NAMIC Wiki - User contributions [en]

2015 Summer Project Week:SlicerCardboard

2015-06-24T15:22:39Z

Utsav Pardasani: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:SlicerCardboard.png
</gallery>

==Key Investigators==
* Utsav Pardasani (Robarts)
* Adam Rankin (Robarts)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Add the capability for Slicer to render stereo views on mobile-phone based viewers.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Develop a websocket server in Slicer to serve up rendered stereo views to cheap vr goggles
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*Successful websocket server implementation, however the image-compression is blocking the renderloop. Also needed is lens-distortion correction
*Plan to implement Steve's model from SlicerWeb to bring potential for interactivity.
*Github Page: https://github.com/Utsavvy/SlicerCardboard
*Planned collaboration with Frankie to integrate rift player with Slicer Cardboard
</div>
</div>

2015 Summer Project Week:SlicerCardboard

2015-06-24T15:19:10Z

Utsav Pardasani: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:SlicerCardboard.png
</gallery>

==Key Investigators==
* Utsav Pardasani
* Adam Rankin

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Add the capability for Slicer to render stereo views on mobile-phone based viewers.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Develop a websocket server in Slicer to serve up rendered stereo views to cheap vr goggles
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*Successful websocket server implementation, however the image-compression is blocking the renderloop. Also needed is lens-distortion correction
*Plan to implement Steve's model from SlicerWeb to bring potential for interactivity.
*Github Page: https://github.com/Utsavvy/SlicerCardboard
*Planned collaboration with Frankie to integrate rift player with Slicer Cardboard
</div>
</div>

2015 Summer Project Week:TrackerlessMRIUSFusion

2015-06-24T15:07:37Z

Utsav Pardasani: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Utsav Pardasani
* Adam Rankin
* Robert Owen, BK
* Andrey Fedorov, BWH

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Work toward a real-time trackerless image-based registration that is constrained by a clinically relevant geometry. (With special emphasis on intra-operative neuroimaging)
* Can support calibration / registration with tracked-systems
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Evaluate and develop various image-similarity metrics in a geometrically constrained search space.
* Rather than relying on an optimizer, the goal would be to find a fast similarity metric that enables a dense sampling of the objective function search space.
* Make use of the BITE dataset for US-MRI images. http://www.bic.mni.mcgill.ca/Services/ServicesBITE
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Initial good results with the LC2 metric constrained to a craniotomy site with 3 degrees of freedom.
* Given a pair of registered US-MRI images, the module calculates the similarity metric output perturbed between the two images.
* Plan to integrate information from image-features per Matthew Toews advice.
* Working toward expanding the code to work with prostate dataset from Andre
</div>
</div>

2015 Summer Project Week:TrackerlessMRIUSFusion

2015-06-24T15:01:11Z

Utsav Pardasani: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Utsav Pardasani
* Adam Rankin
* Robert Owen, BK
* Andrey Fedorov, BWH

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Work toward a real-time trackerless image-based registration that is constrained by a clinically relevant geometry. (With special emphasis on intra-operative neuroimaging)
* Can support calibration / registration with tracked-systems
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Evaluate and develop various image-similarity metrics in a geometrically constrained search space.
* Rather than relying on an optimizer, the goal would be to find a fast similarity metric that enables a dense sampling of the objective function search space.
* Make use of the BITE dataset for US-MRI images. http://www.bic.mni.mcgill.ca/Services/ServicesBITE
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Initial good results with the LC2 metric constrained to a craniotomy site with 3 degrees of freedom.
* Given a pair of registered US-MRI images, the module calculates the similarity metric output perturbed between the two images.
* Plan to integrate image-features per Matthew Toews advice.
* Working toward expanding the code to work with prostate dataset from Andre Federov
</div>
</div>

2015 Summer Project Week:SlicerCardboard

2015-06-24T14:59:22Z

Utsav Pardasani:

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:SlicerCardboard.png
</gallery>

==Key Investigators==
* Utsav Pardasani
* Adam Rankin

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Add the capability for Slicer to render stereo views on mobile-phone based viewers.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Develop a websocket server in Slicer to serve up rendered stereo views to cheap vr goggles
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*Successful websocket server implementation, however the image-compression is blocking the renderloop. Also needed is lens-distortion correction
*Github Page: https://github.com/Utsavvy/SlicerCardboard
*Planned collaboration with Frankie to integrate rift player with Slicer Cardboard
</div>
</div>

2015 Summer Project Week:Volume rendering with DCMJS and THREEJS

2015-06-22T10:31:27Z

Utsav Pardasani: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Nicolas Rannou
* Steve Pieper
* Utsav Pardasani, Adam Rankin, Diego Cantor? (remote, maybe!)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Simulate 3D texture in the GLSL shader.
* Implement a basic volume rendering of DICOM data.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Implement a JS DICOM parser.
* Create 3D textures "polyfill" in Fragment Shader.
* Implement Volume Rendering with THREEJS.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2015 Summer Project Week:Volume rendering with DCMJS and THREEJS

2015-06-22T10:25:21Z

Utsav Pardasani: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Nicolas Rannou
* Steve Pieper
* Utsav Pardasani, Adam Rankin, Diego Cantor (remote, maybe!)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Simulate 3D texture in the GLSL shader.
* Implement a basic volume rendering of DICOM data.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Implement a JS DICOM parser.
* Create 3D textures "polyfill" in Fragment Shader.
* Implement Volume Rendering with THREEJS.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2015 Summer Project Week:T1 mapping

2015-06-22T10:03:52Z

Utsav Pardasani: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Xiao Da (MGH), Yangming Ou (MGH), Andriy Fedorov (BWH), Jayashree Kalpathy-Cramer (MGH)
* Utsav Pardasani (Observing)

==Project Description==
T1 mapping estimates effective tissue parameter maps (T1) from multi-spectral FLASH MRI scans with different flip angles. T1 mapping can be used to optimize parameters for a sequence, monitor diseased tissue, measure Ktrans in DCE-MRI and etc.
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Estimate effective T1 from multi-spectral FLASH MRI scans with different flip angles
* Implement T1 mapping algorithm as a Slicer extension using C++
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Start with [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DWModeling prostate diffusion module]
* Update equations for T1 mapping
* Compare the results using C++, [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/T1_Mapping Python], [https://surfer.nmr.mgh.harvard.edu/fswiki/mri_ms_fitparms Freesurfer ] with ground truth of T1 for [https://dblab.duhs.duke.edu/modules/QIBAcontent/index.php?id=1 QIBA phantom]
* Test the Slicer module on MGH Brain Tumor MR Data with multiple flip angles

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Equations have already been updated
* Working on the GUI
* Working on the comparison
</div>
</div>

==References==

* [https://dblab.duhs.duke.edu/modules/QIBAcontent/index.php?id=1 QIBA T1 phantom]
* [http://europepmc.org/articles/pmc3620726 Basic equations for T1 mapping]

2015 Summer Project Week:T1 mapping

2015-06-22T10:03:13Z

Utsav Pardasani: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Xiao Da (MGH), Yangming Ou (MGH), Andriy Fedorov (BWH), Jayashree Kalpathy-Cramer (MGH)
* Utsav (Observing)

==Project Description==
T1 mapping estimates effective tissue parameter maps (T1) from multi-spectral FLASH MRI scans with different flip angles. T1 mapping can be used to optimize parameters for a sequence, monitor diseased tissue, measure Ktrans in DCE-MRI and etc.
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Estimate effective T1 from multi-spectral FLASH MRI scans with different flip angles
* Implement T1 mapping algorithm as a Slicer extension using C++
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Start with [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/DWModeling prostate diffusion module]
* Update equations for T1 mapping
* Compare the results using C++, [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Modules/T1_Mapping Python], [https://surfer.nmr.mgh.harvard.edu/fswiki/mri_ms_fitparms Freesurfer ] with ground truth of T1 for [https://dblab.duhs.duke.edu/modules/QIBAcontent/index.php?id=1 QIBA phantom]
* Test the Slicer module on MGH Brain Tumor MR Data with multiple flip angles

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Equations have already been updated
* Working on the GUI
* Working on the comparison
</div>
</div>

==References==

* [https://dblab.duhs.duke.edu/modules/QIBAcontent/index.php?id=1 QIBA T1 phantom]
* [http://europepmc.org/articles/pmc3620726 Basic equations for T1 mapping]

2015 Summer Project Week:BigDataFeatures

2015-06-22T09:35:02Z

Utsav Pardasani: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Matthew Toews, École de Technologie Supérieure
* William Wells, BWH, Harvard Medical School
* Raul San Jose Estepar, BWH, Harvard Medical School
* Tina Kapur, BWH, Harvard Medical School
* Utsav Pardasani, Robarts (Observing!)

==3D SIFT-Rank Visualization, SLC 2015, IPMI 2015 ==
[[File:Lung-ct.png|300px|thumb|left|Lung CT Features]]
[[File:Img-feat.png‎|300px|thumb|left|Data Reduction for 20000 lung CT volumes]]
[[File:3D_SIFT_Prostate.png|300px|thumb|left|Prostate US Features]]

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* This project will investigate the use of 3D SIFT-RANK image features for organizing and deriving information from 3D medical image volumes.
* Technology: invariant feature extraction, descriptor representation.
* Application domains: registration, segmentation, classification.
* Image domains: lung CT, brain MR, prostate and brain ultrasound.
* Clinical use case scenarios: chronic obstructive pulmonary disease, Alzheimer's disease, cancer.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Discussion and documentation
* Algorithms: fast KNN methods, hashing, robust estimation (RANSAC, Hough transform).
* Mathematical formalisms: probabilistic inference, kernel methods, manifold learning.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

==References==
[http://www.na-mic.org/Wiki/index.php/3D_SIFT_VIEW] SIFT View, NAMIC 2015 SLC Project Week <br>
[http://www.matthewtoews.com/publications.html] "A Feature-based Approach to Big Data Analysis of Medical Images", M. Toews, C. Wachinger, R. S. J. Estepar, W.M. Wells III.
Information Processing in Medical Imaging (IPMI), 2015.<br>
[http://www.matthewtoews.com/publications.html] "Keypoint Transfer Segmentation", C. Wachinger, M. Toews, G. Langs, W.M. Wells IIIi, P. Golland. Information Processing in Medical Imaging (IPMI), 2015.

2015 Summer Project Week:Slicer Conda

2015-06-22T09:31:14Z

Utsav Pardasani: /* Project Description */

<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Jorge Onieva
* Raúl San José
* Alex Yarmarkovich
* Utsav Pardasani
* Steve Pieper
* JC

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Integrate Slicer with Conda Python so that the community could use Conda packages easily in Slicer.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
An initial approach and a proof of concept has already been done using Miniconda. During the NAMIC week we will try to take the final steps for the integration in all the platforms

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Windows Installer! https://github.com/Utsavvy/SlicerCondaWinBin
</div>
</div>

2015 Summer Project Week:OpenSource MRTRUS Fusion for Prostate biopsy

2015-06-22T09:22:55Z

Utsav Pardasani: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Andrey Fedorov, BWH
* Andras Lasso, Queen's
* Clare Tempany, BWH
* Utsav Pardasani, Robarts (Observer)

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Continue work on open-source system for tracked MRI-TRUS fusion for prostate IGT interventions (targeted biopsy primarily)
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* discuss optimal Plus setup to address the issue of 32-bit only tracker drivers and 64-bit volume reconstruction
** command line invocation vs OpenIGTLink communication for Plus sequence operations
* discuss the use of slicelet as user interface
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
First use of EM-tracked freehand TRUS during prostate biopsy attempted at BWH on June 9; identified issues that need to be discussed with the Plus team:
* disconnect of framegrabber freezes everything
* sensor out of the box is not reported as a warning
* need to record sensor quality
* error messages about missing frames from framegrabber
* sometime Slicer/Plus get into a state where it is not possible to establish OpenIGTLink connection; the only solution was to restart the PC!
* need to consider separate Plus instances for tracker data collection (32 bit) and framegrabber data (64bit for volume reconstruction)
</div>
</div>

2015 Summer Project Week:TrackerlessMRIUSFusion

2015-06-22T09:16:30Z

Utsav Pardasani: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Utsav Pardasani
* Adam Rankin

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Work toward a real-time trackerless image-based registration that is constrained by a clinically relevant geometry. (With special emphasis on intra-operative neuroimaging)
* Can support calibration / registration with tracked-systems
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Evaluate and develop various image-similarity metrics in a geometrically constrained search space.
* Rather than relying on an optimizer, the goal would be to find a fast similarity metric that enables a dense sampling of the objective function search space.
* Make use of the BITE dataset for US-MRI images. http://www.bic.mni.mcgill.ca/Services/ServicesBITE
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Initial good results with the LC2 metric constrained to a craniotomy site.
* Given a pair of registered US-MRI images, the module calculates the similarity metric output perturbed between the two images.
</div>
</div>

2015 Summer Project Week:TrackerlessMRIUSFusion

2015-06-22T09:15:58Z

Utsav Pardasani: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Utsav Pardasani
* Adam Rankin

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Work toward a real-time trackerless image-based registration that is constrained by a clinically relevant geometry. (With special emphasis on intra-operative neuroimaging)
* Can support calibration / registration with tracked-systems
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Evaluate and develop various image-similarity metrics in a geometrically constrained search space.
* Rather than relying on an optimizer, the goal would be to find a fast similarity metric that enables a dense sampling of the objective function search space.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Initial good results with the LC2 metric constrained to a craniotomy site.
* Given a pair of registered US-MRI images, the module calculates the similarity metric output perturbed between the two images.
</div>
</div>

2015 Summer Project Week:TrackerlessMRIUSFusion

2015-06-22T09:12:57Z

Utsav Pardasani:

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Utsav Pardasani
* Adam Rankin

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Work toward a real-time trackerless image-based registration that is constrained by a clinically relevant geometry.
* Can support calibration / registration with tracked-systems
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Evaluate and develop various image-similarity metrics in a geometrically constrained search space.
* Rather than relying on an optimizer, the goal would be to find a fast similarity metric that enables a dense sampling of the objective function search space.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Initial good results with the LC2 metric constrained to a craniotomy site.
* Given a pair of registered US-MRI images, the module calculates the similarity metric output perturbed between the two images.
</div>
</div>

2015 Summer Project Week:TrackerlessMRIUSFusion

2015-06-22T09:07:47Z

Utsav Pardasani: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Utsav Pardasani

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Work toward a real-time trackerless image-based registration that is constrained by a clinically relevant geometry.
* Can support calibration / registration with tracked-systems
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Evaluate and develop various image-similarity metrics in a geometrically constrained search space.
* Rather than relying on an optimizer, the goal would be to find a fast similarity metric that enables a dense sampling of the objective function search space.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Initial good results with the LC2 metric constrained to a craniotomy site.
* Given a pair of registered US-MRI images, the module calculates the similarity metric output perturbed between the two images.
</div>
</div>

2015 Summer Project Week:TrackerlessMRIUSFusion

2015-06-22T08:57:08Z

Utsav Pardasani: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Utsav Pardasani

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Work toward a real-time trackerless image-based registration that is constrained by a clinically relevant geometry.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Evaluate and develop various image-similarity metrics in a geometrically constrained search space.
* Rather than relying on an optimizer, the goal would be to find a fast similarity metric that enables a dense sampling of the objective function search space.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Initial good results with the LC2 metric constrained to a craniotomy site.
* Given a pair of registered US-MRI images, the module calculates the similarity metric output perturbed between the two images.
</div>
</div>

2015 Summer Project Week:TrackerlessMRIUSFusion

2015-06-22T08:55:24Z

Utsav Pardasani: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Utsav Pardasani

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Work toward a real-time trackerless image-based registration that is constrained by a clinically relevant geometry.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Evaluate and develop various image-similarity metrics in a geometrically constrained search space.
* Implement the kernels in PyCuda
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Initial good results with the LC2 metric constrained to a craniotomy site.
* Given a pair of registered US-MRI images, the module calculates the similarity metric output perturbed between the two images.
</div>
</div>

2015 Summer Project Week:TrackerlessMRIUSFusion

2015-06-22T08:54:26Z

Utsav Pardasani: /* Project Description */

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Utsav Pardasani

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Work toward a real-time trackerless image-based registration
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Evaluate and develop various image-similarity metrics in a geometrically constrained search space.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Initial good results with the LC2 metric constrained to a craniotomy site.
* Given a pair of registered US-MRI images, the module calculates the similarity metric output perturbed between the two images.
</div>
</div>

2015 Summer Project Week

2015-06-22T08:52:10Z

Utsav Pardasani: /* Image-Guided Therapy */

__NOTOC__

[[image:PW-Summer2015.png|300px]]
<br>

'''Welcome to the web page for the 21st Project Week! This is the first Project Week that is being held in conjunction with the [http://www.cars-int.org/ CARS conference].'''

==Logistics==

*'''Dates:''' June 21-24, 2015.
*'''Location:''' [http://www.nh-collection.com/hotel/nh-collection-barcelona-constanza NH Collection Constanza Hotel, Barcelona, Spain]
*'''REGISTRATION:''' Please register by adding your name to the list at the end of this page
*'''Registration Fee:''' None. The organizers will cover the charge for the conference room, while all attendees are responsible for their own hotel rooms as well as food.
*'''Hotel:''' You are welcome to book a room using the CARS 2015 conference services ([http://www.cars-int.org/fileadmin/templates/download/2015/CARS_2015_accomondation.pdf Click here for form])
*To attend the CARS meeting, please visit [http://www.cars-int.org/ http://www.cars-int.org/]

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Sunday, June 21
!style="width:18%" |Monday, June 22 <br> Room Berlin
!style="width:18%" |Tuesday, June 23 <br> Room Berlin
!style="width:18%" |Wednesday, June 24 <br> Room Berlin
|-
|bgcolor="#ffffdd"|'''9:00am-3:00pm:'''
|rowspan=3 valign=bottom|<hr>'''6pm''' Meeting with All Participants in Hotel Constanza Lobby
|'''10:00-11am:''' <font color="#503020">Rapid Introduction of all Projects and Teams <br>
'''11am-3pm''' <font color="#503020">Work <br>

|
'''10:00am-11am:''' <font color="#503020">'''Breakout Session:'''</font><br>[[2014_Project_Week_Breakout_Session: Slicer for users| Slicer for users]] (Ron Kikinis) <br>
'''11am-3pm''' <font color="#503020">Work
| <font color="#503020">Work <br>
|-
|bgcolor="#ffffdd"|'''2:00pm-4:00pm'''
|bgcolor="#ffffaa"|Lunch <br> [[Barcelona Restaurants|Places to Eat]]
|bgcolor="#ffffaa"|Lunch<br> [[Barcelona Restaurants|Places to Eat]]
|bgcolor="#ffffaa"|Lunch<br> [[Barcelona Restaurants|Places to Eat]]
|-
|bgcolor="#ffffdd"|'''4:00-7:00pm'''
|<font color="#503020"> Work
|'''5:00-7:00pm:''' <font color="#503020">'''Breakout Session:'''</font><br>[[2015_Summer_Project_Week/SoftwareStack| Open Software Stack]] (Steve Pieper) <br>4pm-6pm: Registration Desk Open for CARS attendees. Please pick up badges. <br>
|'''4:00-5:00pm:''' <font color="#503020"> Work <br>
'''5:00-6pm:''' Report Progress
|-
|bgcolor="#ffffdd"|'''7:00pm'''
|bgcolor="#f0e68b"|
|bgcolor="#f0e68b"|Adjourn for the day <br> [[Barcelona Restaurants|Places to Eat]]
|bgcolor="#f0e68b"|Adjourn for the day <br> [[Barcelona Restaurants|Places to Eat]]
|bgcolor="#f0e68b"|'''6:00pm''' Adjourn Project Week and relocate to CARS Opening<br> '''7:30pm''' CARS Welcome Reception
|}

*Please note that start, end, and mealtimes have been set to match local schedules in Barcelona.
*Here is a list of [[Barcelona Restaurants | locally recommended places to eat]] in the vicinity of the conference hotel. All participants are responsible for their own meals.

== '''Background''' ==

Founded in 2005, the National Alliance for Medical Image Computing (NAMIC), was chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], built using [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws researchers from around the world. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO], and [https://www.ncigt.org/IGTWiki/index.php/Projects/IGTWeb:R25 NCI Funded Image-Guided Fellowship Program].

A summary of all previous Project Events is available [[Project_Events#Past|here]].

This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.

The 21st Project Week is being held on conjunction with the [http://www.cars-int.org/ CARS conference].

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

=Projects=
* [[2015_Summer_Project_Week_Template | Template for project pages]]

==Equipment==

*[[2015_Summer_Project_Week:Equipment|Specialized equipment people are going to bring]] (Please add to this list if you are bringing anything)

==Image-Guided Therapy==
*[[2015_Summer_Project_Week:SlicerIGT|SlicerIGT tutorials for use cases]] (Tamas Ungi, Andras Lasso, Jayender Jagadeesan, Alvaro Gomez, Noby Hata)
*[http://www.na-mic.org/Wiki/index.php/2015_Refinement_Registration_Module Refinement of RegistrationModule] (Peter Behringer, Andrey Fedorov)
*[[2015_Summer_Project_Week:IGTSliceletBase| Create base classes for IGT slicelet]] (Andras Lasso, Andrey Fedorov, Adam Rankin)
*[http://www.na-mic.org/Wiki/index.php/2015_BRAINSFit_registration_in_SimpleITK BRAINSFit registration in SimpleITK] (Peter Behringer, Andrey Fedorov, Dženan Zukić)
*[http://www.na-mic.org/Wiki/index.php/2015_Multi_atlas_based_prostate_segmentation Multi atlas based prostate segmentation] (Paolo Zaffino, Giampaolo Pileggi, Salvatore Scaramuzzino, Peter Behringer, Andrey Fedorov, Maria Francesca Spadea)
*[http://www.na-mic.org/Wiki/index.php/2015_Multimodal_Guidance_for_Breast_Cancer_Surgery Multimodal Guidance for Breast Cancer Surgery] (Mikael Brudfors, Javier Pascau)
*[[2015_pilot trajectory planning | Pilot Trajectory Planning(Caroline Essert, Sonia Pujol)]]
*[[2015_Summer_Project_Week:LinearFeatureRegistration|Linear Feature Registration]] (Matthew Holden)
*[[2015_Summer_Project_Week:LightWeightRobotIGT | Integration of a KUKA robot using OpenIGTLink ]] (Sebastian Tauscher, Junichi Tokuda)
*[[2015_Summer_Project_Week:USReconstruction | Gated 3D Ultrasound Reconstructions with the Help of a Single-Element US Transducer ]] (Frank Preiswerk, Laurent Chauvin)
*[[2015 Orthognathic Surgery|Orthognathic Surgery]] (Dženan Zukić, Kitware)
*[[2015_Summer_Project_Week:SlicerTAVI | SlicerTAVI ]] (Adam Rankin)
*[http://www.na-mic.org/Wiki/index.php/2015_pyDBS pyDBS module update to Slicer4.4 (Sara Fernandez-Vidal, Yulong Zhao, Sonia Pujol)]
*[[2015_Summer_Project_Week:OpenSource_MRTRUS_Fusion_for_Prostate_biopsy|Open-source MRI-TRUS Fusion for Prostate biopsy]] (Andrey Fedorov, Andras Lasso)
*[[2015_Summer_Project_Week:TrackerlessMRIUSFusion | Trackerless MRI - US Registration ]] (Utsav Pardasani)

==Feature Based Image Analysis==
*[[2015_Summer_Project_Week:LungCAD| LungCAD]] (Jayender Jagadeesan, Tobias Penzkofer, Sandy Wells)
*[[2015_Summer_Project_Week:QuantitativeProstate | Texture Analysis for Prostate Imaging]] (Tobias Penzkofer, Jay Jagadeesan, Tina Kapur)
*[[2015_Summer_Project_Week:BigDataFeatures | Big Data Medical Image Analysis using Local Features]] (Matthew Toews, William Wells, Raul San Jose Estepar, Tina Kapur)
*[[2015_Summer_Project_Week:AutomaticCephalometric | Automatic Cephalometric Analysis ]] (J. Jesus Montufar, Marcelo Romero)

==Chest Imaging Platform==
*[[2015_Summer_Project_Week:Slicer_CIP | Slicer CIP: advanced features and deployment ]] (Raúl San José, Alex Yarmarkovich, Jorge Onieva)
*[[2015_Summer_Project_Week:PAA_Ratio | PAA Ratio Module ]] (Jorge Onieva,Raúl San José)
*[[2015_Summer_Project_Week:Tracheal_Stent_Planning | Planning for tracheal stents ]] (Raúl San José, Jorge Onieva, George Cheng)

==QIICR==
*[[2015_Summer_Project_Week:DSC | Dynamic Susceptibility Contrast (DSC) MRI for brain ]] (Xiao Da, Yangming Ou, Andriy Fedorov, Steve Pieper, Jayashree Kalpathy-Cramer)
*[[2015_Summer_Project_Week:T1 mapping | T1 mapping for Dynamic Contrast Enhanced (DCE) MRI ]] (Xiao Da, Yangming Ou, Andriy Fedorov, Jayashree Kalpathy-Cramer)
*[[2015_Summer_Project_Week:DCMTK| Integration and testing of new DCMTK with Slicer]] (Michael Onken, Andrey Fedorov, Steve Pieper)

==Infrastructure==
*[[2015_Summer_Project_Week:Python_scripts_from_command_line|Simplify use of python scripts from the command line]] (Andrey Fedorov, Steve Pieper, Robin Weiss, Artem Mamonov)
*[[2015_Summer_Project_Week:Return_Fiducials_from_CLIs | Return fiducials from CLIs]] (Nicole Aucoin,Hans Meine)
*[[2015_Summer_Project_Week:Update Checker | Update Checker]] (Franklin King, BWH)
*[[2015_Summer_Project_Week:Integrated Virtual Reality Viewer | Integrated Virtual Reality Viewer]] (Franklin King, BWH, Utsav Pardasani)
*[[2015_Summer_Project_Week:SegmentationNode| Use new Segmentation node in Editor]] (Andras Lasso, Steve Pieper)
*[[2015_Summer_Project_Week:Slicer_Conda | Integrate Conda Python in Slicer]] (Raúl San José, Jorge Onieva, Utsav Pardasani)
*[[2015_Summer_Project_Week:CLIModules_Backgrounding_in_MeVisLab | Running CLI Modules in the background in MeVisLab]] (Hans Meine)
*[[2015_Summer_Project_Week:CLIModules_Indexing | CLI Modules elasticsearch / kibana dashboard]] (Hans Meine, JC, Steve Pieper)
*[[2015_Summer_Project_Week:CTK_Interative_Plugins | CTK plugins / paths towards interoperability with GUI & interaction]] (Hans Meine, Steve Pieper, Nicolas Rannou)
*[[2015_Summer_Project_Week:BRAINSFit_in_MeVisLab | Interoperability tests with "interesting" CLI modules (BRAINSFit, CIP, UKFTractography?) in MeVisLab (/Frontier)]] (Hans Meine, Steve Pieper)

==Web==
*[[2015_Summer_Project_Week:Dicom parsing with DCMJS | Dicom parsing with DCMJS]] (Nicolas Rannou, Michael Onken, Steve Pieper)
*[[2015_Summer_Project_Week:Volume rendering with DCMJS and THREEJS | Volume Rendering with DCMJS and THREEJS]] (Nicolas Rannou, Steve Pieper)
*[[2015_Summer_Project_Week:CTK for the web and touch devices| CTK for the web and touch devices]] (Nicolas Rannou, Yves Martelli, Steve Pieper)
*[[2015_Summer_Project_Week:SlicerCardboard| Slicer for mobile-based vr goggles]] (Utsav Pardasani, Adam Rankin)

==Astronomy==
*[[2015_Summer_Project_Week:Astronomy | visualization of HI in galaxies]] (Davide Punzo)

== '''Registrants''' ==

Please add your name to the list. This is the registration mechanism for this project week.
#Tina Kapur, BWH
#Ron Kikinis, BWH & Fraunhofer
#Steve Pieper, Isomics
#Tamas Ungi, Queen's University, Canada
#Andras Lasso, Queen's University, Canada
#Paolo Zaffino, ImagEngLab, Magna Graecia University, Italy
#Salvatore Scaramuzzino, ImagEngLab, Magna Graecia University, Italy
#Giampaolo Pileggi, ImagEngLab, Magna Graecia University, Italy
#Nicole Aucoin, BWH
#Sonia Pujol, BWH
#Dženan Zukić, Kitware, Carrboro, NC
#Jayender Jagadeesan, BWH
#Guido Gerig, Utah
#Sandy Wells, BWH
#Matthew Toews, École de Technologie Supérieure, Montreal, Canada
#Frank Preiswerk, BWH
#Raul San Jose, BWH
#Jorge Onieva, BWH
#Yulong Zhao, Université de Rennes
#Laurent Chauvin, BWH
#Michael Onken, Open Connections
#Tobias Penzkofer, Department of Radiology, Charité Berlin, Germany
#Javier Pascau, Universidad Carlos III de Madrid, Spain
#Angel Torrado-Carvajal, Universidad Rey Juan Carlos, Madrid, Spain
#Nobuhiko Hata, BWH
#Robert H. Owen, BK Medical ApS, Denmark
#Clare Tempany, BWH
#Adam Rankin, Robarts
#Utsav Pardasani, Robarts
#Marcelo Romero, Facultad de Ingenieria, Universidad Autonoma del Estado de Mexico, Mexico
#J. Jesus Montufar, Facultad de Ingenieria, Universidad Autonoma del Estado de Mexico, Mexico
#Davide Punzo, Kapteyn Astronomical Institute, University of Groningen, Netherlands
#Andrey Fedorov, BWH
#Nicolas Rannou, BCH
#Mikael Brudfors, Universidad Carlos III de Madrid, Spain
#Laura Sanz, Universidad Carlos III de Madrid, Spain
#Eugenio Marinetto, Universidad Carlos III de Madrid, Spain
#David García, Universidad Carlos III de Madrid, Spain
#Franklin King, Queen's University / BWH
#Jorge García, Universidad Politécnica de Madrid, Spain
#Peter Behringer, BWH
#Caroline Essert, University of Strasbourg
#Sebastian Tauscher, Institute of Mechatronic Systems, Leibniz Universität Hannover, Germany
#Matthew Holden, Queen's University, Canada
#Sara Fernandez Vidal, ICM, France
#Laszlo Kanyasi, Perk Lab affiliate, Hungary
#Xiao Da, MGH
#Arnaud De Bruecker, École supérieure d'informatique, Brussels, Belgium
#Ali Gottschalk, École supérieure d'informatique, Brussels, Belgium
#Christophe Teixeira Pereira, École supérieure d'informatique, Brussels, Belgium
#Tsotne Shonia, École supérieure d'informatique, Brussels, Belgium
#Clara Meinzer, Semmelweis University, Hungary
#Yves Martelli, Galgo Medical, Barcelona, Spain

2015 Summer Project Week

2015-06-22T08:52:06Z

Utsav Pardasani: /* Feature Based Image Analysis */

__NOTOC__

[[image:PW-Summer2015.png|300px]]
<br>

'''Welcome to the web page for the 21st Project Week! This is the first Project Week that is being held in conjunction with the [http://www.cars-int.org/ CARS conference].'''

==Logistics==

*'''Dates:''' June 21-24, 2015.
*'''Location:''' [http://www.nh-collection.com/hotel/nh-collection-barcelona-constanza NH Collection Constanza Hotel, Barcelona, Spain]
*'''REGISTRATION:''' Please register by adding your name to the list at the end of this page
*'''Registration Fee:''' None. The organizers will cover the charge for the conference room, while all attendees are responsible for their own hotel rooms as well as food.
*'''Hotel:''' You are welcome to book a room using the CARS 2015 conference services ([http://www.cars-int.org/fileadmin/templates/download/2015/CARS_2015_accomondation.pdf Click here for form])
*To attend the CARS meeting, please visit [http://www.cars-int.org/ http://www.cars-int.org/]

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Sunday, June 21
!style="width:18%" |Monday, June 22 <br> Room Berlin
!style="width:18%" |Tuesday, June 23 <br> Room Berlin
!style="width:18%" |Wednesday, June 24 <br> Room Berlin
|-
|bgcolor="#ffffdd"|'''9:00am-3:00pm:'''
|rowspan=3 valign=bottom|<hr>'''6pm''' Meeting with All Participants in Hotel Constanza Lobby
|'''10:00-11am:''' <font color="#503020">Rapid Introduction of all Projects and Teams <br>
'''11am-3pm''' <font color="#503020">Work <br>

|
'''10:00am-11am:''' <font color="#503020">'''Breakout Session:'''</font><br>[[2014_Project_Week_Breakout_Session: Slicer for users| Slicer for users]] (Ron Kikinis) <br>
'''11am-3pm''' <font color="#503020">Work
| <font color="#503020">Work <br>
|-
|bgcolor="#ffffdd"|'''2:00pm-4:00pm'''
|bgcolor="#ffffaa"|Lunch <br> [[Barcelona Restaurants|Places to Eat]]
|bgcolor="#ffffaa"|Lunch<br> [[Barcelona Restaurants|Places to Eat]]
|bgcolor="#ffffaa"|Lunch<br> [[Barcelona Restaurants|Places to Eat]]
|-
|bgcolor="#ffffdd"|'''4:00-7:00pm'''
|<font color="#503020"> Work
|'''5:00-7:00pm:''' <font color="#503020">'''Breakout Session:'''</font><br>[[2015_Summer_Project_Week/SoftwareStack| Open Software Stack]] (Steve Pieper) <br>4pm-6pm: Registration Desk Open for CARS attendees. Please pick up badges. <br>
|'''4:00-5:00pm:''' <font color="#503020"> Work <br>
'''5:00-6pm:''' Report Progress
|-
|bgcolor="#ffffdd"|'''7:00pm'''
|bgcolor="#f0e68b"|
|bgcolor="#f0e68b"|Adjourn for the day <br> [[Barcelona Restaurants|Places to Eat]]
|bgcolor="#f0e68b"|Adjourn for the day <br> [[Barcelona Restaurants|Places to Eat]]
|bgcolor="#f0e68b"|'''6:00pm''' Adjourn Project Week and relocate to CARS Opening<br> '''7:30pm''' CARS Welcome Reception
|}

*Please note that start, end, and mealtimes have been set to match local schedules in Barcelona.
*Here is a list of [[Barcelona Restaurants | locally recommended places to eat]] in the vicinity of the conference hotel. All participants are responsible for their own meals.

== '''Background''' ==

Founded in 2005, the National Alliance for Medical Image Computing (NAMIC), was chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], built using [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws researchers from around the world. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO], and [https://www.ncigt.org/IGTWiki/index.php/Projects/IGTWeb:R25 NCI Funded Image-Guided Fellowship Program].

A summary of all previous Project Events is available [[Project_Events#Past|here]].

This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.

The 21st Project Week is being held on conjunction with the [http://www.cars-int.org/ CARS conference].

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

=Projects=
* [[2015_Summer_Project_Week_Template | Template for project pages]]

==Equipment==

*[[2015_Summer_Project_Week:Equipment|Specialized equipment people are going to bring]] (Please add to this list if you are bringing anything)

==Image-Guided Therapy==
*[[2015_Summer_Project_Week:SlicerIGT|SlicerIGT tutorials for use cases]] (Tamas Ungi, Andras Lasso, Jayender Jagadeesan, Alvaro Gomez, Noby Hata)
*[http://www.na-mic.org/Wiki/index.php/2015_Refinement_Registration_Module Refinement of RegistrationModule] (Peter Behringer, Andrey Fedorov)
*[[2015_Summer_Project_Week:IGTSliceletBase| Create base classes for IGT slicelet]] (Andras Lasso, Andrey Fedorov, Adam Rankin)
*[http://www.na-mic.org/Wiki/index.php/2015_BRAINSFit_registration_in_SimpleITK BRAINSFit registration in SimpleITK] (Peter Behringer, Andrey Fedorov, Dženan Zukić)
*[http://www.na-mic.org/Wiki/index.php/2015_Multi_atlas_based_prostate_segmentation Multi atlas based prostate segmentation] (Paolo Zaffino, Giampaolo Pileggi, Salvatore Scaramuzzino, Peter Behringer, Andrey Fedorov, Maria Francesca Spadea)
*[http://www.na-mic.org/Wiki/index.php/2015_Multimodal_Guidance_for_Breast_Cancer_Surgery Multimodal Guidance for Breast Cancer Surgery] (Mikael Brudfors, Javier Pascau)
*[[2015_pilot trajectory planning | Pilot Trajectory Planning(Caroline Essert, Sonia Pujol)]]
*[[2015_Summer_Project_Week:LinearFeatureRegistration|Linear Feature Registration]] (Matthew Holden)
*[[2015_Summer_Project_Week:LightWeightRobotIGT | Integration of a KUKA robot using OpenIGTLink ]] (Sebastian Tauscher, Junichi Tokuda)
*[[2015_Summer_Project_Week:USReconstruction | Gated 3D Ultrasound Reconstructions with the Help of a Single-Element US Transducer ]] (Frank Preiswerk, Laurent Chauvin)
*[[2015 Orthognathic Surgery|Orthognathic Surgery]] (Dženan Zukić, Kitware)
*[[2015_Summer_Project_Week:SlicerTAVI | SlicerTAVI ]] (Adam Rankin)
*[http://www.na-mic.org/Wiki/index.php/2015_pyDBS pyDBS module update to Slicer4.4 (Sara Fernandez-Vidal, Yulong Zhao, Sonia Pujol)]
*[[2015_Summer_Project_Week:OpenSource_MRTRUS_Fusion_for_Prostate_biopsy|Open-source MRI-TRUS Fusion for Prostate biopsy]] (Andrey Fedorov, Andras Lasso)

==Feature Based Image Analysis==
*[[2015_Summer_Project_Week:LungCAD| LungCAD]] (Jayender Jagadeesan, Tobias Penzkofer, Sandy Wells)
*[[2015_Summer_Project_Week:QuantitativeProstate | Texture Analysis for Prostate Imaging]] (Tobias Penzkofer, Jay Jagadeesan, Tina Kapur)
*[[2015_Summer_Project_Week:BigDataFeatures | Big Data Medical Image Analysis using Local Features]] (Matthew Toews, William Wells, Raul San Jose Estepar, Tina Kapur)
*[[2015_Summer_Project_Week:AutomaticCephalometric | Automatic Cephalometric Analysis ]] (J. Jesus Montufar, Marcelo Romero)

==Chest Imaging Platform==
*[[2015_Summer_Project_Week:Slicer_CIP | Slicer CIP: advanced features and deployment ]] (Raúl San José, Alex Yarmarkovich, Jorge Onieva)
*[[2015_Summer_Project_Week:PAA_Ratio | PAA Ratio Module ]] (Jorge Onieva,Raúl San José)
*[[2015_Summer_Project_Week:Tracheal_Stent_Planning | Planning for tracheal stents ]] (Raúl San José, Jorge Onieva, George Cheng)

==QIICR==
*[[2015_Summer_Project_Week:DSC | Dynamic Susceptibility Contrast (DSC) MRI for brain ]] (Xiao Da, Yangming Ou, Andriy Fedorov, Steve Pieper, Jayashree Kalpathy-Cramer)
*[[2015_Summer_Project_Week:T1 mapping | T1 mapping for Dynamic Contrast Enhanced (DCE) MRI ]] (Xiao Da, Yangming Ou, Andriy Fedorov, Jayashree Kalpathy-Cramer)
*[[2015_Summer_Project_Week:DCMTK| Integration and testing of new DCMTK with Slicer]] (Michael Onken, Andrey Fedorov, Steve Pieper)

==Infrastructure==
*[[2015_Summer_Project_Week:Python_scripts_from_command_line|Simplify use of python scripts from the command line]] (Andrey Fedorov, Steve Pieper, Robin Weiss, Artem Mamonov)
*[[2015_Summer_Project_Week:Return_Fiducials_from_CLIs | Return fiducials from CLIs]] (Nicole Aucoin,Hans Meine)
*[[2015_Summer_Project_Week:Update Checker | Update Checker]] (Franklin King, BWH)
*[[2015_Summer_Project_Week:Integrated Virtual Reality Viewer | Integrated Virtual Reality Viewer]] (Franklin King, BWH, Utsav Pardasani)
*[[2015_Summer_Project_Week:SegmentationNode| Use new Segmentation node in Editor]] (Andras Lasso, Steve Pieper)
*[[2015_Summer_Project_Week:Slicer_Conda | Integrate Conda Python in Slicer]] (Raúl San José, Jorge Onieva, Utsav Pardasani)
*[[2015_Summer_Project_Week:CLIModules_Backgrounding_in_MeVisLab | Running CLI Modules in the background in MeVisLab]] (Hans Meine)
*[[2015_Summer_Project_Week:CLIModules_Indexing | CLI Modules elasticsearch / kibana dashboard]] (Hans Meine, JC, Steve Pieper)
*[[2015_Summer_Project_Week:CTK_Interative_Plugins | CTK plugins / paths towards interoperability with GUI & interaction]] (Hans Meine, Steve Pieper, Nicolas Rannou)
*[[2015_Summer_Project_Week:BRAINSFit_in_MeVisLab | Interoperability tests with "interesting" CLI modules (BRAINSFit, CIP, UKFTractography?) in MeVisLab (/Frontier)]] (Hans Meine, Steve Pieper)

==Web==
*[[2015_Summer_Project_Week:Dicom parsing with DCMJS | Dicom parsing with DCMJS]] (Nicolas Rannou, Michael Onken, Steve Pieper)
*[[2015_Summer_Project_Week:Volume rendering with DCMJS and THREEJS | Volume Rendering with DCMJS and THREEJS]] (Nicolas Rannou, Steve Pieper)
*[[2015_Summer_Project_Week:CTK for the web and touch devices| CTK for the web and touch devices]] (Nicolas Rannou, Yves Martelli, Steve Pieper)
*[[2015_Summer_Project_Week:SlicerCardboard| Slicer for mobile-based vr goggles]] (Utsav Pardasani, Adam Rankin)

==Astronomy==
*[[2015_Summer_Project_Week:Astronomy | visualization of HI in galaxies]] (Davide Punzo)

== '''Registrants''' ==

Please add your name to the list. This is the registration mechanism for this project week.
#Tina Kapur, BWH
#Ron Kikinis, BWH & Fraunhofer
#Steve Pieper, Isomics
#Tamas Ungi, Queen's University, Canada
#Andras Lasso, Queen's University, Canada
#Paolo Zaffino, ImagEngLab, Magna Graecia University, Italy
#Salvatore Scaramuzzino, ImagEngLab, Magna Graecia University, Italy
#Giampaolo Pileggi, ImagEngLab, Magna Graecia University, Italy
#Nicole Aucoin, BWH
#Sonia Pujol, BWH
#Dženan Zukić, Kitware, Carrboro, NC
#Jayender Jagadeesan, BWH
#Guido Gerig, Utah
#Sandy Wells, BWH
#Matthew Toews, École de Technologie Supérieure, Montreal, Canada
#Frank Preiswerk, BWH
#Raul San Jose, BWH
#Jorge Onieva, BWH
#Yulong Zhao, Université de Rennes
#Laurent Chauvin, BWH
#Michael Onken, Open Connections
#Tobias Penzkofer, Department of Radiology, Charité Berlin, Germany
#Javier Pascau, Universidad Carlos III de Madrid, Spain
#Angel Torrado-Carvajal, Universidad Rey Juan Carlos, Madrid, Spain
#Nobuhiko Hata, BWH
#Robert H. Owen, BK Medical ApS, Denmark
#Clare Tempany, BWH
#Adam Rankin, Robarts
#Utsav Pardasani, Robarts
#Marcelo Romero, Facultad de Ingenieria, Universidad Autonoma del Estado de Mexico, Mexico
#J. Jesus Montufar, Facultad de Ingenieria, Universidad Autonoma del Estado de Mexico, Mexico
#Davide Punzo, Kapteyn Astronomical Institute, University of Groningen, Netherlands
#Andrey Fedorov, BWH
#Nicolas Rannou, BCH
#Mikael Brudfors, Universidad Carlos III de Madrid, Spain
#Laura Sanz, Universidad Carlos III de Madrid, Spain
#Eugenio Marinetto, Universidad Carlos III de Madrid, Spain
#David García, Universidad Carlos III de Madrid, Spain
#Franklin King, Queen's University / BWH
#Jorge García, Universidad Politécnica de Madrid, Spain
#Peter Behringer, BWH
#Caroline Essert, University of Strasbourg
#Sebastian Tauscher, Institute of Mechatronic Systems, Leibniz Universität Hannover, Germany
#Matthew Holden, Queen's University, Canada
#Sara Fernandez Vidal, ICM, France
#Laszlo Kanyasi, Perk Lab affiliate, Hungary
#Xiao Da, MGH
#Arnaud De Bruecker, École supérieure d'informatique, Brussels, Belgium
#Ali Gottschalk, École supérieure d'informatique, Brussels, Belgium
#Christophe Teixeira Pereira, École supérieure d'informatique, Brussels, Belgium
#Tsotne Shonia, École supérieure d'informatique, Brussels, Belgium
#Clara Meinzer, Semmelweis University, Hungary
#Yves Martelli, Galgo Medical, Barcelona, Spain

2015 Summer Project Week:TrackerlessMRIUSFusion

2015-06-22T08:47:34Z

Utsav Pardasani: /* Project Description */

2015 Summer Project Week:TrackerlessMRIUSFusion

2015-06-22T08:45:43Z

Utsav Pardasani: Created page with '__NOTOC__ <gallery> Image:PW-Summer2015.png|Projects List </gallery> ==Key Investigators== * Utsav Pardasani ==Project Description== <div…'

2015 Summer Project Week

2015-06-22T08:42:53Z

Utsav Pardasani: /* Feature Based Image Analysis */

__NOTOC__

[[image:PW-Summer2015.png|300px]]
<br>

'''Welcome to the web page for the 21st Project Week! This is the first Project Week that is being held in conjunction with the [http://www.cars-int.org/ CARS conference].'''

==Logistics==

*'''Dates:''' June 21-24, 2015.
*'''Location:''' [http://www.nh-collection.com/hotel/nh-collection-barcelona-constanza NH Collection Constanza Hotel, Barcelona, Spain]
*'''REGISTRATION:''' Please register by adding your name to the list at the end of this page
*'''Registration Fee:''' None. The organizers will cover the charge for the conference room, while all attendees are responsible for their own hotel rooms as well as food.
*'''Hotel:''' You are welcome to book a room using the CARS 2015 conference services ([http://www.cars-int.org/fileadmin/templates/download/2015/CARS_2015_accomondation.pdf Click here for form])
*To attend the CARS meeting, please visit [http://www.cars-int.org/ http://www.cars-int.org/]

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Sunday, June 21
!style="width:18%" |Monday, June 22 <br> Room Berlin
!style="width:18%" |Tuesday, June 23 <br> Room Berlin
!style="width:18%" |Wednesday, June 24 <br> Room Berlin
|-
|bgcolor="#ffffdd"|'''9:00am-3:00pm:'''
|rowspan=3 valign=bottom|<hr>'''6pm''' Meeting with All Participants in Hotel Constanza Lobby
|'''10:00-11am:''' <font color="#503020">Rapid Introduction of all Projects and Teams <br>
'''11am-3pm''' <font color="#503020">Work <br>

|
'''10:00am-11am:''' <font color="#503020">'''Breakout Session:'''</font><br>[[2014_Project_Week_Breakout_Session: Slicer for users| Slicer for users]] (Ron Kikinis) <br>
'''11am-3pm''' <font color="#503020">Work
| <font color="#503020">Work <br>
|-
|bgcolor="#ffffdd"|'''2:00pm-4:00pm'''
|bgcolor="#ffffaa"|Lunch <br> [[Barcelona Restaurants|Places to Eat]]
|bgcolor="#ffffaa"|Lunch<br> [[Barcelona Restaurants|Places to Eat]]
|bgcolor="#ffffaa"|Lunch<br> [[Barcelona Restaurants|Places to Eat]]
|-
|bgcolor="#ffffdd"|'''4:00-7:00pm'''
|<font color="#503020"> Work
|'''5:00-7:00pm:''' <font color="#503020">'''Breakout Session:'''</font><br>[[2015_Summer_Project_Week/SoftwareStack| Open Software Stack]] (Steve Pieper) <br>4pm-6pm: Registration Desk Open for CARS attendees. Please pick up badges. <br>
|'''4:00-5:00pm:''' <font color="#503020"> Work <br>
'''5:00-6pm:''' Report Progress
|-
|bgcolor="#ffffdd"|'''7:00pm'''
|bgcolor="#f0e68b"|
|bgcolor="#f0e68b"|Adjourn for the day <br> [[Barcelona Restaurants|Places to Eat]]
|bgcolor="#f0e68b"|Adjourn for the day <br> [[Barcelona Restaurants|Places to Eat]]
|bgcolor="#f0e68b"|'''6:00pm''' Adjourn Project Week and relocate to CARS Opening<br> '''7:30pm''' CARS Welcome Reception
|}

*Please note that start, end, and mealtimes have been set to match local schedules in Barcelona.
*Here is a list of [[Barcelona Restaurants | locally recommended places to eat]] in the vicinity of the conference hotel. All participants are responsible for their own meals.

== '''Background''' ==

Founded in 2005, the National Alliance for Medical Image Computing (NAMIC), was chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], built using [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws researchers from around the world. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO], and [https://www.ncigt.org/IGTWiki/index.php/Projects/IGTWeb:R25 NCI Funded Image-Guided Fellowship Program].

A summary of all previous Project Events is available [[Project_Events#Past|here]].

This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.

The 21st Project Week is being held on conjunction with the [http://www.cars-int.org/ CARS conference].

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

=Projects=
* [[2015_Summer_Project_Week_Template | Template for project pages]]

==Equipment==

*[[2015_Summer_Project_Week:Equipment|Specialized equipment people are going to bring]] (Please add to this list if you are bringing anything)

==Image-Guided Therapy==
*[[2015_Summer_Project_Week:SlicerIGT|SlicerIGT tutorials for use cases]] (Tamas Ungi, Andras Lasso, Jayender Jagadeesan, Alvaro Gomez, Noby Hata)
*[http://www.na-mic.org/Wiki/index.php/2015_Refinement_Registration_Module Refinement of RegistrationModule] (Peter Behringer, Andrey Fedorov)
*[[2015_Summer_Project_Week:IGTSliceletBase| Create base classes for IGT slicelet]] (Andras Lasso, Andrey Fedorov, Adam Rankin)
*[http://www.na-mic.org/Wiki/index.php/2015_BRAINSFit_registration_in_SimpleITK BRAINSFit registration in SimpleITK] (Peter Behringer, Andrey Fedorov, Dženan Zukić)
*[http://www.na-mic.org/Wiki/index.php/2015_Multi_atlas_based_prostate_segmentation Multi atlas based prostate segmentation] (Paolo Zaffino, Giampaolo Pileggi, Salvatore Scaramuzzino, Peter Behringer, Andrey Fedorov, Maria Francesca Spadea)
*[http://www.na-mic.org/Wiki/index.php/2015_Multimodal_Guidance_for_Breast_Cancer_Surgery Multimodal Guidance for Breast Cancer Surgery] (Mikael Brudfors, Javier Pascau)
*[[2015_pilot trajectory planning | Pilot Trajectory Planning(Caroline Essert, Sonia Pujol)]]
*[[2015_Summer_Project_Week:LinearFeatureRegistration|Linear Feature Registration]] (Matthew Holden)
*[[2015_Summer_Project_Week:LightWeightRobotIGT | Integration of a KUKA robot using OpenIGTLink ]] (Sebastian Tauscher, Junichi Tokuda)
*[[2015_Summer_Project_Week:USReconstruction | Gated 3D Ultrasound Reconstructions with the Help of a Single-Element US Transducer ]] (Frank Preiswerk, Laurent Chauvin)
*[[2015 Orthognathic Surgery|Orthognathic Surgery]] (Dženan Zukić, Kitware)
*[[2015_Summer_Project_Week:SlicerTAVI | SlicerTAVI ]] (Adam Rankin)
*[http://www.na-mic.org/Wiki/index.php/2015_pyDBS pyDBS module update to Slicer4.4 (Sara Fernandez-Vidal, Yulong Zhao, Sonia Pujol)]

==Feature Based Image Analysis==
*[[2015_Summer_Project_Week:LungCAD| LungCAD]] (Jayender Jagadeesan, Tobias Penzkofer, Sandy Wells)
*[[2015_Summer_Project_Week:QuantitativeProstate | Texture Analysis for Prostate Imaging]] (Tobias Penzkofer, Jay Jagadeesan, Tina Kapur)
*[[2015_Summer_Project_Week:BigDataFeatures | Big Data Medical Image Analysis using Local Features]] (Matthew Toews, William Wells, Raul San Jose Estepar, Tina Kapur)
*[[2015_Summer_Project_Week:AutomaticCephalometric | Automatic Cephalometric Analysis ]] (J. Jesus Montufar, Marcelo Romero)
*[[2015_Summer_Project_Week:TrackerlessMRIUSFusion | Trackerless MRI - US Registration ]] (Utsav Pardasani)

==Chest Imaging Platform==
*[[2015_Summer_Project_Week:Slicer_CIP | Slicer CIP: advanced features and deployment ]] (Raúl San José, Alex Yarmarkovich, Jorge Onieva)
*[[2015_Summer_Project_Week:PAA_Ratio | PAA Ratio Module ]] (Jorge Onieva,Raúl San José)
*[[2015_Summer_Project_Week:Tracheal_Stent_Planning | Planning for tracheal stents ]] (Raúl San José, Jorge Onieva, George Cheng)

==QIICR==
*[[2015_Summer_Project_Week:DSC | Dynamic Susceptibility Contrast (DSC) MRI for brain ]] (Xiao Da, Yangming Ou, Andriy Fedorov, Steve Pieper, Jayashree Kalpathy-Cramer)
*[[2015_Summer_Project_Week:T1 mapping | T1 mapping for Dynamic Contrast Enhanced (DCE) MRI ]] (Xiao Da, Yangming Ou, Andriy Fedorov, Jayashree Kalpathy-Cramer)
*[[2015_Summer_Project_Week:DCMTK| Integration and testing of new DCMTK with Slicer]] (Michael Onken, Andrey Fedorov, Steve Pieper)

==Infrastructure==
*[[2015_Summer_Project_Week:Python_scripts_from_command_line|Simplify use of python scripts from the command line]] (Andrey Fedorov, Steve Pieper, Robin Weiss, Artem Mamonov)
*[[2015_Summer_Project_Week:Return_Fiducials_from_CLIs | Return fiducials from CLIs]] (Nicole Aucoin,Hans Meine)
*[[2015_Summer_Project_Week:Update Checker | Update Checker]] (Franklin King, BWH)
*[[2015_Summer_Project_Week:Integrated Virtual Reality Viewer | Integrated Virtual Reality Viewer]] (Franklin King, BWH, Utsav Pardasani)
*[[2015_Summer_Project_Week:SegmentationNode| Use new Segmentation node in Editor]] (Andras Lasso, Steve Pieper)
*[[2015_Summer_Project_Week:Slicer_Conda | Integrate Conda Python in Slicer]] (Raúl San José, Jorge Onieva, Utsav Pardasani)
*[[2015_Summer_Project_Week:CLIModules_Backgrounding_in_MeVisLab | Running CLI Modules in the background in MeVisLab]] (Hans Meine)
*[[2015_Summer_Project_Week:CLIModules_Indexing | CLI Modules elasticsearch / kibana dashboard]] (Hans Meine, JC, Steve Pieper)
*[[2015_Summer_Project_Week:CTK_Interative_Plugins | CTK plugins / paths towards interoperability with GUI & interaction]] (Hans Meine, Steve Pieper, Nicolas Rannou)
*[[2015_Summer_Project_Week:BRAINSFit_in_MeVisLab | Interoperability tests with "interesting" CLI modules (BRAINSFit, CIP, UKFTractography?) in MeVisLab (/Frontier)]] (Hans Meine, Steve Pieper)

==Web==
*[[2015_Summer_Project_Week:Dicom parsing with DCMJS | Dicom parsing with DCMJS]] (Nicolas Rannou, Michael Onken, Steve Pieper)
*[[2015_Summer_Project_Week:Volume rendering with DCMJS and THREEJS | Volume Rendering with DCMJS and THREEJS]] (Nicolas Rannou, Steve Pieper)
*[[2015_Summer_Project_Week:CTK for the web and touch devices| CTK for the web and touch devices]] (Nicolas Rannou, Yves Martelli, Steve Pieper)
*[[2015_Summer_Project_Week:SlicerCardboard| Slicer for mobile-based vr goggles]] (Utsav Pardasani, Adam Rankin)

==Astronomy==
*[[2015_Summer_Project_Week:Astronomy | visualization of HI in galaxies]] (Davide Punzo)

== '''Registrants''' ==

Please add your name to the list. This is the registration mechanism for this project week.
#Tina Kapur, BWH
#Ron Kikinis, BWH & Fraunhofer
#Steve Pieper, Isomics
#Tamas Ungi, Queen's University, Canada
#Andras Lasso, Queen's University, Canada
#Paolo Zaffino, ImagEngLab, Magna Graecia University, Italy
#Salvatore Scaramuzzino, ImagEngLab, Magna Graecia University, Italy
#Giampaolo Pileggi, ImagEngLab, Magna Graecia University, Italy
#Nicole Aucoin, BWH
#Sonia Pujol, BWH
#Dženan Zukić, Kitware, Carrboro, NC
#Jayender Jagadeesan, BWH
#Guido Gerig, Utah
#Sandy Wells, BWH
#Matthew Toews, École de Technologie Supérieure, Montreal, Canada
#Frank Preiswerk, BWH
#Raul San Jose, BWH
#Jorge Onieva, BWH
#Yulong Zhao, Université de Rennes
#Laurent Chauvin, BWH
#Michael Onken, Open Connections
#Tobias Penzkofer, Department of Radiology, Charité Berlin, Germany
#Javier Pascau, Universidad Carlos III de Madrid, Spain
#Angel Torrado-Carvajal, Universidad Rey Juan Carlos, Madrid, Spain
#Nobuhiko Hata, BWH
#Robert H. Owen, BK Medical ApS, Denmark
#Clare Tempany, BWH
#Adam Rankin, Robarts
#Utsav Pardasani, Robarts
#Marcelo Romero, Facultad de Ingenieria, Universidad Autonoma del Estado de Mexico, Mexico
#J. Jesus Montufar, Facultad de Ingenieria, Universidad Autonoma del Estado de Mexico, Mexico
#Davide Punzo, Kapteyn Astronomical Institute, University of Groningen, Netherlands
#Andrey Fedorov, BWH
#Nicolas Rannou, BCH
#Mikael Brudfors, Universidad Carlos III de Madrid, Spain
#Laura Sanz, Universidad Carlos III de Madrid, Spain
#Eugenio Marinetto, Universidad Carlos III de Madrid, Spain
#David García, Universidad Carlos III de Madrid, Spain
#Franklin King, Queen's University / BWH
#Jorge García, Universidad Politécnica de Madrid, Spain
#Peter Behringer, BWH
#Caroline Essert, University of Strasbourg
#Sebastian Tauscher, Institute of Mechatronic Systems, Leibniz Universität Hannover, Germany
#Matthew Holden, Queen's University, Canada
#Sara Fernandez Vidal, ICM, France
#Laszlo Kanyasi, Perk Lab affiliate, Hungary
#Xiao Da, MGH
#Arnaud De Bruecker, École supérieure d'informatique, Brussels, Belgium
#Ali Gottschalk, École supérieure d'informatique, Brussels, Belgium
#Christophe Teixeira Pereira, École supérieure d'informatique, Brussels, Belgium
#Tsotne Shonia, École supérieure d'informatique, Brussels, Belgium
#Clara Meinzer, Semmelweis University, Hungary
#Yves Martelli, Galgo Medical, Barcelona, Spain

2015 Summer Project Week

2015-06-22T08:38:46Z

Utsav Pardasani: /* Infrastructure */

__NOTOC__

[[image:PW-Summer2015.png|300px]]
<br>

'''Welcome to the web page for the 21st Project Week! This is the first Project Week that is being held in conjunction with the [http://www.cars-int.org/ CARS conference].'''

==Logistics==

*'''Dates:''' June 21-24, 2015.
*'''Location:''' [http://www.nh-collection.com/hotel/nh-collection-barcelona-constanza NH Collection Constanza Hotel, Barcelona, Spain]
*'''REGISTRATION:''' Please register by adding your name to the list at the end of this page
*'''Registration Fee:''' None. The organizers will cover the charge for the conference room, while all attendees are responsible for their own hotel rooms as well as food.
*'''Hotel:''' You are welcome to book a room using the CARS 2015 conference services ([http://www.cars-int.org/fileadmin/templates/download/2015/CARS_2015_accomondation.pdf Click here for form])
*To attend the CARS meeting, please visit [http://www.cars-int.org/ http://www.cars-int.org/]

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Sunday, June 21
!style="width:18%" |Monday, June 22 <br> Room Berlin
!style="width:18%" |Tuesday, June 23 <br> Room Berlin
!style="width:18%" |Wednesday, June 24 <br> Room Berlin
|-
|bgcolor="#ffffdd"|'''9:00am-3:00pm:'''
|rowspan=3 valign=bottom|<hr>'''6pm''' Meeting with All Participants in Hotel Constanza Lobby
|'''10:00-11am:''' <font color="#503020">Rapid Introduction of all Projects and Teams <br>
'''11am-3pm''' <font color="#503020">Work <br>

|
'''10:00am-11am:''' <font color="#503020">'''Breakout Session:'''</font><br>[[2014_Project_Week_Breakout_Session: Slicer for users| Slicer for users]] (Ron Kikinis) <br>
'''11am-3pm''' <font color="#503020">Work
| <font color="#503020">Work <br>
|-
|bgcolor="#ffffdd"|'''2:00pm-4:00pm'''
|bgcolor="#ffffaa"|Lunch <br> [[Barcelona Restaurants|Places to Eat]]
|bgcolor="#ffffaa"|Lunch<br> [[Barcelona Restaurants|Places to Eat]]
|bgcolor="#ffffaa"|Lunch<br> [[Barcelona Restaurants|Places to Eat]]
|-
|bgcolor="#ffffdd"|'''4:00-7:00pm'''
|<font color="#503020"> Work
|'''5:00-7:00pm:''' <font color="#503020">'''Breakout Session:'''</font><br>[[2015_Summer_Project_Week/SoftwareStack| Open Software Stack]] (Steve Pieper) <br>4pm-6pm: Registration Desk Open for CARS attendees. Please pick up badges. <br>
|'''4:00-5:00pm:''' <font color="#503020"> Work <br>
'''5:00-6pm:''' Report Progress
|-
|bgcolor="#ffffdd"|'''7:00pm'''
|bgcolor="#f0e68b"|
|bgcolor="#f0e68b"|Adjourn for the day <br> [[Barcelona Restaurants|Places to Eat]]
|bgcolor="#f0e68b"|Adjourn for the day <br> [[Barcelona Restaurants|Places to Eat]]
|bgcolor="#f0e68b"|'''6:00pm''' Adjourn Project Week and relocate to CARS Opening<br> '''7:30pm''' CARS Welcome Reception
|}

*Please note that start, end, and mealtimes have been set to match local schedules in Barcelona.
*Here is a list of [[Barcelona Restaurants | locally recommended places to eat]] in the vicinity of the conference hotel. All participants are responsible for their own meals.

== '''Background''' ==

Founded in 2005, the National Alliance for Medical Image Computing (NAMIC), was chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], built using [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws researchers from around the world. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO], and [https://www.ncigt.org/IGTWiki/index.php/Projects/IGTWeb:R25 NCI Funded Image-Guided Fellowship Program].

A summary of all previous Project Events is available [[Project_Events#Past|here]].

This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.

The 21st Project Week is being held on conjunction with the [http://www.cars-int.org/ CARS conference].

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

=Projects=
* [[2015_Summer_Project_Week_Template | Template for project pages]]

==Equipment==

*[[2015_Summer_Project_Week:Equipment|Specialized equipment people are going to bring]] (Please add to this list if you are bringing anything)

==Image-Guided Therapy==
*[[2015_Summer_Project_Week:SlicerIGT|SlicerIGT tutorials for use cases]] (Tamas Ungi, Andras Lasso, Jayender Jagadeesan, Alvaro Gomez, Noby Hata)
*[http://www.na-mic.org/Wiki/index.php/2015_Refinement_Registration_Module Refinement of RegistrationModule] (Peter Behringer, Andrey Fedorov)
*[[2015_Summer_Project_Week:IGTSliceletBase| Create base classes for IGT slicelet]] (Andras Lasso, Andrey Fedorov, Adam Rankin)
*[http://www.na-mic.org/Wiki/index.php/2015_BRAINSFit_registration_in_SimpleITK BRAINSFit registration in SimpleITK] (Peter Behringer, Andrey Fedorov, Dženan Zukić)
*[http://www.na-mic.org/Wiki/index.php/2015_Multi_atlas_based_prostate_segmentation Multi atlas based prostate segmentation] (Paolo Zaffino, Giampaolo Pileggi, Salvatore Scaramuzzino, Peter Behringer, Andrey Fedorov, Maria Francesca Spadea)
*[http://www.na-mic.org/Wiki/index.php/2015_Multimodal_Guidance_for_Breast_Cancer_Surgery Multimodal Guidance for Breast Cancer Surgery] (Mikael Brudfors, Javier Pascau)
*[[2015_pilot trajectory planning | Pilot Trajectory Planning(Caroline Essert, Sonia Pujol)]]
*[[2015_Summer_Project_Week:LinearFeatureRegistration|Linear Feature Registration]] (Matthew Holden)
*[[2015_Summer_Project_Week:LightWeightRobotIGT | Integration of a KUKA robot using OpenIGTLink ]] (Sebastian Tauscher, Junichi Tokuda)
*[[2015_Summer_Project_Week:USReconstruction | Gated 3D Ultrasound Reconstructions with the Help of a Single-Element US Transducer ]] (Frank Preiswerk, Laurent Chauvin)
*[[2015 Orthognathic Surgery|Orthognathic Surgery]] (Dženan Zukić, Kitware)
*[[2015_Summer_Project_Week:SlicerTAVI | SlicerTAVI ]] (Adam Rankin)
*[http://www.na-mic.org/Wiki/index.php/2015_pyDBS pyDBS module update to Slicer4.4 (Sara Fernandez-Vidal, Yulong Zhao, Sonia Pujol)]

==Feature Based Image Analysis==
*[[2015_Summer_Project_Week:LungCAD| LungCAD]] (Jayender Jagadeesan, Tobias Penzkofer, Sandy Wells)
*[[2015_Summer_Project_Week:QuantitativeProstate | Texture Analysis for Prostate Imaging]] (Tobias Penzkofer, Jay Jagadeesan, Tina Kapur)
*[[2015_Summer_Project_Week:BigDataFeatures | Big Data Medical Image Analysis using Local Features]] (Matthew Toews, William Wells, Raul San Jose Estepar, Tina Kapur)
*[[2015_Summer_Project_Week:AutomaticCephalometric | Automatic Cephalometric Analysis ]] (J. Jesus Montufar, Marcelo Romero)

==Chest Imaging Platform==
*[[2015_Summer_Project_Week:Slicer_CIP | Slicer CIP: advanced features and deployment ]] (Raúl San José, Alex Yarmarkovich, Jorge Onieva)
*[[2015_Summer_Project_Week:PAA_Ratio | PAA Ratio Module ]] (Jorge Onieva,Raúl San José)
*[[2015_Summer_Project_Week:Tracheal_Stent_Planning | Planning for tracheal stents ]] (Raúl San José, Jorge Onieva, George Cheng)

==QIICR==
*[[2015_Summer_Project_Week:DSC | Dynamic Susceptibility Contrast (DSC) MRI for brain ]] (Xiao Da, Yangming Ou, Andriy Fedorov, Steve Pieper, Jayashree Kalpathy-Cramer)
*[[2015_Summer_Project_Week:T1 mapping | T1 mapping for Dynamic Contrast Enhanced (DCE) MRI ]] (Xiao Da, Yangming Ou, Andriy Fedorov, Jayashree Kalpathy-Cramer)
*[[2015_Summer_Project_Week:DCMTK| Integration and testing of new DCMTK with Slicer]] (Michael Onken, Andrey Fedorov, Steve Pieper)

==Infrastructure==
*[[2015_Summer_Project_Week:Python_scripts_from_command_line|Simplify use of python scripts from the command line]] (Andrey Fedorov, Steve Pieper, Robin Weiss, Artem Mamonov)
*[[2015_Summer_Project_Week:Return_Fiducials_from_CLIs | Return fiducials from CLIs]] (Nicole Aucoin,Hans Meine)
*[[2015_Summer_Project_Week:Update Checker | Update Checker]] (Franklin King, BWH)
*[[2015_Summer_Project_Week:Integrated Virtual Reality Viewer | Integrated Virtual Reality Viewer]] (Franklin King, BWH, Utsav Pardasani)
*[[2015_Summer_Project_Week:SegmentationNode| Use new Segmentation node in Editor]] (Andras Lasso, Steve Pieper)
*[[2015_Summer_Project_Week:Slicer_Conda | Integrate Conda Python in Slicer]] (Raúl San José, Jorge Onieva, Utsav Pardasani)
*[[2015_Summer_Project_Week:CLIModules_Backgrounding_in_MeVisLab | Running CLI Modules in the background in MeVisLab]] (Hans Meine)
*[[2015_Summer_Project_Week:CLIModules_Indexing | CLI Modules elasticsearch / kibana dashboard]] (Hans Meine, JC, Steve Pieper)
*[[2015_Summer_Project_Week:CTK_Interative_Plugins | CTK plugins / paths towards interoperability with GUI & interaction]] (Hans Meine, Steve Pieper, Nicolas Rannou)
*[[2015_Summer_Project_Week:BRAINSFit_in_MeVisLab | Interoperability tests with "interesting" CLI modules (BRAINSFit, CIP, UKFTractography?) in MeVisLab (/Frontier)]] (Hans Meine, Steve Pieper)

==Web==
*[[2015_Summer_Project_Week:Dicom parsing with DCMJS | Dicom parsing with DCMJS]] (Nicolas Rannou, Michael Onken, Steve Pieper)
*[[2015_Summer_Project_Week:Volume rendering with DCMJS and THREEJS | Volume Rendering with DCMJS and THREEJS]] (Nicolas Rannou, Steve Pieper)
*[[2015_Summer_Project_Week:CTK for the web and touch devices| CTK for the web and touch devices]] (Nicolas Rannou, Yves Martelli, Steve Pieper)
*[[2015_Summer_Project_Week:SlicerCardboard| Slicer for mobile-based vr goggles]] (Utsav Pardasani, Adam Rankin)

==Astronomy==
*[[2015_Summer_Project_Week:Astronomy | visualization of HI in galaxies]] (Davide Punzo)

== '''Registrants''' ==

Please add your name to the list. This is the registration mechanism for this project week.
#Tina Kapur, BWH
#Ron Kikinis, BWH & Fraunhofer
#Steve Pieper, Isomics
#Tamas Ungi, Queen's University, Canada
#Andras Lasso, Queen's University, Canada
#Paolo Zaffino, ImagEngLab, Magna Graecia University, Italy
#Salvatore Scaramuzzino, ImagEngLab, Magna Graecia University, Italy
#Giampaolo Pileggi, ImagEngLab, Magna Graecia University, Italy
#Nicole Aucoin, BWH
#Sonia Pujol, BWH
#Dženan Zukić, Kitware, Carrboro, NC
#Jayender Jagadeesan, BWH
#Guido Gerig, Utah
#Sandy Wells, BWH
#Matthew Toews, École de Technologie Supérieure, Montreal, Canada
#Frank Preiswerk, BWH
#Raul San Jose, BWH
#Jorge Onieva, BWH
#Yulong Zhao, Université de Rennes
#Laurent Chauvin, BWH
#Michael Onken, Open Connections
#Tobias Penzkofer, Department of Radiology, Charité Berlin, Germany
#Javier Pascau, Universidad Carlos III de Madrid, Spain
#Angel Torrado-Carvajal, Universidad Rey Juan Carlos, Madrid, Spain
#Nobuhiko Hata, BWH
#Robert H. Owen, BK Medical ApS, Denmark
#Clare Tempany, BWH
#Adam Rankin, Robarts
#Utsav Pardasani, Robarts
#Marcelo Romero, Facultad de Ingenieria, Universidad Autonoma del Estado de Mexico, Mexico
#J. Jesus Montufar, Facultad de Ingenieria, Universidad Autonoma del Estado de Mexico, Mexico
#Davide Punzo, Kapteyn Astronomical Institute, University of Groningen, Netherlands
#Andrey Fedorov, BWH
#Nicolas Rannou, BCH
#Mikael Brudfors, Universidad Carlos III de Madrid, Spain
#Laura Sanz, Universidad Carlos III de Madrid, Spain
#Eugenio Marinetto, Universidad Carlos III de Madrid, Spain
#David García, Universidad Carlos III de Madrid, Spain
#Franklin King, Queen's University / BWH
#Jorge García, Universidad Politécnica de Madrid, Spain
#Peter Behringer, BWH
#Caroline Essert, University of Strasbourg
#Sebastian Tauscher, Institute of Mechatronic Systems, Leibniz Universität Hannover, Germany
#Matthew Holden, Queen's University, Canada
#Sara Fernandez Vidal, ICM, France
#Laszlo Kanyasi, Perk Lab affiliate, Hungary
#Xiao Da, MGH
#Arnaud De Bruecker, École supérieure d'informatique, Brussels, Belgium
#Ali Gottschalk, École supérieure d'informatique, Brussels, Belgium
#Christophe Teixeira Pereira, École supérieure d'informatique, Brussels, Belgium
#Tsotne Shonia, École supérieure d'informatique, Brussels, Belgium
#Clara Meinzer, Semmelweis University, Hungary
#Yves Martelli, Galgo Medical, Barcelona, Spain

2015 Summer Project Week:SlicerCardboard

2015-06-22T08:36:53Z

Utsav Pardasani:

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:SlicerCardboard.png
</gallery>

==Key Investigators==
* Utsav Pardasani
* Adam Rankin

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Add the capability for Slicer to render stereo views on mobile-phone based viewers.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Develop a websocket server in Slicer to serve up rendered stereo views to cheap vr goggles
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*Successful websocket server implementation, however the image-compression is blocking the renderloop. Also needed is lens-distortion correction
*Github Page: https://github.com/Utsavvy/SlicerCardboard
</div>
</div>

2015 Summer Project Week:SlicerCardboard

2015-06-22T08:36:19Z

Utsav Pardasani:

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
Image:SlicerCardboard.png
</gallery>

==Key Investigators==
* Utsav Pardasani
* Adam Rankin

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Add the capability for Slicer to render stereo views on mobile-phone based viewers.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Develop a websocket server in Slicer to serve up rendered stereo views to cheap vr goggles
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*Successful websocket server implementation, however the image-compression is blocking the renderloop. Also needed is lens-distortion correction
</div>
</div>

File:SlicerCardboard.png

2015-06-22T08:35:10Z

Utsav Pardasani: Screenshot of SlicerCardboard

Screenshot of SlicerCardboard

2015 Summer Project Week:SlicerCardboard

2015-06-22T08:34:16Z

Utsav Pardasani:

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
[[File:SlicerCardboard.png]]
</gallery>

==Key Investigators==
* Utsav Pardasani
* Adam Rankin

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Add the capability for Slicer to render stereo views on mobile-phone based viewers.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Develop a websocket server in Slicer to serve up rendered stereo views to cheap vr goggles
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*Successful websocket server implementation, however the image-compression is blocking the renderloop. Also needed is lens-distortion correction
</div>
</div>

2015 Summer Project Week:SlicerCardboard

2015-06-21T16:23:38Z

Utsav Pardasani:

2015 Summer Project Week:SlicerCardboard

2015-06-21T16:22:50Z

Utsav Pardasani: Created page with ' ==Project Description== <div style="margin: 20px;"> <div style="width: 27%; float: left; padding-right: 3%;"> <h3>Objective</h3> * Add the capability for Slicer to render stere…'

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Add the capability for Slicer to render stereo views on mobile-phone based viewers.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Develop a websocket server in Slicer to serve up rendered stereo views to cheap vr goggles
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*Successful websocket server implementation, however the image-compression is blocking the renderloop. Also needed is lens-distortion correction
</div>
</div>

2015 Summer Project Week

2015-06-21T16:20:41Z

Utsav Pardasani:

__NOTOC__

[[image:PW-Summer2015.png|300px]]
<br>

'''Welcome to the web page for the 21st Project Week! This is the first Project Week that is being held in conjunction with the [http://www.cars-int.org/ CARS conference].'''

==Logistics==

*'''Dates:''' June 21-24, 2015.
*'''Location:''' [http://www.nh-collection.com/hotel/nh-collection-barcelona-constanza NH Collection Constanza Hotel, Barcelona, Spain]
*'''REGISTRATION:''' Please register by adding your name to the list at the end of this page
*'''Registration Fee:''' None. The organizers will cover the charge for the conference room, while all attendees are responsible for their own hotel rooms as well as food.
*'''Hotel:''' You are welcome to book a room using the CARS 2015 conference services ([http://www.cars-int.org/fileadmin/templates/download/2015/CARS_2015_accomondation.pdf Click here for form])
*To attend the CARS meeting, please visit [http://www.cars-int.org/ http://www.cars-int.org/]

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Sunday, June 21
!style="width:18%" |Monday, June 22 <br> Room Berlin
!style="width:18%" |Tuesday, June 23 <br> Room Berlin
!style="width:18%" |Wednesday, June 24 <br> Room Berlin
|-
|bgcolor="#ffffdd"|'''9:00am-3:00pm:'''
|rowspan=3 valign=bottom|<hr>'''6pm''' Meeting with All Participants in Hotel Constanza Lobby
|'''10:00-11am:''' <font color="#503020">Rapid Introduction of all Projects and Teams <br>
'''11am-3pm''' <font color="#503020">Work <br>

|
'''10:00am-11am:''' <font color="#503020">'''Breakout Session:'''</font><br>[[2014_Project_Week_Breakout_Session: Slicer for users| Slicer for users]] (Ron Kikinis) <br>
'''11am-3pm''' <font color="#503020">Work
| <font color="#503020">Work <br>
|-
|bgcolor="#ffffdd"|'''2:00pm-4:00pm'''
|bgcolor="#ffffaa"|Lunch <br> [[Barcelona Restaurants|Places to Eat]]
|bgcolor="#ffffaa"|Lunch<br> [[Barcelona Restaurants|Places to Eat]]
|bgcolor="#ffffaa"|Lunch<br> [[Barcelona Restaurants|Places to Eat]]
|-
|bgcolor="#ffffdd"|'''4:00-7:00pm'''
|<font color="#503020"> Work
|'''5:00-7:00pm:''' <font color="#503020">'''Breakout Session:'''</font><br>[[2015_Summer_Project_Week/SoftwareStack| Open Software Stack]] (Steve Pieper) <br>4pm-6pm: Registration Desk Open for CARS attendees. Please pick up badges. <br>
|'''4:00-5:00pm:''' <font color="#503020"> Work <br>
'''5:00-6pm:''' Report Progress
|-
|bgcolor="#ffffdd"|'''7:00pm'''
|bgcolor="#f0e68b"|
|bgcolor="#f0e68b"|Adjourn for the day <br> [[Barcelona Restaurants|Places to Eat]]
|bgcolor="#f0e68b"|Adjourn for the day <br> [[Barcelona Restaurants|Places to Eat]]
|bgcolor="#f0e68b"|'''6:00pm''' Adjourn Project Week and relocate to CARS Opening<br> '''7:30pm''' CARS Welcome Reception
|}

*Please note that start, end, and mealtimes have been set to match local schedules in Barcelona.
*Here is a list of [[Barcelona Restaurants | locally recommended places to eat]] in the vicinity of the conference hotel. All participants are responsible for their own meals.

== '''Background''' ==

Founded in 2005, the National Alliance for Medical Image Computing (NAMIC), was chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], built using [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an event called Project Week.

[[Engineering:Programming_Events|Project Week]] is a semi-annual event which draws researchers from around the world. As of August 2014, it is a MICCAI endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event.

Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.

Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO], and [https://www.ncigt.org/IGTWiki/index.php/Projects/IGTWeb:R25 NCI Funded Image-Guided Fellowship Program].

A summary of all previous Project Events is available [[Project_Events#Past|here]].

This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.

The 21st Project Week is being held on conjunction with the [http://www.cars-int.org/ CARS conference].

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

=Projects=
* [[2015_Summer_Project_Week_Template | Template for project pages]]

==Equipment==

*[[2015_Summer_Project_Week:Equipment|Specialized equipment people are going to bring]] (Please add to this list if you are bringing anything)

==Image-Guided Therapy==
*[[2015_Summer_Project_Week:SlicerIGT|SlicerIGT tutorials for use cases]] (Tamas Ungi)
*[http://www.na-mic.org/Wiki/index.php/2015_Refinement_Registration_Module Refinement of RegistrationModule] (Peter Behringer, Andrey Fedorov)
*[[2015_Summer_Project_Week:IGTSliceletBase| Create base classes for IGT slicelet]] (Andras Lasso, Andrey Fedorov, Adam Rankin)
*[http://www.na-mic.org/Wiki/index.php/2015_BRAINSFit_registration_in_SimpleITK BRAINSFit registration in SimpleITK] (Peter Behringer, Andrey Fedorov, Dženan Zukić)
*[http://www.na-mic.org/Wiki/index.php/2015_Multi_atlas_based_prostate_segmentation Multi atlas based prostate segmentation] (Paolo Zaffino, Giampaolo Pileggi, Salvatore Scaramuzzino, Peter Behringer, Andrey Fedorov, Maria Francesca Spadea)
*[[2015 Orthognathic Surgery|Orthognathic Surgery]] (Dženan Zukić, Kitware)
*[http://www.na-mic.org/Wiki/index.php/2015_Multimodal_Guidance_for_Breast_Cancer_Surgery Multimodal Guidance for Breast Cancer Surgery] (Mikael Brudfors, Javier Pascau)
*[http://www.na-mic.org/Wiki/index.php/2015_pyDBS pyDBS module update to Slicer4.4 (Sara Fernandez-Vidal, Yulong Zhao, Sonia Pujol)]
*[[2015_pilot trajectory planning | Pilot Trajectory Planning(Caroline Essert, Sonia Pujol)]]
*[[2015_Summer_Project_Week:LinearFeatureRegistration|Linear Feature Registration]] (Matthew Holden)
*[[2015_Summer_Project_Week:LightWeightRobotIGT | Integration of a KUKA robot using OpenIGTLink ]] (Sebastian Tauscher, Junichi Tokuda)
*[[Slicer_CIP | Slicer CIP: advanced features and deployment ]] (Raúl San José, Alex Yarmarkovich, Jorge Onieva, James Ross, Rola Harmouche)
*[[2015_Summer_Project_Week:PAA_Ratio | PAA Ratio ]] (Raúl San José, Alex Yarmarkovich, Jorge Onieva, James Ross, Rola Harmouche)
*[[2015_Summer_Project_Week:SlicerTAVI | SlicerTAVI ]] (Adam Rankin)

==Feature Based Image Analysis==
*[[2015_Summer_Project_Week:LungCAD| LungCAD]] (Jayender Jagadeesan, Tobias Penzkofer, Sandy Wells)
*[[2015_Summer_Project_Week:QuantitativeProstate | Texture Analysis for Prostate Imaging]] (Tobias Penzkofer, Jay Jagadeesan, Tina Kapur)
*[[2015_Summer_Project_Week:BigDataFeatures | Big Data Medical Image Analysis using Local Features]] (Matthew Toews, William Wells, Raul San Jose Estepar, Tina Kapur)
*[[2015_Summer_Project_Week:USReconstruction | Gated 3D Ultrasound Reconstructions with the Help of a Single-Element US Transducer ]] (Frank Preiswerk, Laurent Chauvin)
*[[2015_Summer_Project_Week:AutomaticCephalometric | Automatic Cephalometric Analysis ]] (J. Jesus Montufar, Marcelo Romero)

==QIICR==
*[[2015_Summer_Project_Week:DSC | Dynamic Susceptibility Contrast (DSC) MRI for brain ]] (Xiao Da, Yangming Ou, Andriy Fedorov, Steve Pieper, Jayashree Kalpathy-Cramer)
*[[2015_Summer_Project_Week:T1 mapping | T1 mapping for Dynamic Contrast Enhanced (DCE) MRI ]] (Xiao Da, Yangming Ou, Andriy Fedorov, Jayashree Kalpathy-Cramer)
*[[2015_Summer_Project_Week:DCMTK| Integration and testing of new DCMTK with Slicer]] (Michael Onken, Andrey Fedorov, Steve Pieper)

==Infrastructure==
*[[2015_Summer_Project_Week:Python_scripts_from_command_line|Simplify use of python scripts from the command line]] (Andrey Fedorov, Steve Pieper, Robin Weiss, Artem Mamonov)
*[[2015_Summer_Project_Week:CLIModules_Backgrounding_in_MeVisLab | Running CLI Modules in the background in MeVisLab]] (Hans Meine)
*[[2015_Summer_Project_Week:CLIModules_Indexing | CLI Modules elasticsearch / kibana dashboard]] (Hans Meine, JC, Steve Pieper)
*[[2015_Summer_Project_Week:CTK_Interative_Plugins | CTK plugins / paths towards interoperability with GUI & interaction]] (Hans Meine, Steve Pieper, Nicolas Rannou)
*[[2015_Summer_Project_Week:BRAINSFit_in_MeVisLab | Interoperability tests with "interesting" CLI modules (BRAINSFit, CIP, UKFTractography?) in MeVisLab (/Frontier)]] (Hans Meine, Steve Pieper)
*[[2015_Summer_Project_Week:Return_Fiducials_from_CLIs | Return fiducials from CLIs]] (Nicole Aucoin,Hans Meine)
*[[2015_Summer_Project_Week:Update Checker | Update Checker]] (Franklin King, BWH)
*[[2015_Summer_Project_Week:Integrated Virtual Reality Viewer | Integrated Virtual Reality Viewer]] (Franklin King, BWH)
*[[2015_Summer_Project_Week:SegmentationNode| Use new Segmentation node in Editor]] (Andras Lasso, Steve Pieper)
*[[2015_Summer_Project_Week:Slicer_Conda | Integrate Conda Python in Slicer]] (Raúl San José, Jorge Onieva)

==Web==
*[[2015_Summer_Project_Week:Dicom parsing with DCMJS | Dicom parsing with DCMJS]] (Nicolas Rannou, Michael Onken, Steve Pieper)
*[[2015_Summer_Project_Week:Volume rendering with DCMJS and THREEJS | Volume Rendering with DCMJS and THREEJS]] (Nicolas Rannou, Steve Pieper)
*[[2015_Summer_Project_Week:CTK for the web and touch devices| CTK for the web and touch devices]] (Nicolas Rannou, Yves Martelli, Steve Pieper)
*[[2015_Summer_Project_Week:SlicerCardboard| Slicer for mobile-based vr goggles]] (Utsav Pardasani, Adam Rankin)

==Astronomy==
*[[2015_Summer_Project_Week:Astronomy | visualization of HI in galaxies]] (Davide Punzo)

== '''Registrants''' ==

Please add your name to the list. This is the registration mechanism for this project week.
#Tina Kapur, BWH
#Ron Kikinis, BWH & Fraunhofer
#Steve Pieper, Isomics
#Tamas Ungi, Queen's University, Canada
#Andras Lasso, Queen's University, Canada
#Paolo Zaffino, ImagEngLab, Magna Graecia University, Italy
#Salvatore Scaramuzzino, ImagEngLab, Magna Graecia University, Italy
#Giampaolo Pileggi, ImagEngLab, Magna Graecia University, Italy
#''Hans Meine, University of Bremen / Fraunhofer MEVIS, Germany'' – canceled due to personal circumstances
#Nicole Aucoin, BWH
#Sonia Pujol, BWH
#Dženan Zukić, Kitware, Carrboro, NC
#Jayender Jagadeesan, BWH
#Guido Gerig, Utah
#Sandy Wells, BWH
#Matthew Toews, École de Technologie Supérieure, Montreal, Canada
#Frank Preiswerk, BWH
#Raul San Jose, BWH
#Jorge Onieva, BWH
#Yulong Zhao, Université de Rennes
#Laurent Chauvin, BWH
#Michael Onken, Open Connections
#Tobias Penzkofer, Department of Radiology, Charité Berlin, Germany
#Javier Pascau, Universidad Carlos III de Madrid, Spain
#Angel Torrado-Carvajal, Universidad Rey Juan Carlos, Madrid, Spain
#Nobuhiko Hata, BWH
#Robert H. Owen, BK Medical ApS, Denmark
#Clare Tempany, BWH
#Adam Rankin, Robarts
#Utsav Pardasani, Robarts
#Marcelo Romero, Facultad de Ingenieria, Universidad Autonoma del Estado de Mexico, Mexico
#J. Jesus Montufar, Facultad de Ingenieria, Universidad Autonoma del Estado de Mexico, Mexico
#Davide Punzo, Kapteyn Astronomical Institute, University of Groningen, Netherlands
#Andrey Fedorov, BWH
#Nicolas Rannou, BCH
#Mikael Brudfors, Universidad Carlos III de Madrid, Spain
#Laura Sanz, Universidad Carlos III de Madrid, Spain
#Eugenio Marinetto, Universidad Carlos III de Madrid, Spain
#David García, Universidad Carlos III de Madrid, Spain
#Franklin King, Queen's University / BWH
#Jorge García, Universidad Politécnica de Madrid, Spain
#Peter Behringer, BWH
#Caroline Essert, University of Strasbourg
#Sebastian Tauscher, Institute of Mechatronic Systems, Leibniz Universität Hannover, Germany
#Matthew Holden, Queen's University, Canada
#Sara Fernandez Vidal, ICM, France
#Laszlo Kanyasi, Perk Lab affiliate, Hungary
#Xiao Da, MGH
#Arnaud De Bruecker, École supérieure d'informatique, Brussels, Belgium
#Ali Gottschalk, École supérieure d'informatique, Brussels, Belgium
#Christophe Teixeira Pereira, École supérieure d'informatique, Brussels, Belgium
#Tsotne Shonia, École supérieure d'informatique, Brussels, Belgium
#Clara Meinzer, Semmelweis University, Hungary
#Yves Martelli, Galgo Medical, Barcelona, Spain

2015 Summer Project Week:Slicer Conda

2015-06-21T16:19:08Z

Utsav Pardasani:

<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Raúl San José
* Jorge Onieva
* Alex Yarmarkovich
* Utsav Pardasani

==Project Description==
<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Integrate Slicer with Conda Python so that the community could use Conda packages easily in Slicer.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
An initial approach and a proof of concept has already been done using Miniconda. During the NAMIC week we will try to take the final steps for the integration in all the platforms

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
*
</div>
</div>

2015 Summer Project Week:Integrated Virtual Reality Viewer

2015-06-21T16:18:25Z

Utsav Pardasani:

__NOTOC__
<gallery>
Image:PW-Summer2015.png|[[2015_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
*Franklin King
*Steve Pieper
*Jayender Jagadeesan
*Tina Kapur
*Utsav Pardasani
==Project Description==

Previous [[2014_Project_Week:ImmersiveVR | virtual reality projects]] for Slicer have either been limited to specific hardware or have required the use of third party applications. The plan is to create an integrated virtual reality viewer as a module within 3D Slicer that can be used with the variety of consumer virtual reality devices releasing in the coming year.

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Create virtual reality viewer module
** Allow a user to pick a point in a Slicer scene to place themselves and render a 360° panoramic view of the scene for virtual reality headsets
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
* Module allows user to position a point in the scene to view from
* Opens a window to be viewed using a VR HMD
** Create a view of the scene (exported as MP4[1]?), display using [https://va3c.github.io/three.js/examples/misc_controls_oculusrift.html three.js], and handle distortion and tracking
* Investigate making 'canned' animation types like flythroughs or rotations
* Use the Endoscopy module
* Investigate exporting mp4 regular movies as well (e.g. for youtube)
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress: </h3>
*
</div>
</div>

==References==
[1] http://www.openh264.org/