z

Kfritscher76 at 22:28, 20 June 2013

2013-06-20T22:28:04Z

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

2013-06-14T07:54:20Z

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

Kfritscher76 at 16:14, 10 June 2013

2013-06-10T16:14:01Z

Kfritscher76 at 16:11, 10 June 2013

2013-06-10T16:11:14Z

Kfritscher76 at 16:01, 10 June 2013

2013-06-10T16:01:42Z

Kfritscher76 at 15:59, 10 June 2013

2013-06-10T15:59:37Z

Kfritscher76 at 15:58, 10 June 2013

2013-06-10T15:58:13Z

Kfritscher76 at 15:53, 10 June 2013

2013-06-10T15:53:27Z

Kfritscher76 at 15:43, 10 June 2013

2013-06-10T15:43:54Z

@@ Line 10: / Line 10: @@
 Acknowledgments:
 This work has been funded by the Austrian Science Fund.<br>
-Author: Karl Fritscher, UMIT, BWH, MGH , contact: kfritscher@gmail.com
+Author: Karl Fritscher, UMIT, BWH, MGH , contact: kfritscher@gmail.com<br>
 Contributors: Peter Karasev, Steve Pieper, Ron Kikinis

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-<!-- ---------------------------- -->
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 {{documentation/{{documentation/version}}/module-section|Information for Developers}}
-* Source code of the module: https://github.com/???
+* Source code of the module: https://github.com/kfritscher/VirtualFractureReconstructionSlicerExtension
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← Older revision		Revision as of 07:54, 14 June 2013
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← Older revision		Revision as of 16:14, 10 June 2013
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	Please note that this module is under active development, and is being made available for the purposes of beta testing and feedback evaluation! The functionality, GUI and workflows may change in the subsequent releases of the module. Moreover, parts of the original algorithm are written in CUDA. Due to some limitations for Slicer extensions, this CUDA code can currently not be provided in this extension. The CUDA part of the code is implementing a more flexible registration algorithm (EM-ICP), which can potentially lead to better reconstruction results. If you are interested in using this extended version of the code, please contact me.		Please note that this module is under active development, and is being made available for the purposes of beta testing and feedback evaluation! The functionality, GUI and workflows may change in the subsequent releases of the module. Moreover, parts of the original algorithm are written in CUDA. Due to some limitations for Slicer extensions, this CUDA code can currently not be provided in this extension. The CUDA part of the code is implementing a more flexible registration algorithm (EM-ICP), which can potentially lead to better reconstruction results. If you are interested in using this extended version of the code, please contact me.
		+
		+	At the moment ICP and EM-ICP were used for the actual registration part. However, the module has been designed in a way that the integration of additional algorithms for point set registration can easily be added. So if you are interested in testing and/or providing suitable registration algorithms, please contact me.

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@@ Line 10: / Line 10: @@
 This work has been funded by the Austrian Science Fund.<br>
 Author: Karl Fritscher, UMIT, BWH, MGH , contact: kfritscher@gmail.com
-Contributors: Peter Karasev, STeve Pieper, Ron Kikinis
+Contributors: Peter Karasev, Steve Pieper, Ron Kikinis
@@ Line 19: / Line 19: @@
 {|
 The reposition of bone fragments after a fracture, a process also referred to as fracture reduction, is a crucial task during the operative treatment of complex bone fractures. The repositioning of fracture fragments often requires a trial and error approach, which leads to a significant prolongation of the surgery and causes additional trauma to the fragments and the surrounding soft tissue. Wound healing failure, infections, or joint stiffness can be the consequence. Therefore, there is a clear trend towards the development of less invasive techniques to reconstruct complex fractures. In order to support this trend, software tools for calculating and visualizing the optimal way of repositioning fracture fragments based on the usage of segmented CT images as input data have been developed. In several studies, they have successfully demonstrated their potential to decrease operation times and increase reduction accuracy. However, existing software tools are often restricted to particular types of fractures and require a large amount of user interaction.<br>
-Hence, the main objective of the proposed project is to overcome these limitations by developing an algorithmic pipeline that is calculating and visualizing the optimal way of repositioning fracture fragments with a minimal amount of user interaction and without restrictions to particular types of fractures. For this purpose, texture information coming from CT image, surface properties of the bone fragments as well as prior knowledge about the shape of the healthy (=non-fractured) bone are used for the reconstruction process.<br>
+Hence, the main objective of the proposed project is to overcome these limitations by developing an algorithmic pipeline that is calculating and visualizing the optimal way of repositioning fracture fragments with a minimal amount of user interaction and without restrictions to particular types of fractures. In a two step approach, the fracture fragments will first be pre-aligned to a healthy reference bone and then aligned against each other. For these steps, texture information coming from CT images, surface properties of the bone fragments as well as prior knowledge about the shape of the healthy (=non-fractured) bone are used in order to identify candidate points for the registration using a nearest neighbor approach based on Mahalanobis distances between fragment surface points.<br>
 The module shall provide the possibility to perform a fully automated fracture reconstruction, but also to perform user guided reconstruction for very complex fractures with a large number of (small) bone fragments.
+|
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 The extensions provides the possibility to reconstruction/realign fracture fragments and visualize the correct reconstruction of the fracture and switch between reconstructed and not reconstructed fragment position for individual fragments. In combination with a volume rendering a better/more detailed pre-surgical planning process shall be supported. Furthermore, the optimal reconstruction provided by the extension can a also act as a reference for post-operative quality assessment of the "real" reconstruction.
 <!-- ---------------------------- -->
-{{documentation/{{documentation/version}}/module-section|Panels and their use}}
+{{documentation/{{documentation/version}}/module-section|Tutorial and description of panels }}
 Using the first tab of the loadable module the user should provide the following input data: <br>
   -3D CT image(volume) of non fractured bone (='Reference image') <br>
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← Older revision		Revision as of 16:01, 10 June 2013
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	[[File:Loadable_ResultStepFinal.png\|300px\|thumb\|center\|Final tab of the loadable module after second step of reconstruction process]]		[[File:Loadable_ResultStepFinal.png\|300px\|thumb\|center\|Final tab of the loadable module after second step of reconstruction process]]
−	[[File:Loadable Screen-ResultFinal+VR.png\|300px\|thumb\|center\|Updated 2D and 3D views after final step of reconstruction. Note that the visible gaps are due to missing bone that has been "simulated" in this (toy) example]]	+	[[File:Loadable Screen-ResultFinal+VR.png\|300px\|thumb\|center\|Updated 2D and 3D views after final step of reconstruction. Note that the visible gaps are due to missing bone that has been "simulated" in this (toy) example. This view was generated using a wireframe representatioin of the fragments in combination with a volume rendering of CT dataset of the (healthy) reference bone ]]

← Older revision		Revision as of 15:59, 10 June 2013
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	[[File:Loadable_ResultStepFinal.png\|300px\|thumb\|center\|Final tab of the loadable module after second step of reconstruction process]]		[[File:Loadable_ResultStepFinal.png\|300px\|thumb\|center\|Final tab of the loadable module after second step of reconstruction process]]
−	[[File:~~Loadable_ScreenStep1~~.png\|300px\|thumb\|center\|Updated 2D and 3D views after final step of reconstruction. Note that the visible gaps are due to missing bone that has been "simulated" in this (toy) example]]	+	[[File:Loadable Screen-ResultFinal+VR.png\|300px\|thumb\|center\|Updated 2D and 3D views after final step of reconstruction. Note that the visible gaps are due to missing bone that has been "simulated" in this (toy) example]]

@@ Line 80: / Line 80: @@
 [[File:Loadable_Para3.png|300px|thumb|center|Parameter section for first reconstruction step]]
-[[File:Loadable_ResultStep1.png|300px|thumb|center|Third tab of the loadable module after first step of reconstruction is finished]]
+After the calculations for the fine tuning step are finished, the last tab will be opened ("Result step 2"). Again 2D and 3D views will be updated accordingly and the same 4 scenarios as in the previous step are possible.
-[[File:Loadable_ScreenStep1.png|300px|thumb|center|Updated 2D and 3D views after first step of reconstruction. In this case only 2 of the 3 fragments were selected for registration in the second ("Fragment models") tab]]

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 ) Good registration - Accept registration without performing further registration (fine tuning part will be skipped).<br>
 ) Good registration - Accept registration and perform fine tuning<br>
-) Registration not good enough - Go back to previous tab and alter parameters. BEFORE going back to the previous tab, the user should select which fragments shall be realigned (with different parameters). If no fragments are selected all fragments will be pre-aligned again.<br>
+) Registration not good enough - Go back to previous tab and alter parameters. BEFORE going back to the previous tab, the user should select which fragments shall be re-   aligned (with different parameters). If no fragments are selected all fragments will be pre-aligned again.<br>
 ) Registration not good enough - Perform manual repositioning using transform sliders and accept registration or continue with fine tuning step.<br>
 <br>
-In any case the user can switch between views of aligned and unaligned fragments in the 3D and 2D viewers using the "toggle aligned <--> unaligned" button.
+In any case the user can switch between views of aligned and unaligned fragments in the 3D and 2D viewers using the "toggle aligned <--> unaligned" button. <br>
 [[File:Loadable_ResultStep1.png|300px|thumb|center|Third tab of the loadable module after first step of reconstruction is finished]]
-[[File:Loadable_ScreenStep1.png|300px|thumb|center|Updated 2D and 3D views after first step of reconstruction is finished. In this case only 2 of the 3 fragments were selected for registration in the second ("Fragment models") tab]]
+[[File:Loadable_ScreenStep1.png|300px|thumb|center|Updated 2D and 3D views after first step of reconstruction. In this case only 2 of the 3 fragments were selected for registration in the second ("Fragment models") tab]]

← Older revision		Revision as of 15:43, 10 June 2013
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	[[File:Loadable_ResultStep1.png\|300px\|thumb\|center\|Third tab of the loadable module after first step of reconstruction is finished]]		[[File:Loadable_ResultStep1.png\|300px\|thumb\|center\|Third tab of the loadable module after first step of reconstruction is finished]]
−	[[File:Loadable_ScreenStep1.png\|300px\|thumb\|center\|Updated 2D and 3D views after first step of reconstruction is finished]]	+	[[File:Loadable_ScreenStep1.png\|300px\|thumb\|center\|Updated 2D and 3D views after first step of reconstruction is finished. In this case only 2 of the 3 fragments were selected for registration in the second ("Fragment models") tab]]