NAMIC Wiki - User contributions [en]

2013 Summer Project Week: Is Neurosurgical Rigid Registration Really Rigid?

2013-06-21T13:54:45Z

Athena Lyons:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:ForceIsotropicTemplate.jpg|ForceIsotropic screenshot
</gallery>

==Key Investigators==
* University of Western Australia: Athena Lyons, Karol Miller, Adam Wittek, Grand Joldes

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Rigid registration is performed prior to the application of the ISML’s computational biomechanical models of the brain. For application of computational biomechanics it is required that the rigid components of the image (i.e. the skull) be rigidly aligned without scaling. This project investigates the suitability of Slicer's rigid registration method and if, or at what point, brain shift or tumour size effect registration to the extent that image pre-processing is required.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

Our approach is to compare the effects of rigid registration on whole images to images where only rigid components are considered for both synthetic samples and hospital data. Analysis will be made using an in house developed Canny Edge detection algorithm.
We intend to take advantage of available Slicer experts to better understand the capabilities and limitations of current rigid registration methods and how they may be applicable.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
We have improved our understanding of rigid registration in Slicer and determined how to validate the resulting transform file. We also found that resampling in Slicer requires a template/field of view/grid to map the image to that is in the desired sampling dimensions. Most groups use an atlas for this purpose. We have written a loadable extension to generate a grid so that the atlas is not required. For our purposes it generates an isotropic grid and then requests that either linear or lanczos interpolation is used in the resampling. It can be found at [https://github.com/20359511/IsotropicResampling]. We also learned some methods to produce better masks/label maps.

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a report that can be made available on the NA-MIC web page.

==References==
*Intelligent Systems for Medicine Laboratory (ISML) [http://www.mech.uwa.edu.au/ISML www.mech.uwa.edu.au/ISML]
*Mostayed, A., Garlapati, R. R., Joldes, G. R., Wittek, A., Roy, A., Kikinis, R., Warfield, S. K. & Miller, K. [2013. Biomechanical model as a registration tool for image-guided neurosurgery: evaluation against BSpline registration. Annals of Biomedical Engineering, DOI: 10.1007/s10439-013-0838-y.

2013 Summer Project Week: Is Neurosurgical Rigid Registration Really Rigid?

2013-06-21T13:50:25Z

Athena Lyons:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:ForceIsotropicTemplate.jpg|[[ForceIsotropic screenshot]]
</gallery>

==Key Investigators==
* University of Western Australia: Athena Lyons, Karol Miller, Adam Wittek, Grand Joldes

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Rigid registration is performed prior to the application of the ISML’s computational biomechanical models of the brain. For application of computational biomechanics it is required that the rigid components of the image (i.e. the skull) be rigidly aligned without scaling. This project investigates the suitability of Slicer's rigid registration method and if, or at what point, brain shift or tumour size effect registration to the extent that image pre-processing is required.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

Our approach is to compare the effects of rigid registration on whole images to images where only rigid components are considered for both synthetic samples and hospital data. Analysis will be made using an in house developed Canny Edge detection algorithm.
We intend to take advantage of available Slicer experts to better understand the capabilities and limitations of current rigid registration methods and how they may be applicable.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
We have improved our understanding of rigid registration in Slicer and determined how to validate the resulting transform file. We also found that resampling in Slicer requires a template/field of view/grid to map the image to that is in the desired sampling dimensions. Most groups use an atlas for this purpose. We have written a loadable extension to generate a grid so that the atlas is not required. For our purposes it generates an isotropic grid and then requests that either linear or lanczos interpolation is used in the resampling. It can be found at [https://github.com/20359511/IsotropicResampling]. We also learned some methods to produce better masks/label maps.

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a report that can be made available on the NA-MIC web page.

==References==
*Intelligent Systems for Medicine Laboratory (ISML) [http://www.mech.uwa.edu.au/ISML www.mech.uwa.edu.au/ISML]
*Mostayed, A., Garlapati, R. R., Joldes, G. R., Wittek, A., Roy, A., Kikinis, R., Warfield, S. K. & Miller, K. [2013. Biomechanical model as a registration tool for image-guided neurosurgery: evaluation against BSpline registration. Annals of Biomedical Engineering, DOI: 10.1007/s10439-013-0838-y.

File:ForceIsotropicTemplate.jpg

2013-06-21T11:26:43Z

Athena Lyons: uploaded a new version of "File:ForceIsotropicTemplate.jpg"

2013 Summer Project Week: Is Neurosurgical Rigid Registration Really Rigid?

2013-06-21T05:56:57Z

Athena Lyons:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:ForceIsotropicTemplate.jpg|[[ForceIsotropic screenshot]]
</gallery>

==Key Investigators==
* University of Western Australia: Athena Lyons, Karol Miller, Adam Wittek, Grand Joldes

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Objective</h3>
Rigid registration is performed prior to the application of the ISML’s computational biomechanical models of the brain. For application of computational biomechanics it is required that the rigid components of the image (i.e. the skull) be rigidly aligned without scaling. This project investigates the suitability of Slicer's rigid registration method and if, or at what point, brain shift or tumour size effect registration to the extent that image pre-processing is required.

</div>

<div style="width: 27%; float: left; padding-right: 3%;">

<h3>Approach, Plan</h3>

Our approach is to compare the effects of rigid registration on whole images to images where only rigid components are considered for both synthetic samples and hospital data. Analysis will be made using an in house developed Canny Edge detection algorithm.
We intend to take advantage of available Slicer experts to better understand the capabilities and limitations of current rigid registration methods and how they may be applicable.

</div>

<div style="width: 40%; float: left;">

<h3>Progress</h3>
We have improved our understanding of rigid registration in Slicer and determined how to validate the resulting transform file. We also found that resampling in Slicer requires a template to map the resampled image to. Most groups use an atlas for this purpose. We have written a loadable extension to generate the template. For our purposes it generates an isotropic template and then requests that either linear or lanczos interpolation is used in the resampling.

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a report that can be made available on the NA-MIC web page.

==References==
*Intelligent Systems for Medicine Laboratory (ISML) [http://www.mech.uwa.edu.au/ISML www.mech.uwa.edu.au/ISML]
*Mostayed, A., Garlapati, R. R., Joldes, G. R., Wittek, A., Roy, A., Kikinis, R., Warfield, S. K. & Miller, K. [2013. Biomechanical model as a registration tool for image-guided neurosurgery: evaluation against BSpline registration. Annals of Biomedical Engineering, DOI: 10.1007/s10439-013-0838-y.

File:ForceIsotropicTemplate.jpg

2013-06-21T05:43:27Z

Athena Lyons:

2013 Summer Project Week

2013-06-05T09:10:47Z

Athena Lyons: /* IGT */

Back to [[Events]]
[[image:PW-MIT2013.png|300px]]

Dates: June 17-21, 2013.

Location: MIT, Cambridge, MA.

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 17
!style="width:18%" |Tuesday, June 18
!style="width:18%" |Wednesday, June 19
!style="width:18%" |Thursday, June 20
!style="width:18%" |Friday, June 21
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT and RT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''10-11am''' [[2013 Project Week Breakout Session:Slicer4Python|Slicer4 Python Modules, Testing, Q&A]] <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
|'''9:30-11pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Project Week Breakout Session: SimpleITK|Slicer and SimpleITK]] (Hans)
[[MIT_Project_Week_Rooms#32-D507|32-D507]]
|'''10am-12pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2013 Project Week Breakout Session: IGT|Image-Guided Therapy]] (Tina)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm''' [[2013 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (Jean-Christophe Fillion-Robin) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''1-3pm:''' [[Renewal-06-2013|NA-MIC Renewal]] <br>PIs <br>Closed Door Session with Ron
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
<br>----------------------------------------<br>
'''3-4pm:''' [[2013_Tutorial_Contest|Tutorial Contest Presentations]] <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2013|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''3-5:30pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2013 Summer Project Week Breakout Session:RT|Radiation Therapy]] (Greg, Csaba)
[[MIT_Project_Week_Rooms#32-D407|32-D407]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

== '''Projects''' ==

Please use [http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template this template] to create wiki pages for your project. Then link the page here with a list of key personnel.

===Huntington's Disease===
* [[Dynamically Configurable Quality Assurance Module for Large Huntington's Disease Database Frontend]] (Dave)
* [[DWIConvert]] (Kent)
* [[Learn and Apply FiberBundleLabelSelect for Huntington's Disease Data]] (Hans, Demian)
* [[Investigate Potential Tensor Computation Improvement via Positive Semi-Definite (PSD) Tensor Estimation]] (Hans)
* [[Enhance and update SPL atlas]] (Dave, Hans)

===Traumatic Brain Injury===
* Validation and testing of 3D Slicer modules implementing the Utah segmentation algorithm for traumatic brain injury (Andrei Irimia, Micah Chambers, Bo Wang, Marcel Prastawa, Guido Gerig, Jack van Horn)
* Visualization and quantification of peri-contusional white matter bundles in traumatic brain injury using diffusion tensor imaging (Andrei Irimia, Micah Chambers, Ron Kikinis, Jack van Horn)
* Clinically oriented assessment of local changes in the properties of white matter affected by intra-cranial hemorrhage (Andrei Irimia, Micah Chambers, Ron Kikinis, Jack van Horn)
* Investigation of the peri-lesional penumbra in traumatic brain injury using diffusion tensor imaging to isolate longitudinal changes in white matter integrity (Andrei Irimia, Micah Chambers, Ron Kikinis, Jack van Horn)
* Reconstruction and visualization of the corticospinal tract in traumatic brain injury in the presence of severe hematoma and CSF-perfused edematous tissue using diffusion tensor imaging (Andrei Irimia, Micah Chambers, Ron Kikinis, Jack van Horn)

===Atrial Fibrillation===
* [[2013_Summer_Project_Week:CARMA_workflow_wizard|Cardiac MRI Toolkit LA segmentation and enhancement quantification workflow wizard]] (Salma Bengali, Alan Morris, Brian Zenger, Josh Cates, Rob MacLeod)
* [[2013_Summer_Project_Week:CARMA_Documentataion|Cardiac MRI Toolkit Documentation Project]] (Salma Bengali, Alan Morris, Brian Zenger, Josh Cates, Rob MacLeod)
* [[2013_Summer_Project_Week:CARMA_Visualization|LA model visualization]] (Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod)
* [[2013_Summer_Project_Week:CARMA_AutoLASeg|Cardiac MRI Toolkit: Automatic LA Segmentation with Graph Cuts Module]] (Salma Bengali, Alan Morris, Josh Cates, Gopal, Ross Whitaker, Rob MacLeod)
* [[2013_Summer_Project_Week:Sobolev_Segmenter|Medical Volume Segmentation Using Sobolev Active Contours]] (Arie Nakhmani, Yi Gao, LiangJia Zhu, Rob MacLeod, Josh Cates, Ron Kikinis, Allen Tannenbaum)
* [[2013_Summer_Project_Week:Fibrosis_analysis|Fibrosis distribution analysis]] (Yi Gao, LiangJia Zhu, Rob MacLeod, Josh Cates, Ron Kikinis, Allen Tannenbaum)

===Radiation Therapy===
* Landmark Registration (Steve, Nadya, Greg, Paolo, Erol)
* [[Slicer RT: DICOM-RT Export]] (Greg Sharp, Kevin Wang, Csaba Pinter)
* [[2013_Summer_Project_Week:Proton_dose_calculation | Proton dose calculation]] (Greg Sharp, Kevin Wang, Maxime Desplanques)
* [[2013_Summer_Project_Week:Deformable_registration_validation_toolkit | Deformable registration validation toolkit]] (Greg Sharp, anyone else?)
* [[Analysis of different atlas-based segmentation techniques for parotid glands]] (Christian Wachinger, Karl Fritscher, Greg Sharp, Matthew Brennan)

===Device Integration with Slicer===
* Open-source electromagnetic trackers using OpenIGTLink (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)

===IGT===
* [[2013_Summer_Project_Week:SlicerIGT_Extension| SlicerIGT extension]] (Tamas, Junichi, Laurent)
* [[2013_Summer_Project_Week:Ultrasound_Calibration| Ultrasound Calibration]] (Matthew Toews, Daniel Kostro, William Wells, Steven Aylward, Tamas Ungi)
* Application of Statistical Shape Modeling to Robot Assisted Spine Surgery (Marine Clogenson)
* [[2013_Summer_Project_Week:Epilepsy_Surgery|Identification of MRI Blurring in Temporal Lobe Epilepsy Surgery]] (Luiz Murta)
* [[2013_Summer_Project_Week:_Is_Neurosurgical_Rigid_Registration_Really_Rigid%3F| Is Neurosurgical Rigid Registration Really Rigid?]] (Athena)
* [[2013_Summer_Project_Week:Liver_Trajectory_Management| Liver Trajectory Management]] (Laurent, Junichi)
* [[2013_Summer_Project_Week:4DUltrasound| 4D Ultrasound]] (Laurent, Junichi)
* [[2013_Summer_Project_Week: Individualized Neuroimaging Content Analysis using 3D Slicer in Alzheimer's Disease| Individualized Neuroimaging Content Analysis using 3D Slicer]] (Sidong Liu, Weidong Cai, Sonia Pujol, Ron Kikinis)
* [[2013_Summer_Project_Week: Computer Assisted Surgery| Computer Assisted Reconstruction of Complex Bone Fractures]] (Karl Fritscher, Peter Karasev, Ron Kikinis)
* [[2013_Summer_Project_Week:PerkTutorExtension| Perk Tutor Extension]] (Matthew Holden, Tamas Ungi)

=== '''Informatics'''===
* [[2013_Summer_Project_Week:Biomedical_Image_Computing_Teaching_Modules|3D Slicer based Biomedical image computing teaching modules]] (A.Vilchis, J-C. Avila-Vilchis, S.Pujol)
* [[2013_Summer_Project_Week:Robot_Control| Robot Control]] (A.Vilchis, J-C. Avila-Vilchis, S.Pujol)

==='''Infrastructure'''===
* [[2013_Summer_Project_Week:MarkupsModuleSummer2013| Markups/Annotations rewrite]] (Nicole Aucoin)
* Brain atlas optimisations demo (Marianna)
* Provenance
* [[Patient hierarchy]] (Csaba Pinter)
* Sample data (Steve Pieper, Jim Miller)
** content addressable data, in external data processing in Slicer, cmake file for external data, when write test can decorate the data file name with macro keywords saying it's external
* Plastimatch in NiPype (Paolo, Dave, Hans)
** look for commonalities/reuse of CompareVolumes
* iPython in Slicer (Hans, Jc, Dave)
* Optimizing start time of slicer (Jc)
* [[Common resampling and conversion utility functions in Slicer]] (Steve Pieper, Hans, Kevin Wang, Csaba Pinter)
* [[2013_Summer_Project_Week:CLI_modules_in_MeVisLab| Integrating CTK CLI modules into MeVisLab]] (Hans Meine, Steve, Jc)

==='''Brain Segmentation'''===
* Multi-Atlas-Based Multi-Image Segmentation for Brain MR Images (Minjeong Kim, Xiaofeng Liu, Jim Miller, Dinggang Shen)

== '''Background''' ==

We are pleased to announce the 17th PROJECT WEEK of hands-on research and development activity for applications in Neuroscience, Image-Guided Therapy and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 25th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself will start off with a short presentation by each project team, driven using their previously created description, and will help all participants get acquainted with others who are doing similar work. In the rest of the week, about half the time will be spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half will be spent in project teams, doing hands-on project work. The hands-on activities will be done in 40-50 small teams of size 2-4, each with a mix of multi-disciplinary expertise. To facilitate this work, a large room at MIT will be setup with several tables, with internet and power access, and each computer software development based team will gather on a table with their individual laptops, connect to the internet to download their software and data, and be able to work on their projects. Teams working on projects that require the use of medical devices will proceed to Brigham and Women's Hospital and carry out their experiments there. On the last day of the event, a closing presentation session will be held in which each project team will present a summary of what they accomplished during the week.

This event is part of the translational research efforts of [http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu/ NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], [http://www.cimit.org CIMIT], and OCAIRO. It is an expansion of the NA-MIC Summer Project Week that has been held annually since 2005. It will be held every summer at MIT and Brigham and Womens Hospital in Boston, typically during the last full week of June, and in Salt Lake City in the winter, typically during the second week of January.

A summary of all past NA-MIC Project Events is available [[Project_Events#Past|here]].

== '''Logistics''' ==

*'''Dates:''' June 17-21, 2013.
*'''Location:''' MIT.
*'''REGISTRATION:''' http://www.regonline.com/namic2013summerprojweek. Please note that as you proceed to the checkout portion of the registration process, RegOnline will offer you a chance to opt into a free trial of ACTIVEAdvantage -- click on "No thanks" in order to finish your Project Week registration.
*'''Registration Fee:''' $300.
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.
*'''Room sharing''': If interested, add your name to the list before May 27th. See [[2013_Summer_Project_Week/RoomSharing|here]]

== '''Preparation''' ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing projects in a their [http://wiki.na-mic.org/Wiki/index.php/Engineering:TCON_2013 weekly teleconferences]. Participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 8, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 6, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 13: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Matt)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Where possible, setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Matt)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## See the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers Developer Section of slicer.org] for information.
## Projects to develop extension modules should be built against the latest Slicer4 trunk.

== '''Registrants''' ==

Do not add your name to this list - it is maintained by the organizers based on your paid registration. ([http://www.regonline.com/Register/Checkin.aspx?EventID=1233699 Please click here to register.])

#Peter Anderson, retired, traneus@verizon.net
#Nicole Aucoin, BWH, nicole@bwh.harvard.edu
#Juan Carlos Avila Vilchis, Univ del Estado de Mexico, jc.avila.vilchis@hotmail.com
#Salma Bengali, Univ UT, salma.bengali@carma.utah.edu
#Anthony Blumfield, Radnostics, Anthony.Blumfield@Radnostics.com
#Vinicius Boen, Univ Michigan, vboen@umich.edu
#Francois Budin, NIRAL-UNC, fbudin@unc.edu
#Josh Cates, Univ UT, cates@sci.utah.edu
#Micah Chambers, UCLA, micahcc@ucla.edu
#Marine Clogenson, Ecole Polytechnique Federale de Lausanne (Switzerland), marine.clogenson@epfl.ch
#Manasi Datar, Univ UT-SCI Institute, datar@sci.utah.edu
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
#Karl Fritscher, MGH, kfritscher@gmail.com
#Yi Gao, Univ AL Birmingham, gaoyi.cn@gmail.com
#Rola Harmouche, BWH, rharmo@bwh.harvard.edu
#Matthew Holden, Queen's Univ (Canada), mholden8@cs.queensu.ca
#Hans Johnson, Univ Iowa, hans-johnson@uiowa.edu
#Tina Kapur, BWH/HMS, tkapur@bwh.harvard.edu
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu
#Daniel Kostro, BWH, dkostro@bwh.harvard.edu
#Andras Lasso, Queen's Univ (Canada), lasso@cs.queensu.ca
#Rui Li, GE Global Research, li.rui@ge.com
#Sidong Liu, Univ Sydney (Australia), sliu7418@uni.sydney.edu.au
#William Lorensen, Bill's Basement, bill.lorensen@gmail.com
#Bradley Lowekamp, Medical Science & Computing Inc, bradley.lowekamp@nih.gov
#Athena Lyons, Univ Western Australia, 20359511@student.uwa.edu.au
#Hans Meine, Fraunhofer MEVIS (Germany), hans.meine@mevis.fraunhofer.de
#Jim Miller, GE Global Research, millerjv@ge.com
#Luis Murta, Univ Sao Paulo (Brazil), lomurta@gmail.com
#Arie Nakhmani, Univ AL Birmingham, anry@uab.edu
#Isaiah Norton, BWH, inorton@bwh.harvard.edu
#Dirk Padfield, GE Global Research, padfield@research.ge.com
#Steve Pieper, Isomics Inc, pieper@isomics.com
#Csaba Pinter, Queen's Univ (Canada), pinter@cs.queensu.ca
#Sonia Pujol, HMS, spujol@bwh.harvard.edu
#Adam Rankin, Queen's Univ (Canada), rankin@cs.queensu.ca
#Nathaniel Reynolds, MGH, reynolds@nmr.mgh.harvard.edu
#Raul San Jose, BWH, rjosest@bwh.harvard.edu
#Greg Sharp, MGH, gcsharp@partners.org
#Nadya Shusharina, MGH, nshusharina@partners.org
#Matthew Toews, BWH/HMS, mt@bwh.harvard.edu
#Tamas Ungi, Queen's Univ (Canada), ungi@cs.queensu.ca
#Adriana Vilchis González, Univ del Estado de Mexico, hvigady@hotmail.com
#Demian Wassermann, BWH, demian@bwh.harvard.edu
#David Welch, Univ Iowa, david-welch@uiowa.edu
#Phillip White, BWH/HMS, white@bwh.harvard.edu
#Paolo Zaffino, Univ Magna Graecia of Catanzaro (Italy), p.zaffino@unicz.it
#Lilla Zollei, MGH, lzollei@nmr.mgh.harvard.edu

User:Athena Lyons

2013-06-05T09:07:26Z

Athena Lyons: moved User:Athena Lyons to 2013 Summer Project Week: Is Neurosurgical Rigid Registration Really Rigid?

#REDIRECT [[2013 Summer Project Week: Is Neurosurgical Rigid Registration Really Rigid?]]

Talk:2013 Summer Project Week: Is Neurosurgical Rigid Registration Really Rigid?

2013-06-05T09:07:26Z

Athena Lyons: moved User talk:Athena Lyons to Talk:2013 Summer Project Week: Is Neurosurgical Rigid Registration Really Rigid?

'''Welcome to ''NAMIC''!'''
We hope you will contribute much and well.
You will probably want to read the [[Help:Contents|help pages]].
Again, welcome and have fun! [[User:Tkapur|Tkapur]] 00:11, 8 May 2013 (UTC)

User talk:Athena Lyons

2013-06-05T09:07:26Z

Athena Lyons: moved User talk:Athena Lyons to Talk:2013 Summer Project Week: Is Neurosurgical Rigid Registration Really Rigid?

#REDIRECT [[Talk:2013 Summer Project Week: Is Neurosurgical Rigid Registration Really Rigid?]]

2013 Summer Project Week: Is Neurosurgical Rigid Registration Really Rigid?

2013-06-05T09:07:26Z

Athena Lyons: moved User:Athena Lyons to 2013 Summer Project Week: Is Neurosurgical Rigid Registration Really Rigid?

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
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==Key Investigators==
* University of Western Australia: Athena Lyons, Karol Miller, Adam Wittek, Grand Joldes

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<h3>Objective</h3>
Rigid registration is performed prior to the application of the ISML’s computational biomechanical models of the brain. For application of computational biomechanics it is required that the rigid components of the image (i.e. the skull) be rigidly aligned without scaling. This project investigates the suitability of Slicer's rigid registration method and if, or at what point, brain shift or tumour size effect registration to the extent that image pre-processing is required.

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<h3>Approach, Plan</h3>

Our approach is to compare the effects of rigid registration on whole images to images where only rigid components are considered for both synthetic samples and hospital data. Analysis will be made using an in house developed Canny Edge detection algorithm.
We intend to take advantage of available Slicer experts to better understand the capabilities and limitations of current rigid registration methods and how they may be applicable.

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<h3>Progress</h3>
A sample surgical case that has a significantly sized tumour and large brain shift has been registered and initial data for whole image vs. solely rigid components has been obtained. This data is currently being compared using the Canny Edge detection algorithm.
Synthetic samples are still being prepared for registration.

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==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a report that can be made available on the NA-MIC web page.

==References==
*Intelligent Systems for Medicine Laboratory (ISML) [http://www.mech.uwa.edu.au/ISML www.mech.uwa.edu.au/ISML]
*Mostayed, A., Garlapati, R. R., Joldes, G. R., Wittek, A., Roy, A., Kikinis, R., Warfield, S. K. & Miller, K. [2013. Biomechanical model as a registration tool for image-guided neurosurgery: evaluation against BSpline registration. Annals of Biomedical Engineering, DOI: 10.1007/s10439-013-0838-y.

2013 Summer Project Week: Is Neurosurgical Rigid Registration Really Rigid?

2013-06-05T09:03:26Z

Athena Lyons: 2013 Summer Project Week: Is Neurosurgical Rigid Registration Really Rigid?

2013 Summer Project Week

2013-05-08T00:21:47Z

Athena Lyons: