NAMIC Wiki - User contributions [en]

UNC 2015

2015-06-11T19:43:14Z

Budin:

=Introduction=
The 3D Slicer UNC workshop is a full day course that will combine a series of lectures and hands-on sessions using the 3D Slicer software. The morning session will provide an introduction to the basics of data loading, 3D visualization and image registration. The afternoon session will focus on fundamental and practical aspects of Diffusion MRI analysis.

=Workshop Organizers=
* Sonia Pujol, Ph.D., Brigham and Women's Hospital, Harvard Medical School
* Martin Styner, Ph.D., University of North Carolina at Chapel Hill

=Local Host=
* Martin Styner, Ph.D., University of North Carolina at Chapel Hill

=Tentative Agenda=
*9:00-9:15 am Computer setup assistance by the instructors
*9:15-9:30 am Welcome and Goals of the Workshop (Martin Styner)
*9:30-10:00 am Introduction to the 3D Slicer software and community (Sonia Pujol)
*10:00-11:00 am Hands-on session 1: [http://www.na-mic.org/Wiki/images/7/71/3DDataLoadingandVisualization_SoniaPujol_slicer4.4.pdf 3D Data Loading and Visualization (partI)](Sonia Pujol)
*11:00-11:15 am Coffee break
*11:15-12:15 pm Hands on session2: [[media:RegistrationTutorial_SoniaPujol_UNC2015.pdf | Image registration (Sonia Pujol)]]
*12:15-1:30 pm Lunch
*1:30 pm-2:15 pm An Introduction to Diffusion Tensor Imaging (Sonia Pujol)
*2:15 pm-2:45 pm The DTI Prep Tool [[Media:2015-DTIPrep.pdf‎ | PDF Slides]] (Martin Styner/Francois Budin)
*2:45 pm -3:00 pm Coffee Break
*3:00-3:45 pm White Matter exploration for Neurosurgical Planning (Sonia Pujol)
*3:45-4:30 pm 3D Slicer UNC demos (Martin Styner/Francois Budin) using DTI-Reg [[Media:2015-DTI-Reg-Tutorial.pptx.pdf | PDF Slides]], FiberViewerLight and DTIAtlasFiberAnalyzer
*4:30-5:00 pm Questions from the audience and concluding remarks

=Logistics=
* Date: Thursday June 11, 2015
* Location: Brooks Hall, FB 141
* Workshop Materials: The workshop will be a series of hands-on sessions using Slicer 4.4 and 4.3.1 release versions (http://slicer.org or http://slicer.kitware.com/midas3/slicerpackages/view) and the following datasets:
**[[Media:3DVisualizationData.zip | 3D Visualization Dataset]]
**[[Media:SlicerWorkshop-UNC-20150611.zip | Diffusion Dataset]]
**[[Media:WhiteMatterExplorationData.zip|White Matter Exploration dataset]]
**[[Media:RegistrationData.zip|Registration dataset]]
* Registration: To register to the event, please fill in the [https://docs.google.com/a/cs.unc.edu/forms/d/1to_wiVc921cbgTYtqrJcB8xnlciLp6C8sAMGU8z3c7A/viewform online registration]. In case that the online registration does not work, you can also use the[[Media:RegistrationForm_SlicerWorkshop_UNC2015.doc‎| UNC registration form]] and send it to Alden Sharpe (ajsharpe at cs.unc.edu).
* Download an Ubuntu Virtual Machine with Slicer 4.4 [https://drive.google.com/file/d/0B024c-nPOGSdVW9jVW15U3YxMUU/view?usp=sharing here]

2014-06-27T05:18:39Z

Budin: Created page with '__NOTOC__ <gallery> Image:PW-MIT2014.png|Projects List Image:Condyles.png|Color map </gallery> ==Key Investigators== * UNC: Francois Budin,…'

__NOTOC__
<gallery>
Image:PW-MIT2014.png|[[2014_Summer_Project_Week#Projects|Projects List]]
Image:Condyles.png|Color map
</gallery>

==Key Investigators==
* UNC: Francois Budin, Beatriz Paniagua
* Michigan: Lucia Cevidanes
* BWH: Nicole Aucoin, Alex Yarmarkovich
* Kitware: Jean-Christophe Fillion-Robin
* Isomics: Steve Pieper

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Find what is available in Slicer and what needs to be added to as Extensions or directly in the core of Slicer to accomplish the goal of this grant.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Meetings with all the people involved in this project to get inputs and advice on what Slicer offers.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Organization of the necessary work for this grant:
** SPHARM-PDM as well as ModelToModelDistance are already available in Slicer as extensions. Distance to corresponding points has to be added to ModelToModelDistance.
** Improving the display of continuous scalar fields on mesh surfaces. The work that has been done is great but there is the necessity of adding the possibility to change the scale of the color bar to allow a similar experience as in ShapePopulationViewer.
** Cropping meshes: Design of a project to crop surfaces loaded in Slicer using the plane clipping information already available in Slicer. This allows to not have to re-implement any interaction with the MRML scene as everything that is necessary to move the clipping planes is already implemented.
** ROI picking on a model: Design of a project that will create an ROI on the surface of a model loaded in Slicer based on a fiducial and a radius chosen by the user and that will compute regional statistics on this ROI.
** Fiducial on surface: Reflection about the addition in Slicer of the possibility to constrain the motion of a fiducial on a surface. This would imply modifying the core of Slicer. This was available in Slicer3, and it is possible to add this in Slicer4, but may not be necessary for this grant.
** Reflection on the creation of a new extension in Slicer to compute Distance Weighted Discrimination (DWD) statistics for models. This extension might eventually be necessary for this grant but the currently available pieces of software that could be used to conduct this project faster are under the GPL license and therefore may not be integrated as a Slicer extension in the current Slicer store.
</div>
</div>

2013-06-21T13:29:28Z

Budin: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:SkulbaseRegistration.png
Image:NonGrowingRegistration.png
Image:GrowingRegistration.png
Image:DownsizeImage.png
</gallery>

==Key Investigators==
* UNC/UofM: Vinicius Boen
* UNC: Beatriz Paniagua, Francois Budin
* UofM: Lucia Cevidanes

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

<h3>Objective</h3>
The goal of this project is to develop a registration package oriented to the Dental Research community. The registration package will work as a user friendly package, easy to install via extension mechanism and easy to use. The registration package will perform superimposition using diverse Cranio-Maxillofacial CMF areas as stable regions of reference. This package provides several modules: mathematical operations on label maps, mask creation and non-growing/growing registrations.
</div>

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

<h3>Approach, Plan</h3>
The plan is to:
* Unify tools already created on Slicer3
* Modify them to compile on Slicer4 on all platforms
* Find the best registration parameters that will be transparent for the user
* Create an extension

</div>

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

<h3>Progress</h3>
The project is working as a CLI module on all 3 platforms and the parameters for Growing and NonGrowing patients were set. But it is not working as a extension yet.
https://github.com/viboen/CMFreg
</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable YES
#Other (Please specify)

==References==

* [http://www.nitrc.org/plugins/mwiki/index.php/cmfreg:MainPage CMFReg page at the NITRC web site ]
* [https://sites.google.com/a/umich.edu/dentistry-image-computing/home-1 Dental and Craniofacial Bionetwork for Image Analysis]

2013 Summer Project Week:CMFReg

2013-06-21T13:27:14Z

Budin: /* Key Investigators */

2013 Summer Project Week:DTIPipelineExtensions

2013-06-21T11:47:50Z

Budin:

__NOTOC__
<gallery>
Image:PW-MIT2013.png|[[2013_Summer_Project_Week#Projects|Projects List]]
Image:FiberViewerLightWindows.PNG|FiberViewerLight working on Windows
</gallery>

==Key Investigators==
* UNC NIRAL: Francois Budin
* UNC NIRAL: Martin Styner
* UNC NIRAL: Adrien Kaiser

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

<h3>Objective</h3>
Analysing Diffusion Tensor Images (DTI) require some specific tools to
* Quality control Diffusion Weighted Images (DTIPrep)
* Provide tools to compute and process DTI (DTIProcess)
* Create an average DTI image from a set of images (DTIAtlasBuilder)
* Visualize and edit tracted fibers (FiberViewerLight)
* Analyze tracts (DTIAtlasFiberAnalyzer)
The goal of this project is to develop Slicer4 extensions providing those tools and verify that they correctly perform on all available platforms.
</div>

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

<h3>Approach, Plan</h3>
* Understand and fixing the libraries issue on MacOS
* Create launchers to start modules with Qt GUI on Windows
* Correct and update packaging process
</div>

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

<h3>Progress</h3>
The Slicer extensions are available at :
https://github.com/Slicer/ExtensionsIndex
* FiberViewerLight runs on Windows thanks to its launcher.
* A launcher has been created for DTIAtlasFiberAnalyzer. Packaging issues still have to be corrected
* Libraries issues on MacOS have been fixed
* DTIProcess now works well on MacOS and Slicer4Extension branch has been merged into the trunk

</div>
</div>

File:FiberViewerLightWindows.PNG

2013-06-21T11:40:57Z

Budin:

2013 Summer Project Week Breakout Session:SlicerExtensions

2013-06-17T20:59:38Z

Budin: /* Is there some documentation that explains how to upload and use test data on a different server? */

[[2013_Summer_Project_Week#Agenda|Back to Summer project week Agenda]]

== Before the breakout session ==

* Complete the [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/StartHere New community member checklist]

* [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Build_Instructions Build Slicer] revision >= 22100 with default options

'''Important: Since building Slicer can be network intensive and can take between 1hr and 3hrs, make sure to build it before coming to the Project week'''

== Goal ==

* During the breakout session we will walk through the resources available for creating, building and distributing extension in Slicer 4. It is based on a build of Slicer r22100 and the wiki documentation as of project week (June 17, 2013).

* We will go through the [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/BuildTestPackageDistributeExtensions updated Slicer wiki documentation], then attendees will install extension developed and published by the other attendees.

* Finally we'll go through the list of questions reported below and look at how the current system could be improved.

== Q&A / Group discussion ==

''Do not hesitate to edit this page and add more questions. Before doing so, make also sure to scan through the existing [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/FAQ/Extensions user] and [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ/Extensions developer] extension FAQs''

=== How much of slicer's core infrastructure should be used by extensions ? ===
<pre>
From Andra Lasso: Currently the picture is quite mixed:
: Source control: separate for all extensions
: Issue tracking: separate for most extensions
: Module documentation: shared between Slicer core and extensions
(extensions appear in a different section)
: Hosting of binary releases: shared between Slicer core and extensions
(extensions appear in a different category)
: Dashboard: shared between Slicer core and extensions (extensions appear in
a different category)
</pre>

=== Can you make a python scripted extension without a built version of slicer ? ===

=== Is the API key only used for 'make Experimental' and 'make ExperimentalUpload'? ===

=== Slicer only allows to download extensions that are build against the same Slicer svn revision. If an extension is built against Slicer which was downloaded from github, will Slicer recognize in that that specific version of Slicer matches the version of Slicer that was used to compile the extension? (ie: if I build the extension against a version of Slicer (downloaded from github) on my computer, can I download that extension in that same Slicer?)===

=== Is there some documentation that explains how to upload and use test data from a server? ===

2013 Summer Project Week Breakout Session:SlicerExtensions

2013-06-17T20:54:37Z

Budin: /* Q&A / Group discussion */

2013 Summer Project Week Breakout Session:SlicerExtensions

2013-06-17T20:52:12Z

Budin: /* Q&A / Group discussion */

2013 Summer Project Week Breakout Session:SlicerExtensions

2013-06-17T20:28:22Z

Budin: /* Q&A / Group discussion */

2013 Summer Project Week

2013-06-17T15:01:38Z

Budin: /* Additional Collaborations */

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]] (Steve Pieper) <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 Johnson, Brad Lowekamp)
[[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 Kapur)
[[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]]
|<br>----------------------------------------<br>'''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===
* [[Learn and Apply FiberBundleLabelSelect for Huntington's Disease Data]] (Hans, Demian)
* [[Investigate Potential Tensor Computation Improvement via Positive Semi-Definite (PSD) Tensor Estimation]] (Hans)
* [[2013_Summer_Project_Week:SinglePrecisionRegistrationITK| Single Precision Registration]] (Hans, Brad Lowekamp, Dave, Ali Ghayoor)
* [[Dynamically Configurable Quality Assurance Module for Large Huntington's Disease Database Frontend]] (Dave)
* [[DWIConvert]] (Dave, Kent Williams)
* [[Enhance and update SPL atlas]] (Dave, Hans)
* [[Linear Mixed-effects shape model to explore Huntington's Disease Data]] (Dave, Manasi, Hans, Ross)

===Traumatic Brain Injury===
* [[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)
* [[Validation and testing of 3D Slicer modules implementing the Utah segmentation algorithm for traumatic brain injury]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Guido Gerig, Jack van Horn)
* [[Exploring multi-modal registration for improved longitudinal modeling of patient-specific 4D DTI data]] (Anuja Sharma, Bo Wang, Andrei Irimia, Micah Chambers, Guido Gerig, Jack van Horn)
* [[2013_Summer_Project_Week: A Portable Ultrasound Device for Intracranial Hemorrhage Detection|A Portable Ultrasound Device for Intracranial Hemorrhage Detection]] (Jason White, Vicki Noble, Kirby Vosburgh)

===Atrial Fibrillation and Cardiac Image Analysis===
* [[2013_Summer_Project_Week:Fibrosis_analysis|Fibrosis distribution analysis]] (Yi Gao, LiangJia Zhu, Rob MacLeod, Josh Cates, Ron Kikinis, Allen Tannenbaum)
* [[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:Left_Ventricle_Motion_Analysis_using_Tagged_MRI|Left Ventricle Motion Analysis using Tagged MRI]] (Yang Yu, Shaoting Zhang, Dimitris Metaxas)

===Radiation Therapy===
* [[2013_Summer_Project_Week:Landmark_Registration| Landmark Registration]] (Steve, Nadya, Greg, Paolo, Erol)
* [[2013_Summer_Project_Week:Slicer_RT:_DICOM-RT_Export | SlicerRT: 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, Kevin Wang, Andrey Fedorov, anyone else?)
* [[2013_Summer_Project_Week:Deformable_transforms | Deformable transform handling in Transforms module]] (Csaba Pinter, Alex Yarmarkovich, Andras Lasso, ?)
* [[2013_Summer_Project_Week:Brachy_HDR_Ultrasound | Using ultrasound for prostate HDR brachytherapy]] (Adam Rankin)
* [[Analysis of different atlas-based segmentation techniques for parotid glands]] (Christian Wachinger, Karl Fritscher, Greg Sharp, Matthew Brennan)
* [[2013_Summer_Project_Week:Prostate_radiotherapy_DICOM_communication|DICOM communication between Slicer and Oncentra Prostate radiation therapy planning system]] (Andrey Fedorov, Csaba Pinter, Emily Neubauer-Sugar, ?)

===IGT and Device Integration with Slicer===
* [[2013_Summer_Project_Week:TractAtlasCluster| Tract Atlas and Clustering for Neurosurgery]] (Lauren O'Donnell)
* [[2013_Summer_Project_Week:SlicerIGT_Extension| SlicerIGT extension]] (Tamas Ungi, Junichi Tokuda, Laurent Chauvin)
* [[2013_Summer_Project_Week:Ultrasound_Calibration| Ultrasound Calibration]] (Matthew Toews, Daniel Kostro, William Wells, Stephen Aylward, Isaiah Norton, Tamas Ungi)
* [[2013_Summer_Project_Week:Liver_Trajectory_Management| Liver Trajectory Management]] (Laurent Chauvin, Junichi Tokuda)
* [[2013_Summer_Project_Week:4DUltrasound| 4D Ultrasound]] (Laurent Chauvin, Junichi Tokuda)
* [[2013_Summer_Project_Week:LabelMapStatistics| Label map statistics]] (Laurent Chauvin, Csaba Pinter)
* [[2013_Summer_Project_Week:PerkTutorExtension| Perk Tutor Extension]] (Matthew Holden, Tamas Ungi)
* [[2013_Summer_Project_Week:Open_source_electromagnetic_trackers_using_OpenIGTLink| Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
* [[2013_Summer_Project_Week:3D_prostate_segmentation_of_Ultrasound_image| Segmentation of Prostate Gland from 3D US for Prostate Interventions]] (Xu Li, Andriy Fedorov, Tina Kapur, William Wells)
* [[2013_Summer_Project_Week:3D_prostate_registration_of_Ultrasound_image_using_MRI| Registration of an MRI delineated image of the Prostate Gland ot a 3D US for Prostate Interventions]] (Demian Wassermann, Andriy Fedorov, Tina Kapur, William Wells)

===Chronic Obstructive Pulmonary Disease===
* [[2013_Summer_Project_Week:Airway_Inspector_Porting | Porting Airway Inspector to Slicer 4]] (Raul San Jose, Demian Wassermann, Rola Harmouche)
* [[2013_Summer_Project_Week:MRML_Infrastructure_Airway_Inspector | Airway Inspector: Slicer Extension and MRML Infrastructure]] (Demian Wassermann, Raul San Jose, Rola Harmouche)
* [[2013_Summer_Project_Week:Nipype_CLI_Integration | Integration of Nipype with CLI modules in the Chest Imaging Platform Library ]] (Rola Harmouche,Demian Wassermann, Raul San Jose)

=== '''Additional Collaborations'''===
* [[2013_Summer_Project_Week:Radnostics |Spine Segmentation & Osteoporosis Detection In CT Imaging Studies]] (Anthony Blumfield, Ron Kikinis)
* [[2013_Summer_Project_Week: Computer Assisted Surgery| Computer Assisted Reconstruction of Complex Bone Fractures]] (Karl Fritscher, Peter Karasev, Ivan Kolesov, Allen Tannenbaum, Ron Kikinis)
* [[2013_Summer_Project_Week:XNAT 3D Viewer| XNAT 3D Viewer]] (Amanda Hartung, Steve Pieper, Daniel Haehn)
* [[2013_Summer_Project_Week:kukarobot| Interface for the integration of a KUKA robot using OpenIGTLink]] (Sebastian Tauscher, Thomas Neff, Junichi Tokuda, Nobuhiko Hata)
* [[2013_Summer_Project_Week:Application of Statistical Shape Modeling to Robot Assisted Spine Surgery | Application of Statistical Shape Modeling to Robot Assisted Spine Surgery]] (Marine Clogenson)
* [[2013_Summer_Project_Week:Robot_Control| Robot Control]] (A.Vilchis, J-C. Avila-Vilchis, S.Pujol)
* [[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: 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:CMFReg | Cranio-Maxillofacial Registration]] (Vinicius Boen)
* [[2013_Summer_Project_Week:DTIPipelineExtensions | DTI Analysis Pipeline as Slicer4 Extensions]] (Francois Budin)
*[[2013_Project_Week:WebbasedAnatomicalTeachingFrameworkSummer2013|Web-based anatomical teaching framework]] (Daniel Haehn, Steve Pieper, Rudolph Pienaar, Lilla Zollei, Nathaniel Reynolds)
* [[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:Analyzing Breast Tumor Heterogeneity Using 3D Slicer|Analyzing Breast Tumor Heterogeneity Using 3D Slicer]] (Sneha Durgapal, Jayender Jagadeesan, Tobias Penzkofer, Vivek Narayan)
* [[2013_Summer_Project_Week:WMH Segmentation for Stroke|WMH Segmentation for Stroke]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)

==='''Infrastructure'''===
* [[2013_Summer_Project_Week:MarkupsModuleSummer2013| Markups/Annotations rewrite]] (Nicole Aucoin, Ron Kikinis)
* [[2013_Summer_Project_Week:Patient_hierarchy | Patient hierarchy]] (Csaba Pinter, Andras Lasso, Steve Pieper)
* [[2013_Summer_Project_Week:CLI_Improvements | CLI Improvements (hierarchy nodes, related nodes, roles)]] (Andras Lasso, Csaba Pinter, Jc, Steve, Jim, ?)
* [[2013_Summer_Project_Week:CLI_Matlab | CLI module implementation in Matlab]] (Andras Lasso, Jc, Steve, Jim, ?)
* [[2013_Summer_Project_Week:Sample_Data | Sample Data]] (Steve Pieper, Jim Miller, Bill Lorensen, Jc)
* [[ITK -VTK wrapper]] (Paolo, Dave, Hans)
* [[2013_Summer_Project_Week:Optimizing start time of slicer| Optimizing start time of slicer]] (Jc, Steve)
* [[Common resampling and conversion utility functions in Slicer]] (Csaba Pinter, Steve Pieper, Hans, Kevin Wang)
* [[2013_Summer_Project_Week:CLI_modules_in_MeVisLab| Integrating CTK CLI modules into MeVisLab]] (Hans Meine, Steve, Jc)
* [[2013_Summer_Project_Week:SimpleITK_GUI| Common Usage GUI for SimpleITK]] (Hans Johnson, Dave Welch, Brad Lowekamp)
* [[2013_Summer_Project_Week:Extension_dependencies| Extension dependencies]] (Jc, Adam Rankin)
* [[2013_Summer_Project_Week:Parameter_heirarchy| Parameter Hierarchy]] (Adam Rankin, ??)

== '''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_Project_Week_Rooms| Stata Center / RLE 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.])

#Parth Amin, WIT, aminp@wit.edu
#Charles Anderson, BWH, canderson26@partners.org
#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
#Matthew Brennan, MIT, brennanm@mit.edu
#Francois Budin, NIRAL-UNC, fbudin@unc.edu
#Ivan Buzurovic, BWH/HMS, ibuzurovic@lroc.harvard.edu
#Josh Cates, Univ UT, cates@sci.utah.edu
#Micah Chambers, UCLA, micahcc@ucla.edu
#Laurent Chauvin, BWH - SPL, lchauvin@bwh.harvard.edu
#Marine Clogenson, Ecole Polytechnique Federale de Lausanne (Switzerland), marine.clogenson@epfl.ch
#Adrian Dalca, MIT, adalca@MIT.EDU
#Matthew D'Artista, BWH - SPL, mdartista7@gmail.com
#Manasi Datar, Univ UT-SCI Institute, datar@sci.utah.edu
#Sneha Durgapal, BWH, durgapalsneha@gmail.com
#Luping Fang, Zhejiang Univ of Technology (China), flp@zjut.edu.cn
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
#Gregory Fischer, WPI, gfischer@wpi.edu
#Barton Fiske, zSpace Inc, bfiske@zspace.com
#Matthew Flynn, WIT, flynnm3@wit.edu
#Karl Fritscher, MGH, kfritscher@gmail.com
#Yi Gao, Univ AL Birmingham, gaoyi.cn@gmail.com
#Maria Gonzalez-Puente, WIT, gonzalezpuentem@wit.edu
#Daniel Haehn, Boston Childrens Hospital, daniel.haehn@childrens.harvard.edu
#Michael Halle, BWH-SPL, mhalle@bwh.harvard.edu
#Rola Harmouche, BWH, rharmo@bwh.harvard.edu
#Amanda Hartung, Rochester Inst of Tech, amh1646@rit.edu
#Nobuhiko Hata, BWH, hata@bwh.harvard.edu
#Nicholas Herlambang, AZE Technology Inc, nicholas.herlambang@azetech.com
#Matthew Holden, Queen's Univ (Canada), mholden8@cs.queensu.ca
#Andrei Irimia, UCLA, andrei.irimia@loni.ucla.edu
#Jayender Jagadeesan, BWH-SPL, jayender@bwh.harvard.edu
#Hans Johnson, Univ Iowa, hans-johnson@uiowa.edu
#Tina Kapur, BWH/HMS, tkapur@bwh.harvard.edu
#Alex Kikinis, BWH, alexkikinis@gmail.com
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu
#Nils Klarlund, IEEE, klarlund@ieee.org
#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
#Xu Li, BWH, lixu0103@gmail.com
#Lichen Liang, MGH, lichenl@nmr.mgh.harvard.edu
#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
#Nikos Makris, MGH, nikos@nmr.mgh.harvard.edu
#Katie Mastrogiacomo, BWH - SPL, kmast@bwh.harvard.edu
#Alireza Mehrtash, BWH - SPL, mehrtash@bwh.harvard.edu
#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
#Lauren O'Donnell, BWH, odonnell@bwh.harvard.edu
#Dirk Padfield, GE Global Research, padfield@research.ge.com
#Jian Pan, Zhejiang Univ of Technology (China), pj@zjut.edu.cn
#George Papadimitriou, MGH, georgep@nmr.mgh.harvard.edu
#Tobias Penzkofer, BWH - SPL, pt@bwh.harvard.edu
#Rudolph Pienaar, Boston Childrens Hospital, Rudolph.Pienaar@childrens.harvard.edu
#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
#Peter Savadjiev, BWH, petersv@bwh.harvard.edu
#Anuja Sharma, Univ UT-SCI Institute, anuja@cs.utah.edu
#Greg Sharp, MGH, gcsharp@partners.org
#Nadya Shusharina, MGH, nshusharina@partners.org
#Sebastian Tauscher, Leibniz Univ Hannover (Germany), sebastian.tauscher@imes.uni-hannover.de
#Clare Tempany, BWH, ctempanyafdhal@partners.org
#Cyrill von Tiesenhausen, KUKA Laboratories (Germany), cyrill.tiesenhausen@kuka.com
#Gaurie Tilak, BWH, gaurie_tilak@hms.harvard.edu
#Matthew Toews, BWH/HMS, mt@bwh.harvard.edu
#Junichi Tokuda, BWH, tokuda@bwh.harvard.edu
#Tamas Ungi, Queen's Univ (Canada), ungi@cs.queensu.ca
#Adriana Vilchis González, Univ del Estado de Mexico, hvigady@hotmail.com
#Kirby Vosburgh, BWH, kirby@bwh.harvard.edu
#Christian Wachinger, MIT, wachinge@mit.edu
#Bo Wang, Univ UT-SCI Institute, bowang@sci.utah.edu
#Demian Wassermann, BWH, demian@bwh.harvard.edu
#David Welch, Univ Iowa, david-welch@uiowa.edu
#William Wells, BWH/HMS, sw@bwh.harvard.edu
#Phillip White, BWH/HMS, white@bwh.harvard.edu
#Alex Yarmarkovich, Isomics Inc, alexy@bwh.harvard.edu
#Kitaro Yoshimitsu, BWH, kitarof1@bwh.harvard.edu
#Yang Yu, Rutgers Univ, yyu@cs.rutgers.edu
#Paolo Zaffino, Univ Magna Graecia of Catanzaro (Italy), p.zaffino@unicz.it
#Lilla Zollei, MGH, lzollei@nmr.mgh.harvard.edu

2013 Summer Project Week:DTIPipelineExtensions

2013-06-17T12:30:43Z

Budin: /* Key Investigators */

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

==Key Investigators==
* UNC NIRAL: Francois Budin
* UNC NIRAL: Martin Styner
* UNC NIRAL: Adrien Kaiser

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

<h3>Objective</h3>
Analysing Diffusion Tensor Images (DTI) require some specific tools to
* Quality control Diffusion Weighted Images (DTIPrep)
* Provide tools to compute and process DTI (DTIProcess)
* Create an average DTI image from a set of images (DTIAtlasBuilder)
* Visualize and edit tracted fibers (FiberViewerLight)
* Analyze tracts (DTIAtlasFiberAnalyzer)
The goal of this project is to develop Slicer4 extensions providing those tools and verify that they correctly perform on all available platforms.
</div>

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

<h3>Approach, Plan</h3>

</div>

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

<h3>Progress</h3>
The Slicer extensions are available at :
https://github.com/Slicer/ExtensionsIndex

</div>
</div>

2013 Summer Project Week:DTIPipelineExtensions

2013-06-17T12:28:59Z

Budin: Created page with '__NOTOC__ <gallery> Image:PW-MIT2013.png|Projects List </gallery> ==Key Investigators== * UNC NIRAL: Francois Budin * UNC NIRAL: Martin Sty…'

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

==Key Investigators==
* UNC NIRAL: Francois Budin
* UNC NIRAL: Martin Styner
* UNC NIRAL: Adrien Kaiser

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

<h3>Objective</h3>
Analysing Diffusion Tensor images require some specific tools to
* Quality control Diffusion Weighted Images
* Create an average DTI image from a set of images
* Visualize and edit tracted fibers
* Analyze tracts
The goal of this project is to develop Slicer4 extensions providing those tools and verify that they correctly perform on all available platforms.
</div>

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

<h3>Approach, Plan</h3>

</div>

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

<h3>Progress</h3>
The Slicer extension is available at :
https://github.com/SNRLab/LightWeightRobotIGT

</div>
</div>

2013 Summer Project Week

2013-06-17T12:21:10Z

2013-01-03T16:05:08Z

Budin: /* Slicer4 Extensions */

Back to [[Project Events]], [[Events]]
Back to [[Project Events]], [[AHM_2013]], [[Events]]

__NOTOC__
[[image:PW-SLC2013.png|300px]]

Project Week is a hands on activity -- programming using the open source [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the NA-MIC, NCIGT, and NAC calendars. It is held in the summer at MIT, typically the last week of June, and a shorter version is held in Salt Lake City in the winter, typically the second week of January.

Active preparation begins 6-8 weeks prior to the meeting, when a kick-off teleconference is hosted by the NA-MIC Engineering, Dissemination, and Leadership teams, the primary hosts of this event. Invitations to this call are sent to all na-mic members, past attendees of the event, as well as any parties who have expressed an interest in working with NA-MIC. 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 NA-MIC coverage for all. Subsequent teleconferences 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 are asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself starts off with a short presentation by each project team, driven using their previously created description, and allows all participants to be acquainted with others who are doing similar work. In the rest of the week, about half the time is spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half is spent in project teams, doing hands-on programming, algorithm design, or clinical application of NA-MIC kit tools. The hands-on activities are done in 10-20 small teams of size 3-5, each with a mix of experts in NA-MIC kit software, algorithms, and clinical. To facilitate this work, a large room is setup with several tables, with internet and power access, and each team gathers on a table with their individual laptops, connects to the internet to download their software and data, and is able to work on their projects. On the last day of the event, a closing presentation session is held in which each project team presents a summary of what they accomplished during the week.

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

Please [[AHM_2013#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

= [[AHM_2013#Agenda|'''AGENDA''']] and Project List=

Please:
* [[AHM_2013#Agenda|'''Click here for the agenda for AHM 2013 and Project Week''']].
* [[#Projects|'''Click here to jump to Project list''']]

=Background and Preparation=

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

Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]

=Projects=
* [[2013_Project_Week_Template | Template for project pages]]

==TBI==
* [[4D DTI tractography in Slicer for TBI]] (Bo Wang, Andrei Irimia, Micah Chambers, Jack Van Horn, Bo Wang, Marcel Prastawa, Guido Gerig)
* [[Clinically oriented TBI connectivity analysis in Slicer]] (Andrei Irimia, Bo Wang, Micah Chambers, Jack Van Horn, Marcel Prastawa, Guido Gerig)
* [[Geometric metamorphosis for TBI]] (Danielle Pace, Stephen Aylward, Andrei Irimia, Micah Chambers)
* [[UKF Tractography in Slicer 4]] (Ryan Eckbo, Yogesh Rathi, Demian Wassermann, C.F Westin, Ron Kikinis)
* [[4D DTI analysis via longitudinal modeling of tract diffusivities]] (Anuja Sharma, Bo Wang, Andrei Irimia, Micah Chambers, Jack Van Horn, Marcel Prastawa, Guido Gerig)

==Atrial Fibrillation==
* [[2013_Project_Week:CARMA_Scar_Segmentation|Scar Identification (LiangJia Zhu, Yi Gao, Josh Cates, Rob MacLeod, Allen Tannenbaum)]]
* [[2013_Project_Week:CARMA_PV_Antrum_Cut|SLICER MODULE: PV Antrum Cut Filter (Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod)]]
* [[2013_Project_Week:CARMA_LA_Seg_Gopal|SLICER MODULE: Automated LA Segmentation by Gopal (Gopal Veni, Salma Bengali, Greg Gardner, Alan Morris, Josh Cates, Rob MacLeod)]]
* [[2013_Project_Week:CARMA_2D_Dilate|SLICER MODULE: 2D Dilate Filter (Salma Bengali, Greg Gardner, Alan Morris, Josh Cates, Rob MacLeod)]]
* [[2013_Project_Week:CARMA_PractialLASeg|SLICER WORKFLOW: Practical Manual LA Segmentation in Slicer (Salma Bengali, Greg Gardner, Alan Morris, Josh Cates, Rob MacLeod)]]
* [[2013_Project_Week:CARMA_RT_MRI|PROJECT PLANNING: Real Time MRI in Slicer with OpenIGT (Alan Morris, Ashvin George, Josh Cates, Rob MacLeod)]]

==Slicer4 Extensions==
* [[2013_Project_Week:DTIExtension|Diffusion Tensor Images processing tools as Slicer4 extensions (Francois Budin, Adrien Kaiser, Martin Styner)]]

==Huntington's Disease==
* [[2013_Project_Week:QualityAssuranceModule|Quality assurance module enhancements]] (Dave Welch, Hans Johnson)
* [[2013_Project_Week:PythonModules|Slicer interface to add Python modules to Slicer environment]] (Dave Welch)
* [[2013_Project_Week:FastFiducialRegistrationModule|Fast fiducial registration module]] (Dave Welch, Nicole Aucoin)

==Head and Neck Cancer==
* [[2013_Winter_Project_Week:MABS|Multi atlas-based segmentation]] (Sharp, Shusharina, Golland)
* [[2013_Winter_Project_Week:Hybrid_registration|Hybrid interactive-automatic registration]] (Shusharina, Sharp, Pieper)

==Prostate Interventions==
* [[2013_Project_Week:BRAINSFit_new_features|BRAINSFit in ITK4: extra functionality and testing for prostate MR registration (Andrey, Hans)]]
* [[2013_Project_Week:PkModeling_for_prostate_DCE_MRI|PkModeling for prostate DCE MRI (Jim, Andrey)]]

==Abdominal Interventions==
* [[2013_Project_Week:AbdominalNavigationModule|Abdominal navigation module (Junichi Tokuda, Atsushi Yamada)]]

==Medical Robotics==
* [[Configurable fiducial-based device to image registration]] (Junichi Tokuda)
* Reviving ultrasound integration for visual servoing (Laurent Chauvin, Noby Hata)
* [[2013_Project_Week:AgileMedicalRobot | Agile medical robotics development with Slicer: Case study with MRI compatible robot(Taka Kato, Atsushi Yamada, Noby Hata, Kazuhumi Onuma)]]
* Investigating role of open source in translational research (Miki Kumekawa)

==General Image Guided Therapy==
* [[2013_Project_Week:UnitedSlicerIGTExtension|United SlicerIGT extension, repository, website]] (Tamas Ungi, Junichi Tokuda, Adam Rankin)
* [[2013_Project_Week:MobileImageOverlay|Mobile image overlay augmented reality needle guidance]] (Adam Rankin, Tamas Ungi)
* [[2013_Project_Week:TemperatureMonitoring|Temperature Monitoring for Laser Ablation intervention]] (Laurent Chauvin, Noby Hata)

==Radiation Therapy==
* [[2013_Project_Week:DicomRtExport|SlicerRT: DICOM RT export]] (Kevin Wang, Greg Sharp, Csaba Pinter)
* [[2013_Project_Week:RtBeamGeometry|SlicerRT: Beam geometry widgets]] (Csaba Pinter, Greg Sharp)
* [[2013_Project_Week:MRIAblation|Thermal monitoring tools for MRI-guided laser ablation therapy of brain tumor]] (Laurent Chauvin)

==NA-MIC Kit Internals==
*[[2013_Project_Week:WebbasedAnatomicalTeachingFramework|Web-based anatomical teaching framework for mi2b2]] (Daniel Haehn, Steve Pieper, Sonia Pujol, Randy Gollub, Rudolph Pienaar, Ellen Grant)
*[[2013_Project_Week:ITKv4Default|ITKv4 Default in Superbuild]] - [http://www.na-mic.org/Bug/search.php?project_id=3&sticky_issues=on&sortby=last_updated&dir=DESC&hide_status_id=80&tag_string=ITKv4 Issues] (Matt McCormick, Luis Ibanez, Hans Johnson, Jc?, Bill Lorensen,Bradley Lowekamp)
*[[2013_Project_Week:MarkupsModule|Slicer4 Markups Module]] (Nicole Aucoin)
*[[2013_Project_Week:ColorHierarchies|Slicer4 Color Hierarchies]] (Nicole Aucoin)
*[[2013_Project_Week:PatientHierarchy|Slicer4 Patient Hierarchy]] (Csaba Pinter, Andrey Fedorov?, Nicole Aucoin, Steve Pieper)
*[[2013_Project_Week:ScalarBar|Slicer4 Scalar bar improvements]] (Kevin Wang, Nicole Aucoin Csaba Pinter)
*[[2013_Project_Week:CliMatlabInterface|Slicer4 CLI Matlab interface]] (Kevin Wang, Steve Pieper, Csaba Pinter)
*[[2013_Project_Week:PETStandardUptakeValueComputation| PET/CT SUV Module for Clinicians]] (Sonia Pujol, Markus Van Tol, Nicole Aucoin)
*[[2013_Project_Week:SelfTests|Slicer4 Self Test and Sample Data Refactor]] (Steve Pieper, Jim Miller, Jc, Sankhesh Jhaveri)
*[[2013_Project_Week:SimplifyMRMLReference|Simplify MRML References]] - Issue [http://www.na-mic.org/Bug/view.php?id=2727 #2727] (Alex Yarmarkovich, Andras Lasso?, Steve Pieper, Julien Finet ?, Sankhesh Jhaveri ?, Jc ?)
*[[2013_Project_Week:SlicerIPythonIntegration|Integration of IPython]] (Jc, Hans Johnson, Dave Welch, Steve Pieper, Matt McCormick)
*[[2013_Project_Week:SlicerDebianPackage|Slicer Debian package]] (Jc, Dominique Belhachemi ?, Greg Sharp)
*[[2013_Project_Week:SimplifyRendererMouseInteraction|Simplify renderer window mouse interaction]] - Mailing list [http://slicer-devel.65872.n3.nabble.com/Left-mouse-button-changes-window-level-Is-it-good-tt4026815.html thread] (Csaba ?, Greg?, Andriy?, Steve, Jc)
*[[2013_Project_Week:PotentialSolutionForDefiningRoleAttributesForVolumes|Potential solutions for defining roles and/or attributes for volumes that are preserved when the volume is processed.]] - Mailing list [http://slicer-devel.65872.n3.nabble.com/Volume-node-subclass-tt4026807.html thread] (Andras?, Greg?, Andriy?, Steve, Jc)
*[[2013_Project_Week:SteeredRegistration|Interactive Registration for Image Guided Therapy]] (Dirk Padfield, Jim Miller, Steve Pieper, Kunlin Cao)
*[[2013_Project_Week:Threaded SimpleITK Modules|Threaded SimpleITK Modules]] (Brad Lowekamp, Steve Pieper)

2013 Project Week:DTIExtension

2013-01-03T16:04:35Z

Budin: Created page with '__NOTOC__ <gallery> Image:PW-SLC2013.png|Projects List Image:DTIEstim-B0.png‎| DTIEstim Image:FiberViewerLight1.2-ScreenShot.png| FiberVie…'

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:DTIEstim-B0.png‎| DTIEstim
Image:FiberViewerLight1.2-ScreenShot.png| FiberViewerLight
</gallery>

==Key Investigators==

* Francois Budin, Adrien Kaiser, Martin Styner, UNC NIRAL

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* We have developed several tools to perform various steps of Diffusion Tensor Images processing such as DTI estimation, DTI registration or DTI atlas building.
* Most of those tools are compatible with Slicer4 and are available in different repository such as NITRC (www.nitrc.org)
* We plan to integrate all those tools as Slicer4 extensions to make them available easily to the entire Slicer community
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Verify compatibility of the different tools with Slicer4
* Integration of those tools as Slicer4 CLI modules
* Integration of those tools as Slicer4 extensions
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

File:FiberViewerLight1.2-ScreenShot.png

2013-01-03T16:03:54Z

Budin:

File:DTIEstim-B0.png

2013-01-03T16:03:12Z

Budin:

2013 Winter Project Week

2013-01-03T15:45:49Z

Budin: /* Projects */

Back to [[Project Events]], [[Events]]
Back to [[Project Events]], [[AHM_2013]], [[Events]]

__NOTOC__
[[image:PW-SLC2013.png|300px]]

Project Week is a hands on activity -- programming using the open source [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, and clinical application -- that has become one of the major events in the NA-MIC, NCIGT, and NAC calendars. It is held in the summer at MIT, typically the last week of June, and a shorter version is held in Salt Lake City in the winter, typically the second week of January.

Active preparation begins 6-8 weeks prior to the meeting, when a kick-off teleconference is hosted by the NA-MIC Engineering, Dissemination, and Leadership teams, the primary hosts of this event. Invitations to this call are sent to all na-mic members, past attendees of the event, as well as any parties who have expressed an interest in working with NA-MIC. 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 NA-MIC coverage for all. Subsequent teleconferences 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 are asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

The event itself starts off with a short presentation by each project team, driven using their previously created description, and allows all participants to be acquainted with others who are doing similar work. In the rest of the week, about half the time is spent in breakout discussions on topics of common interest of subsets of the attendees, and the other half is spent in project teams, doing hands-on programming, algorithm design, or clinical application of NA-MIC kit tools. The hands-on activities are done in 10-20 small teams of size 3-5, each with a mix of experts in NA-MIC kit software, algorithms, and clinical. To facilitate this work, a large room is setup with several tables, with internet and power access, and each team gathers on a table with their individual laptops, connects to the internet to download their software and data, and is able to work on their projects. On the last day of the event, a closing presentation session is held in which each project team presents a summary of what they accomplished during the week.

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

Please [[AHM_2013#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

= [[AHM_2013#Agenda|'''AGENDA''']] and Project List=

Please:
* [[AHM_2013#Agenda|'''Click here for the agenda for AHM 2013 and Project Week''']].
* [[#Projects|'''Click here to jump to Project list''']]

=Background and Preparation=

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

Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]

=Projects=
* [[2013_Project_Week_Template | Template for project pages]]

==TBI==
* [[4D DTI tractography in Slicer for TBI]] (Bo Wang, Andrei Irimia, Micah Chambers, Jack Van Horn, Bo Wang, Marcel Prastawa, Guido Gerig)
* [[Clinically oriented TBI connectivity analysis in Slicer]] (Andrei Irimia, Bo Wang, Micah Chambers, Jack Van Horn, Marcel Prastawa, Guido Gerig)
* [[Geometric metamorphosis for TBI]] (Danielle Pace, Stephen Aylward, Andrei Irimia, Micah Chambers)
* [[UKF Tractography in Slicer 4]] (Ryan Eckbo, Yogesh Rathi, Demian Wassermann, C.F Westin, Ron Kikinis)
* [[4D DTI analysis via longitudinal modeling of tract diffusivities]] (Anuja Sharma, Bo Wang, Andrei Irimia, Micah Chambers, Jack Van Horn, Marcel Prastawa, Guido Gerig)

==Atrial Fibrillation==
* [[2013_Project_Week:CARMA_Scar_Segmentation|Scar Identification (LiangJia Zhu, Yi Gao, Josh Cates, Rob MacLeod, Allen Tannenbaum)]]
* [[2013_Project_Week:CARMA_PV_Antrum_Cut|SLICER MODULE: PV Antrum Cut Filter (Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod)]]
* [[2013_Project_Week:CARMA_LA_Seg_Gopal|SLICER MODULE: Automated LA Segmentation by Gopal (Gopal Veni, Salma Bengali, Greg Gardner, Alan Morris, Josh Cates, Rob MacLeod)]]
* [[2013_Project_Week:CARMA_2D_Dilate|SLICER MODULE: 2D Dilate Filter (Salma Bengali, Greg Gardner, Alan Morris, Josh Cates, Rob MacLeod)]]
* [[2013_Project_Week:CARMA_PractialLASeg|SLICER WORKFLOW: Practical Manual LA Segmentation in Slicer (Salma Bengali, Greg Gardner, Alan Morris, Josh Cates, Rob MacLeod)]]
* [[2013_Project_Week:CARMA_RT_MRI|PROJECT PLANNING: Real Time MRI in Slicer with OpenIGT (Alan Morris, Ashvin George, Josh Cates, Rob MacLeod)]]

==Slicer4 Extensions==
* [[2013_Project_Week:DTIExtension|Diffusion Tensor Images processing tools as Slicer4 extensions (Francois Budin, Adrien Kaiser)]]

==Huntington's Disease==
* [[2013_Project_Week:QualityAssuranceModule|Quality assurance module enhancements]] (Dave Welch, Hans Johnson)
* [[2013_Project_Week:PythonModules|Slicer interface to add Python modules to Slicer environment]] (Dave Welch)
* [[2013_Project_Week:FastFiducialRegistrationModule|Fast fiducial registration module]] (Dave Welch, Nicole Aucoin)

==Head and Neck Cancer==
* [[2013_Winter_Project_Week:MABS|Multi atlas-based segmentation]] (Sharp, Shusharina, Golland)
* [[2013_Winter_Project_Week:Hybrid_registration|Hybrid interactive-automatic registration]] (Shusharina, Sharp, Pieper)

==Prostate Interventions==
* [[2013_Project_Week:BRAINSFit_new_features|BRAINSFit in ITK4: extra functionality and testing for prostate MR registration (Andrey, Hans)]]
* [[2013_Project_Week:PkModeling_for_prostate_DCE_MRI|PkModeling for prostate DCE MRI (Jim, Andrey)]]

==Abdominal Interventions==
* [[2013_Project_Week:AbdominalNavigationModule|Abdominal navigation module (Junichi Tokuda, Atsushi Yamada)]]

==Medical Robotics==
* [[Configurable fiducial-based device to image registration]] (Junichi Tokuda)
* Reviving ultrasound integration for visual servoing (Laurent Chauvin, Noby Hata)
* [[2013_Project_Week:AgileMedicalRobot | Agile medical robotics development with Slicer: Case study with MRI compatible robot(Taka Kato, Atsushi Yamada, Noby Hata, Kazuhumi Onuma)]]
* Investigating role of open source in translational research (Miki Kumekawa)

==General Image Guided Therapy==
* [[2013_Project_Week:UnitedSlicerIGTExtension|United SlicerIGT extension, repository, website]] (Tamas Ungi, Junichi Tokuda, Adam Rankin)
* [[2013_Project_Week:MobileImageOverlay|Mobile image overlay augmented reality needle guidance]] (Adam Rankin, Tamas Ungi)

==Radiation Therapy==
* [[2013_Project_Week:DicomRtExport|SlicerRT: DICOM RT export]] (Kevin Wang, Greg Sharp, Csaba Pinter)
* [[2013_Project_Week:RtBeamGeometry|SlicerRT: Beam geometry widgets]] (Csaba Pinter, Greg Sharp)
* [[2013_Project_Week:MRIAblation|Thermal monitoring tools for MRI-guided laser ablation therapy of brain tumor]] (Laurent Chauvin)

==NA-MIC Kit Internals==
*[[2013_Project_Week:WebbasedAnatomicalTeachingFramework|Web-based anatomical teaching framework for mi2b2]] (Daniel Haehn, Steve Pieper, Sonia Pujol, Randy Gollub, Rudolph Pienaar, Ellen Grant)
*[[2013_Project_Week:ITKv4Default|ITKv4 Default in Superbuild]] - [http://www.na-mic.org/Bug/search.php?project_id=3&sticky_issues=on&sortby=last_updated&dir=DESC&hide_status_id=80&tag_string=ITKv4 Issues] (Matt McCormick, Luis Ibanez, Hans Johnson, Jc?, Bill Lorensen,Bradley Lowekamp)
*[[2013_Project_Week:MarkupsModule|Slicer4 Markups Module]] (Nicole Aucoin)
*[[2013_Project_Week:ColorHierarchies|Slicer4 Color Hierarchies]] (Nicole Aucoin)
*[[2013_Project_Week:PatientHierarchy|Slicer4 Patient Hierarchy]] (Csaba Pinter, Andrey Fedorov?, Nicole Aucoin, Steve Pieper)
*[[2013_Project_Week:ScalarBar|Slicer4 Scalar bar improvements]] (Kevin Wang, Nicole Aucoin Csaba Pinter)
*[[2013_Project_Week:CliMatlabInterface|Slicer4 CLI Matlab interface]] (Kevin Wang, Steve Pieper, Csaba Pinter)
*[[2013_Project_Week:PETStandardUptakeValueComputation| PET/CT SUV Module for Clinicians]] (Sonia Pujol, Markus Van Tol, Nicole Aucoin)
*[[2013_Project_Week:SelfTests|Slicer4 Self Test and Sample Data Refactor]] (Steve Pieper, Jim Miller, Jc, Sankhesh Jhaveri)
*[[2013_Project_Week:SimplifyMRMLReference|Simplify MRML References]] - Issue [http://www.na-mic.org/Bug/view.php?id=2727 #2727] (Alex Yarmarkovich, Andras Lasso?, Steve Pieper, Julien Finet ?, Sankhesh Jhaveri ?, Jc ?)
*[[2013_Project_Week:SlicerIPythonIntegration|Integration of IPython]] (Jc, Hans Johnson, Dave Welch, Steve Pieper, Matt McCormick)
*[[2013_Project_Week:SlicerDebianPackage|Slicer Debian package]] (Jc, Dominique Belhachemi ?, Greg Sharp)
*[[2013_Project_Week:SimplifyRendererMouseInteraction|Simplify renderer window mouse interaction]] - Mailing list [http://slicer-devel.65872.n3.nabble.com/Left-mouse-button-changes-window-level-Is-it-good-tt4026815.html thread] (Csaba ?, Greg?, Andriy?, Steve, Jc)
*[[2013_Project_Week:PotentialSolutionForDefiningRoleAttributesForVolumes|Potential solutions for defining roles and/or attributes for volumes that are preserved when the volume is processed.]] - Mailing list [http://slicer-devel.65872.n3.nabble.com/Volume-node-subclass-tt4026807.html thread] (Andras?, Greg?, Andriy?, Steve, Jc)
*[[2013_Project_Week:SteeredRegistration|Interactive Registration for Image Guided Therapy]] (Dirk Padfield, Jim Miller, Steve Pieper, Kunlin Cao)
*[[2013_Project_Week:Threaded SimpleITK Modules|Threaded SimpleITK Modules]] (Brad Lowekamp, Steve Pieper)

2012 Summer Project Week:DTI-Reg

2012-06-22T13:14:29Z

Budin: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:Glyphs-coronal-clean.png|DTI image: Color coded FA and glyphs
</gallery>

==Key Investigators==
* UNC: Francois Budin

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

<h3>Objective</h3>
DTI-reg is a tool available on NITRC that allows to register DTI images. It has been developped to work with Slicer3. Other tools such as dtiprocess already exist and work with Slicer3. We want to test and integrate those existing tools in Slicer4 to perform DTI atlas based fiber analysis.

</div>

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

<h3>Approach, Plan</h3>

Existing tools may need re-writing to make them slicer4 compatible. The goal is to integrate them to Slicer4 as extensions.

</div>

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

<h3>Progress</h3>

DTI-reg now compiles with Slicer4 in the svn branch SlicerExtension. DTIProcessToolkit, when downloaded through DTI-reg, also compiles with Slicer4. The next step is to integrate those tools as extensions in Slicer4.

http://www.nitrc.org/projects/dtireg
</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

#Slicer Module
##Extension -- commandline