NAMIC Wiki - User contributions [en]

2012 Winter Project Week:BKPLUSSlicer

2012-01-13T08:07:48Z

Moradi: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
File:bk.PNG|
</gallery>

==Key Investigators==
* BWH: Isaiah Norton, Mehdi Moradi
* Queen's: Tamas Ungi

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

<h3>Objective</h3>
The goal is to integrate and streamline tracked data logging from the BK ultrasound (specifically RF data) using Slicer and PLUS. This will facilitate use of the BK system for on- and off-line visualization and data analysis. In certain clinical applications in BWH AMIGO that use the BK system, such as prostate interventions and brain tumor resection procedures, real time ultrasound-based tissue typing is a very useful addition. Tracking and streaming of the RF data to a high end PC is essential for these purposes.

</div>

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

<h3>Approach, Plan</h3>

The ProFocus BK machine, equipped with the optional research interface has the ability to stream RF data over a CameraLink connection to a frame grabber. This setup is now in use in BWH. The software developed for data logging lacks a GUI, the ability for real time B-mode display, and tracking at the moment. The PLUS library, developed for streaming data from the Ultrasonix machine through an OpenIGTLink, essentially meets the visualization and tracking aims. Since this is all implemented with a different US machine in PLUS, theoretically, we just have to instantiate new subclasses for this specific video source. In practice, we anticipate complications arising from the different hardware platforms.

</div>

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

<h3>Progress</h3>

In meetings with the Queen's group and PLUS developers, we analyzed the architecture of the PLUS library. A blueprint and pseudocode were created for the interface between the PLUS library and the BK SDK. The development is highly hardware dependent and will be completed back in Boston.
</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#Slicer Module (via PLUS and OpenIGTLink)

==References==

</div>

2012 Winter Project Week:PelvicRegistration

2012-01-13T07:56:34Z

Moradi:

Project Title: '''Surface-based 3D deformable registration of ultrasound and MRI prostate volumes'''
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
File:Mr us.JPG|
</gallery>

==Investigators at Brigham and Women's ==
* Computational core: Mehdi Moradi, Firdaus Janoos, Tina Kapur, Jan Egger, Sandy Wells
* Clinical core: Clare Tempany, Paul Nguyen
* Prostate core: Andriy Fedorov
* Present team members in SLC: Mehdi Moradi, Andriy Fedorov, Jan Egger.

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
We will implement a basic surface-based deformable registration solution to register prostate 3D ultrasound data to MRI. This is to enable clinical integration of the diagnostic MRI data with ultrasound during prostate brachytherapy with dynamic intraoperative dose planning.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>

We will first examine solutions available in Slicer.

We have also implemented a surface based registration algorithm with elastic energy as the penalty for the deformation. Ultrasound images are collected using a stepper, with fixed slice spacing in the axial view. The object is segmented (contoured) in both MRI and ultrasound images and a surface model is created.

</div>

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

<h3>Progress</h3>

During the project week, two solutions were applied to an available dataset. The dataset included three sets of 3D ultrasound and MRI images from three different cases. For all these cases manual segmentation provided by a clinician was available. 1) We used Slicer 4 to implement image-based 3D deformable registration of image labels (results of segmentation) and then apply the resulting warping to the moving (MRI) image. 2) We used the Slicer 3.6 implementation of ICP registration to align the 3D models created from the segmented labels from MRI and ultrasound. Based on this initial alignment, we equalized the length of the base-apex axis of the prostate gland in the two modalities. Then, we updated the label volumes and applied image-based registration (Rigid, affine and deformable) to the updated label maps.

Validation is a challenge as landmarks that can be matched from ultrasound and MRI are hard to find in the prostate gland. In one case, calcification is visible in both modalities. Based solely on this landmark, solution (2) appears more accurate. We are planning to consult with clinicians and acquire their feedback on the comparisons of these methods, and validation methods.
<gallery>
File:Mr_us_pros.PNG|[[MR to ultrasound registration, using solutions (1) described in the (progress) section above.]]
</gallery>
</div>

<div style="width: 97%; float: left;">

2012 Winter Project Week:PelvicRegistration

2012-01-13T07:54:31Z

Moradi:

Project Title: '''Surface-based 3D deformable registration of ultrasound and MRI prostate volumes'''
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
File:Mr us.JPG|
</gallery>

==Investigators at Brigham and Women's ==
* Computational core: Mehdi Moradi, Firdaus Janoos, Tina Kapur, Jan Egger, Sandy Wells
* Clinical core: Clare Tempany, Paul Nguyen
* Prostate core: Andriy Fedorov
* Present team members in SLC: Mehdi Moradi, Andriy Fedorov, Jan Egger.

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
We will implement a basic surface-based deformable registration solution to register prostate 3D ultrasound data to MRI. This is to enable clinical integration of the diagnostic MRI data with ultrasound during prostate brachytherapy with dynamic intraoperative dose planning.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>

We will first examine solutions available in Slicer.

We have also implemented a surface based registration algorithm with elastic energy as the penalty for the deformation. Ultrasound images are collected using a stepper, with fixed slice spacing in the axial view. The object is segmented (contoured) in both MRI and ultrasound images and a surface model is created.

</div>

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

<h3>Progress</h3>

During the project week, two solutions were applied to an available dataset. The dataset included three sets of 3D ultrasound and MRI images from three different cases. For all these cases manual segmentation provided by a clinician was available. 1) We used Slicer 4 to implement image-based 3D deformable registration of image labels (results of segmentation) and then apply the resulting warping to the moving (MRI) image. 2) We used the Slicer 3.6 implementation of ICP registration to align the 3D models created from the segmented labels from MRI and ultrasound. Based on this initial alignment, we equalized the length of the base-apex axis of the prostate gland in the two modalities. Then, we updated the label volumes and applied image-based registration (Rigid, affine and deformable) to the updated label maps.

Validation is a challenge as landmarks that can be matched from ultrasound and MRI are hard to find in the prostate gland. In one case, calcification is visible in both modalities. Based solely on this landmark, solution (2) appears more accurate. We are planning to consult with clinicians and acquire their feedback on the comparisons of these methods, and validation methods.
<gallery>
File:Mr_us_pros.PNG
</gallery>
</div>

<div style="width: 97%; float: left;">

2012 Winter Project Week:PelvicRegistration

2012-01-13T07:53:11Z

Moradi:

Project Title: '''Surface-based 3D deformable registration of ultrasound and MRI prostate volumes'''
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
File:Mr us.JPG|
</gallery>

==Investigators at Brigham and Women's ==
* Computational core: Mehdi Moradi, Firdaus Janoos, Tina Kapur, Jan Egger, Sandy Wells
* Clinical core: Clare Tempany, Paul Nguyen
* Prostate core: Andriy Fedorov
* Present team members in SLC: Mehdi Moradi, Andriy Fedorov, Jan Egger.

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
We will implement a basic surface-based deformable registration solution to register prostate 3D ultrasound data to MRI. This is to enable clinical integration of the diagnostic MRI data with ultrasound during prostate brachytherapy with dynamic intraoperative dose planning.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>

We will first examine solutions available in Slicer.

We have also implemented a surface based registration algorithm with elastic energy as the penalty for the deformation. Ultrasound images are collected using a stepper, with fixed slice spacing in the axial view. The object is segmented (contoured) in both MRI and ultrasound images and a surface model is created.

</div>

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

<h3>Progress</h3>

During the project week, two solutions were applied to an available dataset. The dataset included three sets of 3D ultrasound and MRI images from three different cases. For all these cases manual segmentation provided by a clinician was available. 1) We used Slicer 4 to implement image-based 3D deformable registration of image labels (results of segmentation) and then apply the resulting warping to the moving (MRI) image. 2) We used the Slicer 3.6 implementation of ICP registration to align the 3D models created from the segmented labels from MRI and ultrasound. Based on this initial alignment, we equalized the length of the base-apex axis of the prostate gland in the two modalities. Then, we updated the label volumes and applied image-based registration (Rigid, affine and deformable) to the updated label maps.

Validation is a challenge as landmarks that can be matched from ultrasound and MRI are hard to find in the prostate gland. In one case, calcification is visible in both modalities. Based solely on this landmark, solution (2) appears more accurate. We are planning to consult with clinicians and acquire their feedback on the comparisons of these methods, and validation methods.
<gallery>
Image:mr_us_pros.png|
</gallery>
</div>

<div style="width: 97%; float: left;">

2012 Winter Project Week:PelvicRegistration

2012-01-13T07:52:09Z

Moradi:

Project Title: '''Surface-based 3D deformable registration of ultrasound and MRI prostate volumes'''
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
File:Mr us.JPG|
</gallery>

==Investigators at Brigham and Women's ==
* Computational core: Mehdi Moradi, Firdaus Janoos, Tina Kapur, Jan Egger, Sandy Wells
* Clinical core: Clare Tempany, Paul Nguyen
* Prostate core: Andriy Fedorov
* Present team members in SLC: Mehdi Moradi, Andriy Fedorov, Jan Egger.

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
We will implement a basic surface-based deformable registration solution to register prostate 3D ultrasound data to MRI. This is to enable clinical integration of the diagnostic MRI data with ultrasound during prostate brachytherapy with dynamic intraoperative dose planning.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>

We will first examine solutions available in Slicer.

We have also implemented a surface based registration algorithm with elastic energy as the penalty for the deformation. Ultrasound images are collected using a stepper, with fixed slice spacing in the axial view. The object is segmented (contoured) in both MRI and ultrasound images and a surface model is created.

</div>

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

<h3>Progress</h3>

During the project week, two solutions were applied to an available dataset. The dataset included three sets of 3D ultrasound and MRI images from three different cases. For all these cases manual segmentation provided by a clinician was available. 1) We used Slicer 4 to implement image-based 3D deformable registration of image labels (results of segmentation) and then apply the resulting warping to the moving (MRI) image. 2) We used the Slicer 3.6 implementation of ICP registration to align the 3D models created from the segmented labels from MRI and ultrasound. Based on this initial alignment, we equalized the length of the base-apex axis of the prostate gland in the two modalities. Then, we updated the label volumes and applied image-based registration (Rigid, affine and deformable) to the updated label maps.

Validation is a challenge as landmarks that can be matched from ultrasound and MRI are hard to find in the prostate gland. In one case, calcification is visible in both modalities. Based solely on this landmark, solution (2) appears more accurate. We are planning to consult with clinicians and acquire their feedback on the comparisons of these methods, and validation methods.
<gallery>
File:mr_us_pros.png|
</gallery>
</div>

<div style="width: 97%; float: left;">

2012 Winter Project Week:PelvicRegistration

2012-01-13T07:51:24Z

Moradi:

Project Title: '''Surface-based 3D deformable registration of ultrasound and MRI prostate volumes'''
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
File:Mr us.JPG|
</gallery>

==Investigators at Brigham and Women's ==
* Computational core: Mehdi Moradi, Firdaus Janoos, Tina Kapur, Jan Egger, Sandy Wells
* Clinical core: Clare Tempany, Paul Nguyen
* Prostate core: Andriy Fedorov
* Present team members in SLC: Mehdi Moradi, Andriy Fedorov, Jan Egger.

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
We will implement a basic surface-based deformable registration solution to register prostate 3D ultrasound data to MRI. This is to enable clinical integration of the diagnostic MRI data with ultrasound during prostate brachytherapy with dynamic intraoperative dose planning.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>

We will first examine solutions available in Slicer.

We have also implemented a surface based registration algorithm with elastic energy as the penalty for the deformation. Ultrasound images are collected using a stepper, with fixed slice spacing in the axial view. The object is segmented (contoured) in both MRI and ultrasound images and a surface model is created.

</div>

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

<h3>Progress</h3>

During the project week, two solutions were applied to an available dataset. The dataset included three sets of 3D ultrasound and MRI images from three different cases. For all these cases manual segmentation provided by a clinician was available. 1) We used Slicer 4 to implement image-based 3D deformable registration of image labels (results of segmentation) and then apply the resulting warping to the moving (MRI) image. 2) We used the Slicer 3.6 implementation of ICP registration to align the 3D models created from the segmented labels from MRI and ultrasound. Based on this initial alignment, we equalized the length of the base-apex axis of the prostate gland in the two modalities. Then, we updated the label volumes and applied image-based registration (Rigid, affine and deformable) to the updated label maps.

Validation is a challenge as landmarks that can be matched from ultrasound and MRI are hard to find in the prostate gland. In one case, calcification is visible in both modalities. Based solely on this landmark, solution (2) appears more accurate. We are planning to consult with clinicians and acquire their feedback on the comparisons of these methods, and validation methods.

File:mr_us_pros.png|

</div>

<div style="width: 97%; float: left;">

2012 Winter Project Week:PelvicRegistration

2012-01-13T07:50:27Z

Moradi:

Project Title: '''Surface-based 3D deformable registration of ultrasound and MRI prostate volumes'''
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
File:Mr us.JPG|
</gallery>

==Investigators at Brigham and Women's ==
* Computational core: Mehdi Moradi, Firdaus Janoos, Tina Kapur, Jan Egger, Sandy Wells
* Clinical core: Clare Tempany, Paul Nguyen
* Prostate core: Andriy Fedorov
* Present team members in SLC: Mehdi Moradi, Andriy Fedorov, Jan Egger.

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
We will implement a basic surface-based deformable registration solution to register prostate 3D ultrasound data to MRI. This is to enable clinical integration of the diagnostic MRI data with ultrasound during prostate brachytherapy with dynamic intraoperative dose planning.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>

We will first examine solutions available in Slicer.

We have also implemented a surface based registration algorithm with elastic energy as the penalty for the deformation. Ultrasound images are collected using a stepper, with fixed slice spacing in the axial view. The object is segmented (contoured) in both MRI and ultrasound images and a surface model is created.

</div>

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

<h3>Progress</h3>

During the project week, two solutions were applied to an available dataset. The dataset included three sets of 3D ultrasound and MRI images from three different cases. For all these cases manual segmentation provided by a clinician was available. 1) We used Slicer 4 to implement image-based 3D deformable registration of image labels (results of segmentation) and then apply the resulting warping to the moving (MRI) image. 2) We used the Slicer 3.6 implementation of ICP registration to align the 3D models created from the segmented labels from MRI and ultrasound. Based on this initial alignment, we equalized the length of the base-apex axis of the prostate gland in the two modalities. Then, we updated the label volumes and applied image-based registration (Rigid, affine and deformable) to the updated label maps.

Validation is a challenge as landmarks that can be matched from ultrasound and MRI are hard to find in the prostate gland. In one case, calcification is visible in both modalities. Based solely on this landmark, solution (2) appears more accurate. We are planning to consult with clinicians and acquire their feedback on the comparisons of these methods, and validation methods.

Image:mr_us_pros.png

</div>

<div style="width: 97%; float: left;">

File:Mr us pros.PNG

2012-01-13T07:49:01Z

Moradi:

2012 Winter Project Week:PelvicRegistration

2012-01-13T07:34:09Z

Moradi: /* Investigators at Brigham and Women's */

2012 Winter Project Week:PelvicRegistration

2012-01-13T07:32:29Z

Moradi: /* Investigators at Brigham and Women's */

Project Title: '''Surface-based 3D deformable registration of ultrasound and MRI prostate volumes'''
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
File:Mr us.JPG|
</gallery>

==Investigators at Brigham and Women's ==
* Computational core: Mehdi Moradi, Firdaus Janoos, Tina Kapur, Jan Egger, Sandy Wells
* Clinical core: Clare Tempany, Paul Nguyen
* Prostate core: Andriy Fedorov
* Present team members in SLC: Mehdi Moradi, Andriy Fedorov, Jan Egger.

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
We will implement a basic surface-based deformable registration solution to register prostate 3D ultrasound data to MRI. This is to enable clinical integration of the diagnostic MRI data with ultrasound during prostate brachytherapy with dynamic intraoperative dose planning.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>

We will first examine solutions available in Slicer.

We have also implemented a surface based registration algorithm with elastic energy as the penalty for the deformation. Ultrasound images are collected using a stepper, with fixed slice spacing in the axial view. The object is segmented (contoured) in both MRI and ultrasound images and a surface model is created. Gaussian mapping of the surface reduces the registration problem to finding an appropriate rotation of the coordinate systems that minimizes a cost function. This cost is the elastic energy of deforming the surface from MRI to US configuration.

</div>

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

<h3>Progress</h3>

During the project week, two solutions were applied to an available dataset. The dataset included three sets of 3D ultrasound and MRI images from three different cases. For all these cases manual segmentation provided by a clinician was available. 1) We used Slicer 4 to implement image-based 3D deformable registration of image labels (results of segmentation) and then apply the resulting warping to the moving (MRI) image. 2) We used the Slicer 3.6 implementation of ICP registration to align the 3D models created from the segmented labels from MRI and ultrasound. Based on this initial alignment, we equalized the length of the base-apex axis of the prostate gland in the two modalities. Then, we updated the label volumes and applied image-based registration (Rigid, affine and deformable) to the updated label maps.

Validation is a challenge as landmarks that can be matched from ultrasound and MRI are hard to find in the prostate gland. In one case, calcification is visible in both modalities. Based solely on this landmark, solution (2) appears more accurate. We are planning to consult with clinicians and acquire their feedback on the comparisons of these methods, and validation methods.

</div>

<div style="width: 97%; float: left;">

2012 Winter Project Week

2012-01-13T07:08:25Z

Moradi: /* IGT for Surgery and Radiation Treatments */

Back to [[Project Events]], [[Events]]
Back to [[Project Events]], [[AHM_2012]], [[Events]]

__NOTOC__
[[image:PW-SLC2012.png|300px]]

== Dates.Venue.Registration ==

Please [[AHM_2012#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

== [[AHM_2012#Agenda|'''AGENDA''']] and Project List==

Please:
* [[AHM_2012#Agenda|'''Click here for the agenda for AHM 2012 and Project Week''']].
* [[#Projects|'''Click here to jump to Project list''']]

==Background==

From January 9-13, 2012, the 14th project week for hands-on research and development activity in Neuroscience and Image-Guided Therapy applications will be hosted in Salt Lake City, Utah. Participant engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions.

Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project.

On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.

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

==Projects==

===Traumatic Brain Injury ===

* [[2012_Winter_Project_Week:TBIClinicalAnalysis|Segmentation of Serial MRI of TBI patients
using Personalized Atlas Construction]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIDTIAnalysis|Registration and analysis of white matter tract changes in TBI]] (Clement Vachet, Anuja Sharma, Marcel Prastawa, Andrei Irimia, Jack van Horn, Guido Gerig, Martin Styner, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIValidation|Validation, visualization and analysis of segmentation for TBI]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:GeometricMetamorphosisTBI|Geometric Metamorphosis for TBI]] (Danielle Pace, Marc Niethammer, Marcel Prastawa, Andrei Irimia, Jack van Horn, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Multimodal Deformable Registration of Traumatic Brain Injury MR Volumes using Graphics Processing Units]] (Yifei Lou, Andrei Irimia, Patricio Vela, Allen Tannenbaum, Micah C. Chambers, Jack Van Horn and Paul M. Vespa, Danielle Pace, Stephen Aylward)

===Predict Huntington's Disease===
* [[2012_Winter_Project_Week:SPIEWorkshop|SPIE DTI Workshop Preparation: Perform DTI Quality Control]] (Jean-Baptiste Berger, Sonia Pujol, Guido Gerig, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DWIPhantom|DTI tractography phantom: a software for evaluating tractography algorithms]] (Gwendoline Roger,Yundi Shi, Clement Vachet, Martin Styner, Sylvain Gouttard)
* [[2012_Winter_Project_Week:FVLight|FiberViewerLight: a fiber bundle visualization and clustering tool]] (Jean-Baptiste Berger, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DTIAFA|DTIAtlasFiberAnalyzer]] (Jean-Baptiste Berger, Yundi Shi, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:PairWiseDTIRegistration|Pairwise DTI registration: DTI-Reg]] (Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:ShapeAnalysisSubcorticalStructuresHD|Morphometric analysis in subcortical structures in HD]] (Beatriz Paniagua, Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:DTI pipeline|Applying our DTI pipeline to analyse HD data]] (Gopalkrishna Veni, Hans Johnson, Martin Styner, Ross Whitaker)
* [[2012_Winter_Project_Week: DTI Change Modeling | Longitudinal change modeling of fiber tracts in serial HD DTI data]] (Anuja Sharma, Hans Johnson, Guido Gerig)
* [[2012_Winter_Project_Week: Continuous 4D shapes | Continuous 4d shape models from time-discrete data: Subcortical structures in HD]] (James Fishbaugh, Hans Johnson, Guido Gerig)

===Atrial fibrillation ===
* [[2012_Winter_Project_Week:EndoSeg|Endocardial Segmentation in DE-MRI for AFib]] (Yi Gao, Liang-Jia Zhu, Josh Cates, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:LAWallRegistration|Longitudinal Alignment and Visualization of Left-Atrial Wall from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:PVRegistration|Longitudinal Alignment and Visualization of Pulmonary Veins from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:RealTime|OpenIGT for realtime MRI-guided RF ablation]] (Rob MacLeod, and Junichi Tokuda)
* [[2012_Winter_Project_Week:GraphbasedSeg|Graph based segmentation on LGE-MRI data]] (Gopal Veni, Ross Whitaker)

===Head and Neck Cancer ===
* [[2012_Winter_Project_Week:PairwiseLF|Label fusion with pairwise interactions]] (Ramesh Sridharan, Christian Wachinger, Polina Golland)
* [[2012_Winter_Project_Week:PatchBased|A patch-based approach to the segmentation of organs of risk]] (Christian Wachinger, Polina Golland)
* [[RT dose comparison tool for Slicer]] (Nadya Shusharina, Greg Sharp)
* [[2012_Winter_Project_Week:InteractiveSegmentation|Interactive editing tools for segmentation]] (Greg Sharp, Steve Pieper)
* [[2012_Winter_Project_Week:UserInTheLoop_InteractiveSegmn|Interactive 3D Level-Set Segmentation]] (Peter Karasev, Karl Fritscher, Ivan Kolesov, Allen Tannenbaum)
* [[2012_Winter_Project_Week:GBMseg|Segmentation of polymodal images of GBM's in Slicer]] (Misha Milchenko, Dan Marcus, Andrey Fedorov, Jan Egger, Isaiah Norton, Jayashree)

===IGT for Surgery and Radiation Treatments===
*[[2012_Winter_Project_Week:OpenIGTLink_Interface_for_Slicer4| OpenIGTLink interface for Slicer4]] (Junichi Tokuda, Clif Burdette/Jack Blevins, Tamas Ungi, Andras Lasso)
*[[2012_Winter_Project_Week:LiveUltrasound|Live ultrasound in Slicer4 using Plus and OpenIGTLink]] (Tamas Ungi, Elvis Chen, Junichi Tokuda)
*[[2012_Winter_Project_Week:4DUltrasound|4D Ultrasound Storage and Volume Rendering on Slicer 3.6]] (Laurent, Noby)
*[[2012_Winter_Project_Week:BKPLUSSlicer|Integration of BK Ultrasound into PLUS and Slicer]] (Isaiah Norton, Mehdi Moradi, Tamas Ungi)
*[[2012_Winter_Project_Week:LaserAblationAndGuidance|Slicer-BrainLab integration for laser ablation]] (Erol Yeniaras, Isaiah Norton, Pratik Patel)
*[[2012_Winter_Project_Week:PelvicRegistration|Deformable prostate registration: 3D ultrasound to MRI]] (Mehdi Moradi, Jan Egger, Andrey Fedorov)
*[[2012_Winter_Project_Week:iGyne | iGyne: A Software Prototype to support Gynecologic Radiation Treatment in AMIGO]] (Jan Egger, Xiaojun Chen, Radhika Tibrewal, Mehdi Moradi, Antonio Damato, Kanokpis Townamchai, Tina Kapur, Akila Viswanathan)
*[[2012_Winter_Project_Week:hybridMRS | Generation of a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer for Neurosurgery]] (Jan Egger, Isaiah Norton, Bjoern Menze, Daniel Hořínek, Antonín Škoch, Jens Sommer, Christopher Nimsky, Alexandra Golby, Tina Kapur)
*[[2012_Winter_Project_Week:Needle Detection in MR Images for Brachytherapy in AMIGO|Needle Detection in MR Images for Brachytherapy in AMIGO]] (Radhika Tibrewal, Jan Egger, Xiaojun Chen, Matthew Toews, Stephen Aylward)
*[[2012_Winter_Project_Week:Needle Detection in MR Images for Brachytherapy in AMIGO|Needle Detection in MR Images for Brachytherapy in AMIGO]]
*[[2012_Winter_Project_Week:RTTools|RT tools for Slicer4]] (Csaba Pinter, Kevin Wang, Andras Lasso, Greg Sharp)
*[[2012_Winter_Project_Week:RTSS|RT structure set data representation]] (Greg Sharp, Andras Lasso, Steve Pieper, etc.)

===Musculoskeletal System===
* [[2012_Winter_Project_Week:Radnostics|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)

===Registration===
* [[2012_Winter_Project_Week:CMFreg|Framework for Cranio-Maxillo Facial registration in Slicer3]] (Beatriz Paniagua, Lucia Cevidanes, Martin Styner)
* [[2012_Winter_Project_Week:SlidingOrgans|Registration in the presence of sliding between organs (Danielle Pace, Marc Neithammer, Stephen Aylward)]]
* [[2012_Winter_Project_Week:GeometricMetamorphosis|Estimating the infiltration / recession of pathologies independent of background deformations (Danielle Pace, Stephen Aylward, Marc Niethammer)]]
* [[2012_Winter_Project_Week:FastInterpolation|Fast Image Interpolation Given Parameterized Deformations For Image Registration (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)]]
* [[2012_Winter_Project_Week:CTLiverRegistration|Register liver CT images for tumor progress monitoring]] (Karl Diedrich, Nobuhiko Hata, Atsushi Yamada)
* [[2012_Winter_Project_Week:Fast Multi-modal Registration|Fast Registration with User-guidance for AMIGO]] (Dave Welch, Hans Johnson, Nicole Aucoin, Ron Kikinis)

===Shape Analysis===
* [[2012_Winter_Project_Week:PNSnormals|Principal Nested Spheres Normal Consistency in ShapeWorks]] (Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)
* [[2012_Winter_Project_Week:GeomIndicesSlicer4|Porting of White Matter Geometric Indices Module to Slicer4]] (Peter Savadjiev)
* [[2012_Winter_Project_Week:ParticleWrapper|Slicer end-to-end particle correspondence wrapper module]] (Ipek Oguz, Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)
* [[2012_Winter_Project_Week:UKFTractography|Integration of unscented Kalman filter (UKF) based multi-tensor tractography in Slicer]] (Christian Baumgartner, Yogesh Rathi, Carl-Fredrik Westin)

===NA-MIC Kit Internals===
*Slicer4 release (Jean-Christophe Fillion-Robin (JC), and Julien Finet (J2))
*Slicer4 extensions (JC)
*Slicer4 documentation (JC)
*Slicer4 GUI Testing (Benjamin Long, JC, J2)
*Slicer4 data on MIDAS (Josh Cates, Patrick Reynolds)
*[[2012_Project_Week:SceneViews|Slicer4 Scene Views Module]] (Nicole Aucoin, Ron Kikinis, Julien Finet)
*[[2012_Project_Week:AnnotationsFileFormatRefactor|Annotations Module File Format Refactor]] (Nicole Aucoin)
*[[2012_Project_Week:QT3DTextRendering|QT 3D Text rendering proof of concept]] (Julien Finet, Steve Pieper, Nicole Aucoin)
*[[2012_Project_Week:DICOM|DICOM Networking, Database, and Slicer Integration]] (Steve, Andrey, Andras)
*[[2012_Project_Week:EditorExtensions|Editor Extension Examples and Debugging]] (Steve, Andrey, Jc, Hans, Satra)
*[[2012_Project_Week:GeneralGUI|General minor GUI redesign]] (Wendy Plezniak, Julien Finet, Ron Kikinis)
*[[2012_Project_Week:ViewerControls|Redesign of the slice viewer control panels]] (Julien Finet, Ron Kikinis, Hans Johnson, Greg Sharp)
*[[2012_Project_Week:AutomatedTesting |Automated Testing (Sonia Pujol, Steve Pieper, Jc, Benjamin)]]
*[[2012_Project_Week:RemoveSlicerLegacyCode|Remove legacy code from slicer4 (itk, modules, build scripts) (Hans, Jim, Steve, J2, JC)]]
*[[2012_Project_Week:BatchProcessing|Batch Processing with Slicer Modules]] (Steve, Andrey, JC, Hans, Satra, Dave Welch)
*[[2012_Project_Week:4DImageSlicer4|Support for 4D Images in Slicer4]] (Andrey, Steve, Junichi, Alex)
*[[2012_Project_Week:QIN-SAM|QIN Slicer Annotation Module: AIM, DICOM SR and Slicer annotations]] (Andrey, Steve, Nicole, Jayashree)

=== Preparation ===

#Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
#Starting Thursday, October 27th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 27: MGH DBP
#*November 3: Iowa DBP Huntingtons, Engineering Infrastructure Topics
#*November 10: Utah Atrial Fibrillation DBP
#*November 17: UCLA TBI DBP
#*November 24: No call. thanksgiving.
#*December 1:
#*December 8:
#*December 15:Finalize Projects
#*January 5: Loose Ends
#By December 15: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
#By December 15: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
##Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
##Gather test images in any of the Data sharing resources we have (e.g. MIDAS, xNAT). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
##Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
#Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

AHM2012-3D-US-Slicer-Breakout

2012-01-05T20:39:31Z

Moradi: /* Agenda */

[[AHM_2012#Agenda|Back to AHM Schedule]]

=Objective=
The objective of this break out session is discuss 1) the current Slicer activities related to ultrasound guided therapies, 2) identify shared interest effort overlap, and common unmet needs, 3) produce common statement from participants about the action plans. Everyone is welcome to attend.

=Time/Date/Place=
*In 2012 NA-MIC all hands meeting
*8:10-12:00, Wednesday, January 11, 2012
*Amethyst room, Marriott, Salt Lake City, UT

=Coordinator=
*Nobuhiko Hata, PhD, Brigham and Women's Hospital
*Andras Lasso, PhD, Queens University

=Agenda=

*8:10-8:20, Welcome, Goal of the meeting, Meeting logistics, Note taking in wiki
*8:20-8:35, Project introduction 1, PLUS library and/or Canadian projects efforts, Andras Lasso
**Keywords: Plus framework, applications, spatial & temporal calibration, volume reconstruction, ECG
*X:XX-X:XX, Project introduction 2, Tamas Ungi, Tracked real-time 2D ultrasound in Slicer (LiveUltrasound).
**Keywords: OpenIGTLink, needle guidance
*X:XX-X:XX, Project introduction 3, Elvis Chen, GPU volume rendering. We have developed (clean room implementation) a stand-along, CUDA-based, VTK class for volume rendering. It is meant to be a drop-in replacement for vtkVolumeMapper. In addition, we implemented multi-dimentional transfer function, allowing much concise pixel-classification and visualization. Video demo will be given, source code will be made available.
**Keywords: CUDA, volume rendering, transfer function
*X:XX-X:XX, Project introduction 4, Laurent Chauvin, 4D US rendering
**Keywords:
*X:XX-X:XX, Project introduction 5, Mehdi Moradi, Prostate 3D US, BWH Efforts on US imaging. The ProFocus BK machine, equipped with the optional research interface has the ability to stream RF data over a CameraLink connection to a frame grabber. This setup is now in use in BWH. The software developed for data logging lacks a GUI, the ability for real time B-mode display, and tracking at the moment. The PLUS library, developed for streaming data from the Ultrasonix machine through an OpenIGTLink, essentially meets the visualization and tracking aims. We want to integrate the BK RF streaming module with the PLUS/Slicer development.

**Keywords:
*X:XX-X:XX, Project introduction 6, Junichi Tokuda/Steve Pieper, Related engineering effort: Handling 4D Images in Slicer
**Keywords: ,
*X:XX-X:XX, Project introduction 7, Nobuhiko Hata, review of U.S. US efforts
**Keywords: JHU efforts, BWH efforts, more...
*X:XX-X:XX, Project introduction 8, Anyone who is interested in talking
*X:XX-X:XX, Project introduction 8, Anyone who is interested in talking
*X:XX-X:XX, Project introduction 8, Anyone who is interested in talking
*10:00-10:30, Coffee break and
*10:30-11:00, Summary of current US projects, Breakdown of core technologies
*11:00-11:30, Identifying unmet needs,
*11:30-10:00, Group statement, Action Plan, Plan for the next events

2012 Winter Project Week:BKPLUSSlicer

2012-01-04T18:13:39Z

Moradi:

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
File:bk.PNG|
</gallery>

==Key Investigators==
* BWH: Isaiah Norton, Mehdi Moradi
* Queen's: Tamas Ungi

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

<h3>Objective</h3>
The goal is to integrate and streamline tracked data logging from the BK ultrasound (specifically RF data) using Slicer and PLUS. This will facilitate use of the BK system for on- and off-line visualization and data analysis. In certain clinical applications in BWH AMIGO that use the BK system, such as prostate interventions and brain tumor resection procedures, real time ultrasound-based tissue typing is a very useful addition. Tracking and streaming of the RF data to a high end PC is essential for these purposes.

</div>

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

<h3>Approach, Plan</h3>

The ProFocus BK machine, equipped with the optional research interface has the ability to stream RF data over a CameraLink connection to a frame grabber. This setup is now in use in BWH. The software developed for data logging lacks a GUI, the ability for real time B-mode display, and tracking at the moment. The PLUS library, developed for streaming data from the Ultrasonix machine through an OpenIGTLink, essentially meets the visualization and tracking aims. Since this is all implemented with a different US machine in PLUS, theoretically, we just have to instantiate new subclasses for this specific video source. In practice, we anticipate complications arising from the different hardware platforms.

</div>

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

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#Slicer Module (via PLUS and OpenIGTLink)

==References==

</div>

2012 Winter Project Week:BKPLUSSlicer

2012-01-04T18:13:28Z

Moradi:

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
File:bk.png|
</gallery>

==Key Investigators==
* BWH: Isaiah Norton, Mehdi Moradi
* Queen's: Tamas Ungi

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

<h3>Objective</h3>
The goal is to integrate and streamline tracked data logging from the BK ultrasound (specifically RF data) using Slicer and PLUS. This will facilitate use of the BK system for on- and off-line visualization and data analysis. In certain clinical applications in BWH AMIGO that use the BK system, such as prostate interventions and brain tumor resection procedures, real time ultrasound-based tissue typing is a very useful addition. Tracking and streaming of the RF data to a high end PC is essential for these purposes.

</div>

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

<h3>Approach, Plan</h3>

The ProFocus BK machine, equipped with the optional research interface has the ability to stream RF data over a CameraLink connection to a frame grabber. This setup is now in use in BWH. The software developed for data logging lacks a GUI, the ability for real time B-mode display, and tracking at the moment. The PLUS library, developed for streaming data from the Ultrasonix machine through an OpenIGTLink, essentially meets the visualization and tracking aims. Since this is all implemented with a different US machine in PLUS, theoretically, we just have to instantiate new subclasses for this specific video source. In practice, we anticipate complications arising from the different hardware platforms.

</div>

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

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#Slicer Module (via PLUS and OpenIGTLink)

==References==

</div>

2012 Winter Project Week:BKPLUSSlicer

2012-01-04T18:12:19Z

Moradi:

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
File:BK.png|
</gallery>

==Key Investigators==
* BWH: Isaiah Norton, Mehdi Moradi
* Queen's: Tamas Ungi

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

<h3>Objective</h3>
The goal is to integrate and streamline tracked data logging from the BK ultrasound (specifically RF data) using Slicer and PLUS. This will facilitate use of the BK system for on- and off-line visualization and data analysis. In certain clinical applications in BWH AMIGO that use the BK system, such as prostate interventions and brain tumor resection procedures, real time ultrasound-based tissue typing is a very useful addition. Tracking and streaming of the RF data to a high end PC is essential for these purposes.

</div>

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

<h3>Approach, Plan</h3>

The ProFocus BK machine, equipped with the optional research interface has the ability to stream RF data over a CameraLink connection to a frame grabber. This setup is now in use in BWH. The software developed for data logging lacks a GUI, the ability for real time B-mode display, and tracking at the moment. The PLUS library, developed for streaming data from the Ultrasonix machine through an OpenIGTLink, essentially meets the visualization and tracking aims. Since this is all implemented with a different US machine in PLUS, theoretically, we just have to instantiate new subclasses for this specific video source. In practice, we anticipate complications arising from the different hardware platforms.

</div>

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

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#Slicer Module (via PLUS and OpenIGTLink)

==References==

</div>

2012 Winter Project Week:BKPLUSSlicer

2012-01-04T18:10:39Z

Moradi:

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:BK.png|
</gallery>

==Key Investigators==
* BWH: Isaiah Norton, Mehdi Moradi
* Queen's: Tamas Ungi

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

<h3>Objective</h3>
The goal is to integrate and streamline tracked data logging from the BK ultrasound (specifically RF data) using Slicer and PLUS. This will facilitate use of the BK system for on- and off-line visualization and data analysis. In certain clinical applications in BWH AMIGO that use the BK system, such as prostate interventions and brain tumor resection procedures, real time ultrasound-based tissue typing is a very useful addition. Tracking and streaming of the RF data to a high end PC is essential for these purposes.

</div>

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

<h3>Approach, Plan</h3>

The ProFocus BK machine, equipped with the optional research interface has the ability to stream RF data over a CameraLink connection to a frame grabber. This setup is now in use in BWH. The software developed for data logging lacks a GUI, the ability for real time B-mode display, and tracking at the moment. The PLUS library, developed for streaming data from the Ultrasonix machine through an OpenIGTLink, essentially meets the visualization and tracking aims. Since this is all implemented with a different US machine in PLUS, theoretically, we just have to instantiate new subclasses for this specific video source. In practice, we anticipate complications arising from the different hardware platforms.

</div>

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

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#Slicer Module (via PLUS and OpenIGTLink)

==References==

</div>

2012 Winter Project Week:BKPLUSSlicer

2012-01-04T18:10:00Z

Moradi:

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
Image:BK.png
</gallery>

==Key Investigators==
* BWH: Isaiah Norton, Mehdi Moradi
* Queen's: Tamas Ungi

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

<h3>Objective</h3>
The goal is to integrate and streamline tracked data logging from the BK ultrasound (specifically RF data) using Slicer and PLUS. This will facilitate use of the BK system for on- and off-line visualization and data analysis. In certain clinical applications in BWH AMIGO that use the BK system, such as prostate interventions and brain tumor resection procedures, real time ultrasound-based tissue typing is a very useful addition. Tracking and streaming of the RF data to a high end PC is essential for these purposes.

</div>

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

<h3>Approach, Plan</h3>

The ProFocus BK machine, equipped with the optional research interface has the ability to stream RF data over a CameraLink connection to a frame grabber. This setup is now in use in BWH. The software developed for data logging lacks a GUI, the ability for real time B-mode display, and tracking at the moment. The PLUS library, developed for streaming data from the Ultrasonix machine through an OpenIGTLink, essentially meets the visualization and tracking aims. Since this is all implemented with a different US machine in PLUS, theoretically, we just have to instantiate new subclasses for this specific video source. In practice, we anticipate complications arising from the different hardware platforms.

</div>

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

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#Slicer Module (via PLUS and OpenIGTLink)

==References==

</div>

File:Bk.PNG

2012-01-04T18:08:39Z

Moradi:

2012 Winter Project Week:BKPLUSSlicer

2012-01-04T17:52:56Z

Moradi: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* BWH: Isaiah Norton, Mehdi Moradi
* Queen's: Tamas Ungi

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

<h3>Objective</h3>
The goal is to integrate and streamline tracked data logging from the BK ultrasound (specifically RF data) using Slicer and PLUS. This will facilitate use of the BK system for on- and off-line visualization and data analysis. In certain clinical applications in BWH AMIGO that use the BK system, such as prostate interventions and brain tumor resection procedures, real time ultrasound-based tissue typing is a very useful addition. Tracking and streaming of the RF data to a high end PC is essential for these purposes.

</div>

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

<h3>Approach, Plan</h3>

The ProFocus BK machine, equipped with the optional research interface has the ability to stream RF data over a CameraLink connection to a frame grabber. This setup is now in use in BWH. The software developed for data logging lacks a GUI, the ability for real time B-mode display, and tracking at the moment. The PLUS library, developed for streaming data from the Ultrasonix machine through an OpenIGTLink, essentially meets the visualization and tracking aims. Since this is all implemented with a different US machine in PLUS, theoretically, we just have to instantiate new subclasses for this specific video source. In practice, we anticipate complications arising from the different hardware platforms.

</div>

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

<h3>Progress</h3>

</div>
</div>

<div style="width: 97%; float: left;">

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a

#Slicer Module (via PLUS and OpenIGTLink)

==References==

</div>

2012 Winter Project Week:BKPLUSSlicer

2012-01-04T17:29:16Z

Moradi: /* Key Investigators */

2012 Winter Project Week:PelvicRegistration

2011-12-22T04:38:30Z

Moradi:

2012 Winter Project Week:PelvicRegistration

2011-12-22T04:37:49Z

Moradi:

_NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
File:Mr us.JPG|
</gallery>

Project Title: '''Surface-based 3D deformable registration of ultrasound and MRI prostate volumes'''

==Investigators at Brigham and Women's ==
* Computational core: Mehdi Moradi, Firdaus Janoos, Tina Kapur, Jan Egger, Sandy Wells
* Clinical core: Clare Tempany, Paul Nguyen
* Prostate core: Andriy Fedorov
* Present team members in SLC: Mehdi Moradi, Andriy Fedorov, Jan Egger.

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
We will implement a basic surface-based deformable registration solution to register prostate 3D ultrasound data to MRI. This is to enable clinical integration of the diagnostic MRI data with ultrasound during prostate brachytherapy with dynamic intraoperative dose planning.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
We use a surface based registration algorithm with elastic energy as the
penalty for the deformation. Ultrasound images are collected using a stepper, with fixed slice spacing in the axial view. The object is segmented (contoured) in both MRI and ultrasound images and a surface model is created. Gaussian mapping of the surface reduces the registration problem to finding an appropriate rotation of the coordinate systems that minimizes a cost function. This cost is the elastic energy of deforming the surface from MRI to US sconfiguration.

</div>

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

<h3>Progress</h3>

*

</div>

<div style="width: 97%; float: left;">

2012 Winter Project Week:PelvicRegistration

2011-12-22T04:34:47Z

Moradi: /* Investigators at Brigham and Women's */

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
</gallery>

_NOTOC__
<gallery>
File:Mr us.JPG[[2012_Winter_Project_Week#Projects|Projects List]]

Image:IGyneNeedles.png|Screenshot of the iGyne Prototype
</gallery>

Project Title: '''Surface-based 3D deformable registration of ultrasound and MRI prostate volumes'''

==Investigators at Brigham and Women's ==
* Computational core: Mehdi Moradi, Firdaus Janoos, Tina Kapur, Jan Egger, Sandy Wells
* Clinical core: Clare Tempany, Paul Nguyen
* Prostate core: Andriy Fedorov
* Present team members in SLC: Mehdi Moradi, Andriy Fedorov, Jan Egger.

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
We will implement a basic surface-based deformable registration solution to register prostate 3D ultrasound data to MRI. This is to enable clinical integration of the diagnostic MRI data with ultrasound during prostate brachytherapy with dynamic intraoperative dose planning.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
We use a surface based registration algorithm with elastic energy as the
penalty for the deformation. Ultrasound images are collected using a stepper, with fixed slice spacing in the axial view. The object is segmented (contoured) in both MRI and ultrasound images and a surface model is created. Gaussian mapping of the surface reduces the registration problem to finding an appropriate rotation of the coordinate systems that minimizes a cost function. This cost is the elastic energy of deforming the surface from MRI to US sconfiguration.

</div>

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

<h3>Progress</h3>

*

</div>

<div style="width: 97%; float: left;">

File:Mr us.JPG

2011-12-22T04:26:26Z

Moradi: MRI-ultrasound prostate

MRI-ultrasound prostate

2012 Winter Project Week:PelvicRegistration

2011-12-21T19:33:06Z

Moradi: /* Investigators at Brigham and Women's */

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Investigators at Brigham and Women's ==
* Computational core: Mehdi Moradi, Firdaus Janoos, Tina Kapur, Jan Egger, Sandy Wells
* Clinical core: Clare Tempany, Paul Nguyen
* Prostate core: Andriy Fedorov
* Present team members in SLC: Mehdi Moradi, Andriy Fedorov, Jan Egger.

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
We will implement a basic surface-based deformable registration solution to register prostate 3D ultrasound data to MRI. This is to enable clinical integration of the diagnostic MRI data with ultrasound during prostate brachytherapy with dynamic intraoperative dose planning.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
We use a surface based registration algorithm with elastic energy as the
penalty for the deformation. Ultrasound images are collected using a stepper, with fixed slice spacing in the axial view. The object is segmented (contoured) in both MRI and ultrasound images and a surface model is created. Gaussian mapping of the surface reduces the registration problem to finding an appropriate rotation of the coordinate systems that minimizes a cost function. This cost is the elastic energy of deforming the surface from MRI to US sconfiguration.

</div>

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

<h3>Progress</h3>

*

</div>

<div style="width: 97%; float: left;">

2012 Winter Project Week:PelvicRegistration

2011-12-21T19:31:28Z

Moradi: /* Investigators at Brigham and Women's */

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Investigators at Brigham and Women's ==
* Computational core: Mehdi Moradi, Firdaus Janoos, Tina Kapur, Jan Egger, Sandy Wells
* Clinical core: Clare Tempany, Paul Nguyen
* Prostate core: Andriy Fedorov
* Present team members in SLC: Mehdi Moradi, Andriy Fedorov, Jan Egger.

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
We will implement a basic surface-based deformable registration solution to register prostate 3D ultrasound data to MRI. This is to enable clinical integration of the diagnostic MRI data with ultrasound during prostate brachytherapy with dynamic intraoperative dose planning.
</div>

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
We use a surface based registration algorithm with elastic energy as the
penalty for the deformation. Ultrasound images are collected using a stepper, with fixed slice spacing in the axial view. The object is segmented (contoured) in both MRI and ultrasound images and a surface model is created. Gaussian mapping of the surface reduces the registration problem to finding an appropriate rotation of the coordinate systems that minimizes a cost function. This cost is the elastic energy of deforming the surface from pre-operative to intraop configuration.
*

</div>

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

<h3>Progress</h3>

*

</div>

<div style="width: 97%; float: left;">

2012 Winter Project Week:PelvicRegistration

2011-12-21T19:30:59Z

Moradi: /* Investigators at Brigham and Women's */

__NOTOC__
<gallery>
Image:PW-SLC2012.png|[[2012_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Investigators at Brigham and Women's ==
* Computational core: Mehdi Moradi, Firdaus Janoos, Tina Kapur, Jan Egger, Sandy Wells
* Clinical core: Clare Tempany, Paul Nguyen
* Prostate core: Andriy Fedorov
* Present team members in SLC: Mehdi Moradi, Andriy Fedorov, Jan Egger.

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
We will implement a basic surface-based deformable registration solution to register prostate 3D ultrasound data to MRI. This is to enable clinical integration of the diagnostic MRI data with ultrasound during prostate brachytherapy with dynamic intraoperative dose planning.
</div>

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

</div>

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

<h3>Progress</h3>
We use a surface based registration algorithm with elastic energy as the
penalty for the deformation. Ultrasound images are collected using a stepper, with fixed slice spacing in the axial view. The object is segmented (contoured) in both MRI and ultrasound images and a surface model is created. Gaussian mapping of the surface reduces the registration problem to finding an appropriate rotation of the coordinate systems that minimizes a cost function. This cost is the elastic energy of deforming the surface from pre-operative to intraop configuration.
*

</div>

<div style="width: 97%; float: left;">

2012 Winter Project Week:PelvicRegistration

2011-12-14T19:59:16Z

Moradi:

==Investigators at Brigham and Women's ==
* Computational core: Firdaus Janoos, Mehdi Moradi, Andriy Fedorov, Tina Kapur, Jan Egger, Sandy Wells
* Clinical core: Clare Tempany, Paul Nguyen
* Present team members in SLC: Mehdi Moradi, Andriy Fedorov, Jan Egger.

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
We will implement a basic surface-based deformable registration solution to register prostate 3D ultrasound data to MRI. This is to enable clinical integration of the diagnostic MRI data with ultrasound during prostate brachytherapy with dynamic intraoperative dose planning.
</div>

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

</div>

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

<h3>Progress</h3>
*

</div>

<div style="width: 97%; float: left;">

2012 Winter Project Week:PelvicRegistration

2011-12-14T19:56:06Z

Moradi:

==Key Investigators at Brigham and Women's ==
* Computational core: Mehdi Moradi, Andriy Fedorov, Firdaus Janoos, Tina Kapur, Jan Egger, Sandy Wells
* Clinical core: Clare Tempany, Paul Nguyen
* Present team members in SLC: Mehdi Moradi, Andriy Fedorov, Jan Egger.

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
We will implement a basic surface-based deformable registration solution to register prostate 3D ultrasound data to MRI. This is to enable clinical integration of the diagnostic MRI data with ultrasound during prostate brachytherapy with dynamic intraoperative dose planning.
</div>

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

</div>

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

<h3>Progress</h3>
*

</div>

<div style="width: 97%; float: left;">

2012 Winter Project Week:PelvicRegistration

2011-12-14T19:55:54Z

Moradi:

==Key Investigators at Brigham and Women's ==
* Computational core: Mehdi Moradi, Andriy Fedorov, Firdaus Janoos, Tina Kapur, Jan Egger, Sandy Wells
* Clinical core: Clare Tempany, Paul Nguyen
* Present team members in SLC: Mehdi Moradi, Andriy Fedorov, Jan Egger.

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
We will implement a basic surface-based deformable registration solution to register prostate 3D ultrasound data to MRI. This is to enable clinical integration of the diagnostic MRI data with ultrasound during prostate brachytherapy with dynamic intraoperative dose planning.
</div>

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

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

<h3>Progress</h3>
*

</div>

<div style="width: 97%; float: left;">

2012 Winter Project Week

2011-12-14T19:33:29Z

Moradi: /* IGT for Surgery and Radiation Treatments */

Back to [[Project Events]], [[Events]]
Back to [[Project Events]], [[AHM_2012]], [[Events]]

__NOTOC__
[[image:PW-SLC2012.png|300px]]

== Dates.Venue.Registration ==

Please [[AHM_2012#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

== Agenda==

Please [[AHM_2012#Agenda|click here for the agenda for AHM 2012 and Project Week]].

==Background==

From January 9-13, 2012, the 14th project week for hands-on research and development activity in Neuroscience and Image-Guided Therapy applications will be hosted in Salt Lake City, Utah. Participant engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions.

Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project.

On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.

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

==Projects==

===Traumatic Brain Injury DBP===

* [[2012_Winter_Project_Week:TBIClinicalAnalysis|Segmentation of Serial MRI of TBI patients
using Personalized Atlas Construction]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIDTIAnalysis|Registration and analysis of white matter tract changes in TBI]] (Clement Vachet, Anuja Sharma, Marcel Prastawa, Andrei Irimia, Jack van Horn, Guido Gerig, Martin Styner, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIValidation|Validation, visualization and analysis of segmentation for TBI]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
*Geometric Metamorphosis for TBI (Danielle Pace, Marc Niethammer, Marcel Prastawa, Andrei Irimia, Jack van Horn, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Multimodal Deformable Registration of Traumatic Brain Injury MR Volumes using Graphics Processing Units]] (Yifei Lou, Andrei Irimia, Patricio Vela, Allen Tannenbaum, Micah C. Chambers, Jack Van Horn and Paul M. Vespa, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Integration of unscented Kalman filter (UKF) based multi-tensor tractography in Slicer]] (Christian Baumgartner, Yogesh Rathi, Carl-Fredrik Westin)

===Predict Huntington's Disease DBP===
* [[2012_Winter_Project_Week:SPIEWorkshop|SPIE DTI Workshop Preparation: Perform DTI Quality Control]] (Jean-Baptiste Berger, Sonia Pujol, Guido Gerig, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DWIPhantom|DTI tractography phantom: a software for evaluating tractography algorithms]] (Gwendoline Roger,Yundi Shi, Clement Vachet, Martin Styner, Sylvain Gouttard)
* [[2012_Winter_Project_Week:FVLight|FiberViewerLight: a fiber bundle visualization and clustering tool]] (Jean-Baptiste Berger, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DTIAFA|DTIAtlasFiberAnalyzer]] (Jean-Baptiste Berger, Yundi Shi, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:PairWiseDTIRegistration|Pairwise DTI registration: DTI-Reg]] (Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:ShapeAnalysisSubcorticalStructuresHD|Morphometric analysis in subcortical structures in HD]] (Beatriz Paniagua, Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:DTI pipeline|Applying our DTI pipeline to analyse HD data]] (Gopalkrishna Veni, Hans Johnson, Martin Styner, Ross Whitaker)
* [[2012_Winter_Project_Week: DTI Change Modeling | Longitudinal change modeling of fiber tracts in serial HD DTI data]] (Anuja Sharma, Hans Johnson, Guido Gerig)
* [[2012_Winter_Project_Week: Continuous 4D shapes | Continuous 4d shape models from time-discrete data: Subcortical structures in HD]] (James Fishbaugh, Hans Johnson, Guido Gerig)

===Atrial fibrillation DBP===
* [[2012_Winter_Project_Week:EndoSeg|Endocardial Segmentation in DE-MRI for AFib]] (Yi Gao, Liang-Jia Zhu, Josh Cates, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:LAWallRegistration|Longitudinal Alignment and Visualization of Left-Atrial Wall from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:PVRegistration|Longitudinal Alignment and Visualization of Pulmonary Veins from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:RealTime|OpenIGT for realtime MRI-guided RF ablation]] (Gene Payne, Rob MacLeod, and Junichi Tokuda)

===Head and Neck Cancer DBP===
* A patch-based approach to the segmentation of organs of risk (Christian Wachinger, Polina Golland)
* RT dose comparison tool for Slicer (Nadya Shusharina, Greg Sharp)
* [[2012_Winter_Project_Week:InteractiveSegmentation|Interactive editing tools for segmentation]] (Greg Sharp, Steve Pieper)

===IGT for Surgery and Radiation Treatments===
*[[2012_Winter_Project_Week:PelvicRegistration|Deformable prostate registration: 3D ultrasound to MRI]] (Mehdi Moradi, Jan Egger, Andrey Fedorov)
*iGyne (Jan Egger, Xiaojun Chen, Radhika Tibrewal, Mehdi Moradi)
*[[2012_Winter_Project_Week:OpenIGTLink_Interface_for_Slicer4| OpenIGTLink interface for Slicer4]] (Junichi Tokuda, Clif Burdette/Jack Blevins, Tamas Ungi, Andras Lasso)
*[[2012_Winter_Project_Week:Needle Detection in MR Images for Brachytherapy in AMIGO|Needle Detection in MR Images for Brahytherapy in AMIGO]] (Radhika Tibrewal, Jan Egger, Xiaojun Chen)
*[[2012_Winter_Project_Week:LiveUltrasound|Live ultrasound in Slicer4 using Plus and OpenIGTLink]] (Tamas Ungi, Elvis Chen)
*[[2012_Winter_Project_Week:OsteoPlan|Surgical Planning for facial osteotomy (OsteoPlan)]] (Laurent, Noby)
*Generating a hybrid MR Spectroscopic Dataset under Slicer (Isaiah Norton, Jan Egger, Tina Kapur)
* [[2012_Winter_Project_Week:RTTools|RT tools for Slicer4]] (Csaba Pinter, Kevin Wang, Andras Lasso, Greg Sharp)
* [[2012_Winter_Project_Week:RTSS|RT structure set data representation]] (Greg Sharp, Andras Lasso, Steve Pieper, etc.)

===Musculoskeletal System===
* [[2012_Winter_Project_Week:Radnostics|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)

===Registration===
* [[2012_Winter_Project_Week:CMFreg|Framework for Cranio-Maxillo Facial registration in Slicer3]] (Beatriz Paniagua, Lucia Cevidanes, Martin Styner)
* [[2012_Winter_Project_Week:SlidingOrgans|Registration in the presence of sliding between organs (Danielle Pace, Marc Neithammer, Stephen Aylward)]]
* [[2012_Winter_Project_Week:GeometricMetamorphosis|Estimating the infiltration / recession of pathologies independent of background deformations (Danielle Pace, Stephen Aylward, Marc Niethammer)]]

===Shape Analysis===
* [[2012_Winter_Project_Week:PNSnormals|Principal Nested Spheres Normal Consistency in ShapeWorks]] (Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)
* [[2012_Winter_Project_Week:GeomIndicesSlicer4|Porting of White Matter Geometric Indices Module to Slicer4]] (Peter Savadjiev)

===NA-MIC Kit Internals===
*Slicer4 release (Jean-Christophe Fillion-Robin (JC), and Julien Finet (J2))
*Slicer4 extensions (JC)
*Slicer4 documentation (JC)
*Slicer4 GUI Testing (Benjamin Long, J2, JC)
*Slicer4 data on MIDAS (Josh Cates, Patrick Reynolds)
*Slicer4 extension: Slicer4 Scene Views Module (Nicole Aucoin)
*Slicer4 Annotations Module
** File format refactor (Nicole Aucoin)
** QT 3D Text rendering proof of concept (Julien Finet, Steve Pieper, Nicole Aucoin)
*[[2012_Project_Week:DICOM|DICOM Networking, Database, and Slicer Integration]] (Steve, Andrey, Andras)
*[[2012_Project_Week:EditorExtensions|Editor Extension Examples and Debugging]] (Steve, Andrey, Jc, Hans, Satra)
*[[2012_Project_Week:ViewerControls|Redesign of the slice viewer control panels]] (Julien Finet, Ron Kikinis, Hans Johnson, Greg Sharp)
* [[2012_Project_Week:AutomatedTesting |Automated Testing (Sonia Pujol, Steve Pieper, Jc, Benjamin)]]
* Remove legacy code from slicer4 (itk, modules, build scripts) (Hans, Jim, Steve, J2, JC)
*[[2012_Project_Week:BatchProcessing|Batch Processing with Slicer Modules]] (Steve, Andrey, JC, Hans, Satra)
*[[2012_Project_Week:4DImageSlicer4|Support for 4D Images in Slicer4]] (Andrey, Steve, Junichi, Alex)
* AIM, DICOM SR and Slicer annotations (Andrey, Steve, Nicole, Jayashree)

=== Preparation ===

#Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
#Starting Thursday, October 27th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 27: MGH DBP
#*November 3: Iowa DBP Huntingtons, Engineering Infrastructure Topics
#*November 10: Utah Atrial Fibrillation DBP
#*November 17: UCLA TBI DBP
#*November 24: No call. thanksgiving.
#*December 1:
#*December 8:
#*December 15:Finalize Projects
#*January 5: Loose Ends
#By December 15: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
#By December 15: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
##Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
##Gather test images in any of the Data sharing resources we have (e.g. MIDAS, xNAT). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
##Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
#Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

2012 Winter Project Week

2011-12-14T19:33:00Z

Moradi: /* IGT for Surgery and Radiation Treatments */

Back to [[Project Events]], [[Events]]
Back to [[Project Events]], [[AHM_2012]], [[Events]]

__NOTOC__
[[image:PW-SLC2012.png|300px]]

== Dates.Venue.Registration ==

Please [[AHM_2012#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

== Agenda==

Please [[AHM_2012#Agenda|click here for the agenda for AHM 2012 and Project Week]].

==Background==

From January 9-13, 2012, the 14th project week for hands-on research and development activity in Neuroscience and Image-Guided Therapy applications will be hosted in Salt Lake City, Utah. Participant engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions.

Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project.

On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.

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

==Projects==

===Traumatic Brain Injury DBP===

* [[2012_Winter_Project_Week:TBIClinicalAnalysis|Segmentation of Serial MRI of TBI patients
using Personalized Atlas Construction]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIDTIAnalysis|Registration and analysis of white matter tract changes in TBI]] (Clement Vachet, Anuja Sharma, Marcel Prastawa, Andrei Irimia, Jack van Horn, Guido Gerig, Martin Styner, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIValidation|Validation, visualization and analysis of segmentation for TBI]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
*Geometric Metamorphosis for TBI (Danielle Pace, Marc Niethammer, Marcel Prastawa, Andrei Irimia, Jack van Horn, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Multimodal Deformable Registration of Traumatic Brain Injury MR Volumes using Graphics Processing Units]] (Yifei Lou, Andrei Irimia, Patricio Vela, Allen Tannenbaum, Micah C. Chambers, Jack Van Horn and Paul M. Vespa, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Integration of unscented Kalman filter (UKF) based multi-tensor tractography in Slicer]] (Christian Baumgartner, Yogesh Rathi, Carl-Fredrik Westin)

===Predict Huntington's Disease DBP===
* [[2012_Winter_Project_Week:SPIEWorkshop|SPIE DTI Workshop Preparation: Perform DTI Quality Control]] (Jean-Baptiste Berger, Sonia Pujol, Guido Gerig, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DWIPhantom|DTI tractography phantom: a software for evaluating tractography algorithms]] (Gwendoline Roger,Yundi Shi, Clement Vachet, Martin Styner, Sylvain Gouttard)
* [[2012_Winter_Project_Week:FVLight|FiberViewerLight: a fiber bundle visualization and clustering tool]] (Jean-Baptiste Berger, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DTIAFA|DTIAtlasFiberAnalyzer]] (Jean-Baptiste Berger, Yundi Shi, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:PairWiseDTIRegistration|Pairwise DTI registration: DTI-Reg]] (Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:ShapeAnalysisSubcorticalStructuresHD|Morphometric analysis in subcortical structures in HD]] (Beatriz Paniagua, Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:DTI pipeline|Applying our DTI pipeline to analyse HD data]] (Gopalkrishna Veni, Hans Johnson, Martin Styner, Ross Whitaker)
* [[2012_Winter_Project_Week: DTI Change Modeling | Longitudinal change modeling of fiber tracts in serial HD DTI data]] (Anuja Sharma, Hans Johnson, Guido Gerig)
* [[2012_Winter_Project_Week: Continuous 4D shapes | Continuous 4d shape models from time-discrete data: Subcortical structures in HD]] (James Fishbaugh, Hans Johnson, Guido Gerig)

===Atrial fibrillation DBP===
* [[2012_Winter_Project_Week:EndoSeg|Endocardial Segmentation in DE-MRI for AFib]] (Yi Gao, Liang-Jia Zhu, Josh Cates, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:LAWallRegistration|Longitudinal Alignment and Visualization of Left-Atrial Wall from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:PVRegistration|Longitudinal Alignment and Visualization of Pulmonary Veins from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:RealTime|OpenIGT for realtime MRI-guided RF ablation]] (Gene Payne, Rob MacLeod, and Junichi Tokuda)

===Head and Neck Cancer DBP===
* A patch-based approach to the segmentation of organs of risk (Christian Wachinger, Polina Golland)
* RT dose comparison tool for Slicer (Nadya Shusharina, Greg Sharp)
* [[2012_Winter_Project_Week:InteractiveSegmentation|Interactive editing tools for segmentation]] (Greg Sharp, Steve Pieper)

===IGT for Surgery and Radiation Treatments===
*[[2012_Winter_Project_Week:PelvicRegistration|Deformable prostate registration: 3D ultrasound to MRI]] (Mehdi Moradi UBC/BWH, Jan Egger, Andrey Fedorov)
*iGyne (Jan Egger, Xiaojun Chen, Radhika Tibrewal, Mehdi Moradi)
*[[2012_Winter_Project_Week:OpenIGTLink_Interface_for_Slicer4| OpenIGTLink interface for Slicer4]] (Junichi Tokuda, Clif Burdette/Jack Blevins, Tamas Ungi, Andras Lasso)
*[[2012_Winter_Project_Week:Needle Detection in MR Images for Brachytherapy in AMIGO|Needle Detection in MR Images for Brahytherapy in AMIGO]] (Radhika Tibrewal, Jan Egger, Xiaojun Chen)
*[[2012_Winter_Project_Week:LiveUltrasound|Live ultrasound in Slicer4 using Plus and OpenIGTLink]] (Tamas Ungi, Elvis Chen)
*[[2012_Winter_Project_Week:OsteoPlan|Surgical Planning for facial osteotomy (OsteoPlan)]] (Laurent, Noby)
*Generating a hybrid MR Spectroscopic Dataset under Slicer (Isaiah Norton, Jan Egger, Tina Kapur)
* [[2012_Winter_Project_Week:RTTools|RT tools for Slicer4]] (Csaba Pinter, Kevin Wang, Andras Lasso, Greg Sharp)
* [[2012_Winter_Project_Week:RTSS|RT structure set data representation]] (Greg Sharp, Andras Lasso, Steve Pieper, etc.)

===Musculoskeletal System===
* [[2012_Winter_Project_Week:Radnostics|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)

===Registration===
* [[2012_Winter_Project_Week:CMFreg|Framework for Cranio-Maxillo Facial registration in Slicer3]] (Beatriz Paniagua, Lucia Cevidanes, Martin Styner)
* [[2012_Winter_Project_Week:SlidingOrgans|Registration in the presence of sliding between organs (Danielle Pace, Marc Neithammer, Stephen Aylward)]]
* [[2012_Winter_Project_Week:GeometricMetamorphosis|Estimating the infiltration / recession of pathologies independent of background deformations (Danielle Pace, Stephen Aylward, Marc Niethammer)]]

===Shape Analysis===
* [[2012_Winter_Project_Week:PNSnormals|Principal Nested Spheres Normal Consistency in ShapeWorks]] (Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)
* [[2012_Winter_Project_Week:GeomIndicesSlicer4|Porting of White Matter Geometric Indices Module to Slicer4]] (Peter Savadjiev)

===NA-MIC Kit Internals===
*Slicer4 release (Jean-Christophe Fillion-Robin (JC), and Julien Finet (J2))
*Slicer4 extensions (JC)
*Slicer4 documentation (JC)
*Slicer4 GUI Testing (Benjamin Long, J2, JC)
*Slicer4 data on MIDAS (Josh Cates, Patrick Reynolds)
*Slicer4 extension: Slicer4 Scene Views Module (Nicole Aucoin)
*Slicer4 Annotations Module
** File format refactor (Nicole Aucoin)
** QT 3D Text rendering proof of concept (Julien Finet, Steve Pieper, Nicole Aucoin)
*[[2012_Project_Week:DICOM|DICOM Networking, Database, and Slicer Integration]] (Steve, Andrey, Andras)
*[[2012_Project_Week:EditorExtensions|Editor Extension Examples and Debugging]] (Steve, Andrey, Jc, Hans, Satra)
*[[2012_Project_Week:ViewerControls|Redesign of the slice viewer control panels]] (Julien Finet, Ron Kikinis, Hans Johnson, Greg Sharp)
* [[2012_Project_Week:AutomatedTesting |Automated Testing (Sonia Pujol, Steve Pieper, Jc, Benjamin)]]
* Remove legacy code from slicer4 (itk, modules, build scripts) (Hans, Jim, Steve, J2, JC)
*[[2012_Project_Week:BatchProcessing|Batch Processing with Slicer Modules]] (Steve, Andrey, JC, Hans, Satra)
*[[2012_Project_Week:4DImageSlicer4|Support for 4D Images in Slicer4]] (Andrey, Steve, Junichi, Alex)
* AIM, DICOM SR and Slicer annotations (Andrey, Steve, Nicole, Jayashree)

=== Preparation ===

#Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
#Starting Thursday, October 27th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 27: MGH DBP
#*November 3: Iowa DBP Huntingtons, Engineering Infrastructure Topics
#*November 10: Utah Atrial Fibrillation DBP
#*November 17: UCLA TBI DBP
#*November 24: No call. thanksgiving.
#*December 1:
#*December 8:
#*December 15:Finalize Projects
#*January 5: Loose Ends
#By December 15: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
#By December 15: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
##Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
##Gather test images in any of the Data sharing resources we have (e.g. MIDAS, xNAT). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
##Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
#Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

2012 Winter Project Week

2011-12-14T19:32:36Z

Moradi: /* IGT for Surgery and Radiation Treatments */

Back to [[Project Events]], [[Events]]
Back to [[Project Events]], [[AHM_2012]], [[Events]]

__NOTOC__
[[image:PW-SLC2012.png|300px]]

== Dates.Venue.Registration ==

Please [[AHM_2012#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

== Agenda==

Please [[AHM_2012#Agenda|click here for the agenda for AHM 2012 and Project Week]].

==Background==

From January 9-13, 2012, the 14th project week for hands-on research and development activity in Neuroscience and Image-Guided Therapy applications will be hosted in Salt Lake City, Utah. Participant engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions.

Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project.

On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.

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

==Projects==

===Traumatic Brain Injury DBP===

* [[2012_Winter_Project_Week:TBIClinicalAnalysis|Segmentation of Serial MRI of TBI patients
using Personalized Atlas Construction]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIDTIAnalysis|Registration and analysis of white matter tract changes in TBI]] (Clement Vachet, Anuja Sharma, Marcel Prastawa, Andrei Irimia, Jack van Horn, Guido Gerig, Martin Styner, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIValidation|Validation, visualization and analysis of segmentation for TBI]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
*Geometric Metamorphosis for TBI (Danielle Pace, Marc Niethammer, Marcel Prastawa, Andrei Irimia, Jack van Horn, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Multimodal Deformable Registration of Traumatic Brain Injury MR Volumes using Graphics Processing Units]] (Yifei Lou, Andrei Irimia, Patricio Vela, Allen Tannenbaum, Micah C. Chambers, Jack Van Horn and Paul M. Vespa, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Integration of unscented Kalman filter (UKF) based multi-tensor tractography in Slicer]] (Christian Baumgartner, Yogesh Rathi, Carl-Fredrik Westin)

===Predict Huntington's Disease DBP===
* [[2012_Winter_Project_Week:SPIEWorkshop|SPIE DTI Workshop Preparation: Perform DTI Quality Control]] (Jean-Baptiste Berger, Sonia Pujol, Guido Gerig, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DWIPhantom|DTI tractography phantom: a software for evaluating tractography algorithms]] (Gwendoline Roger,Yundi Shi, Clement Vachet, Martin Styner, Sylvain Gouttard)
* [[2012_Winter_Project_Week:FVLight|FiberViewerLight: a fiber bundle visualization and clustering tool]] (Jean-Baptiste Berger, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DTIAFA|DTIAtlasFiberAnalyzer]] (Jean-Baptiste Berger, Yundi Shi, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:PairWiseDTIRegistration|Pairwise DTI registration: DTI-Reg]] (Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:ShapeAnalysisSubcorticalStructuresHD|Morphometric analysis in subcortical structures in HD]] (Beatriz Paniagua, Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:DTI pipeline|Applying our DTI pipeline to analyse HD data]] (Gopalkrishna Veni, Hans Johnson, Martin Styner, Ross Whitaker)
* [[2012_Winter_Project_Week: DTI Change Modeling | Longitudinal change modeling of fiber tracts in serial HD DTI data]] (Anuja Sharma, Hans Johnson, Guido Gerig)
* [[2012_Winter_Project_Week: Continuous 4D shapes | Continuous 4d shape models from time-discrete data: Subcortical structures in HD]] (James Fishbaugh, Hans Johnson, Guido Gerig)

===Atrial fibrillation DBP===
* [[2012_Winter_Project_Week:EndoSeg|Endocardial Segmentation in DE-MRI for AFib]] (Yi Gao, Liang-Jia Zhu, Josh Cates, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:LAWallRegistration|Longitudinal Alignment and Visualization of Left-Atrial Wall from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:PVRegistration|Longitudinal Alignment and Visualization of Pulmonary Veins from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:RealTime|OpenIGT for realtime MRI-guided RF ablation]] (Gene Payne, Rob MacLeod, and Junichi Tokuda)

===Head and Neck Cancer DBP===
* A patch-based approach to the segmentation of organs of risk (Christian Wachinger, Polina Golland)
* RT dose comparison tool for Slicer (Nadya Shusharina, Greg Sharp)
* [[2012_Winter_Project_Week:InteractiveSegmentation|Interactive editing tools for segmentation]] (Greg Sharp, Steve Pieper)

===IGT for Surgery and Radiation Treatments===
*[[2012_Winter_Project_Week:PelvicRegistration|Deformable prostate registration]] (Mehdi Moradi UBC/BWH, Jan Egger, Andrey Fedorov)
*iGyne (Jan Egger, Xiaojun Chen, Radhika Tibrewal, Mehdi Moradi)
*[[2012_Winter_Project_Week:OpenIGTLink_Interface_for_Slicer4| OpenIGTLink interface for Slicer4]] (Junichi Tokuda, Clif Burdette/Jack Blevins, Tamas Ungi, Andras Lasso)
*[[2012_Winter_Project_Week:Needle Detection in MR Images for Brachytherapy in AMIGO|Needle Detection in MR Images for Brahytherapy in AMIGO]] (Radhika Tibrewal, Jan Egger, Xiaojun Chen)
*[[2012_Winter_Project_Week:LiveUltrasound|Live ultrasound in Slicer4 using Plus and OpenIGTLink]] (Tamas Ungi, Elvis Chen)
*[[2012_Winter_Project_Week:OsteoPlan|Surgical Planning for facial osteotomy (OsteoPlan)]] (Laurent, Noby)
*Generating a hybrid MR Spectroscopic Dataset under Slicer (Isaiah Norton, Jan Egger, Tina Kapur)
* [[2012_Winter_Project_Week:RTTools|RT tools for Slicer4]] (Csaba Pinter, Kevin Wang, Andras Lasso, Greg Sharp)
* [[2012_Winter_Project_Week:RTSS|RT structure set data representation]] (Greg Sharp, Andras Lasso, Steve Pieper, etc.)

===Musculoskeletal System===
* [[2012_Winter_Project_Week:Radnostics|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)

===Registration===
* [[2012_Winter_Project_Week:CMFreg|Framework for Cranio-Maxillo Facial registration in Slicer3]] (Beatriz Paniagua, Lucia Cevidanes, Martin Styner)
* [[2012_Winter_Project_Week:SlidingOrgans|Registration in the presence of sliding between organs (Danielle Pace, Marc Neithammer, Stephen Aylward)]]
* [[2012_Winter_Project_Week:GeometricMetamorphosis|Estimating the infiltration / recession of pathologies independent of background deformations (Danielle Pace, Stephen Aylward, Marc Niethammer)]]

===Shape Analysis===
* [[2012_Winter_Project_Week:PNSnormals|Principal Nested Spheres Normal Consistency in ShapeWorks]] (Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)
* [[2012_Winter_Project_Week:GeomIndicesSlicer4|Porting of White Matter Geometric Indices Module to Slicer4]] (Peter Savadjiev)

===NA-MIC Kit Internals===
*Slicer4 release (Jean-Christophe Fillion-Robin (JC), and Julien Finet (J2))
*Slicer4 extensions (JC)
*Slicer4 documentation (JC)
*Slicer4 GUI Testing (Benjamin Long, J2, JC)
*Slicer4 data on MIDAS (Josh Cates, Patrick Reynolds)
*Slicer4 extension: Slicer4 Scene Views Module (Nicole Aucoin)
*Slicer4 Annotations Module
** File format refactor (Nicole Aucoin)
** QT 3D Text rendering proof of concept (Julien Finet, Steve Pieper, Nicole Aucoin)
*[[2012_Project_Week:DICOM|DICOM Networking, Database, and Slicer Integration]] (Steve, Andrey, Andras)
*[[2012_Project_Week:EditorExtensions|Editor Extension Examples and Debugging]] (Steve, Andrey, Jc, Hans, Satra)
*[[2012_Project_Week:ViewerControls|Redesign of the slice viewer control panels]] (Julien Finet, Ron Kikinis, Hans Johnson, Greg Sharp)
* [[2012_Project_Week:AutomatedTesting |Automated Testing (Sonia Pujol, Steve Pieper, Jc, Benjamin)]]
* Remove legacy code from slicer4 (itk, modules, build scripts) (Hans, Jim, Steve, J2, JC)
*[[2012_Project_Week:BatchProcessing|Batch Processing with Slicer Modules]] (Steve, Andrey, JC, Hans, Satra)
*[[2012_Project_Week:4DImageSlicer4|Support for 4D Images in Slicer4]] (Andrey, Steve, Junichi, Alex)
* AIM, DICOM SR and Slicer annotations (Andrey, Steve, Nicole, Jayashree)

=== Preparation ===

#Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
#Starting Thursday, October 27th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 27: MGH DBP
#*November 3: Iowa DBP Huntingtons, Engineering Infrastructure Topics
#*November 10: Utah Atrial Fibrillation DBP
#*November 17: UCLA TBI DBP
#*November 24: No call. thanksgiving.
#*December 1:
#*December 8:
#*December 15:Finalize Projects
#*January 5: Loose Ends
#By December 15: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
#By December 15: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
##Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
##Gather test images in any of the Data sharing resources we have (e.g. MIDAS, xNAT). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
##Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
#Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

2012 Winter Project Week

2011-12-14T19:31:38Z

Moradi: /* IGT for Surgery and Radiation Treatments */

Back to [[Project Events]], [[Events]]
Back to [[Project Events]], [[AHM_2012]], [[Events]]

__NOTOC__
[[image:PW-SLC2012.png|300px]]

== Dates.Venue.Registration ==

Please [[AHM_2012#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

== Agenda==

Please [[AHM_2012#Agenda|click here for the agenda for AHM 2012 and Project Week]].

==Background==

From January 9-13, 2012, the 14th project week for hands-on research and development activity in Neuroscience and Image-Guided Therapy applications will be hosted in Salt Lake City, Utah. Participant engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithms, medical imaging sequence development, tracking experiments, and clinical applications. The main goal of this event is to further the translational research deliverables of the sponsoring centers ([http://www.na-mic.org NA-MIC], [http://www.ncigt.org NCIGT], [http://nac.spl.harvard.edu NAC], [http://catalyst.harvard.edu/home.html Harvard Catalyst], and [http://www.cimit.org CIMIT]) and their collaborators by identifying and solving programming problems during planned and ad hoc break-out sessions.

Active preparation for this conference begins with a kick-off teleconference. Invitations to this call are sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties expressing an interest in working with these centers. The main goal of the initial teleconference is to gather information about which groups/projects would be active at the upcoming event to ensure that there were sufficient resources available to meet everyone's needs. Focused discussions about individual projects are conducted during several subsequent teleconferences and permits the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in break-out sessions. In the final days leading up to the meeting, all project teams are asked to complete a template page on the wiki describing the objectives and research plan for each project.

On the first day of the conference, each project team leader delivers a short presentation to introduce their topic and individual members of their team. These brief presentations serve to both familiarize other teams doing similar work about common problems or practical solutions, and to identify potential subsets of individuals who might benefit from collaborative work. For the remainder of the conference, about 50% time is devoted to break-out discussions on topics of common interest to particular subsets and 50% to hands-on project work. For hands-on project work, attendees are organized into 30-50 small teams comprised of 2-4 individuals with a mix of multi-disciplinary expertise. To facilitate this work, a large room is setup with ample work tables, internet connection, and power access. This enables each computer software development-based team to gather on a table with their individual laptops, connect to the internet, download their software and data, and work on specific projects. On the final day of the event, each project team summarizes their accomplishments in a closing presentation.

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

==Projects==

===Traumatic Brain Injury DBP===

* [[2012_Winter_Project_Week:TBIClinicalAnalysis|Segmentation of Serial MRI of TBI patients
using Personalized Atlas Construction]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIDTIAnalysis|Registration and analysis of white matter tract changes in TBI]] (Clement Vachet, Anuja Sharma, Marcel Prastawa, Andrei Irimia, Jack van Horn, Guido Gerig, Martin Styner, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIValidation|Validation, visualization and analysis of segmentation for TBI]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig, Danielle Pace, Stephen Aylward)
*Geometric Metamorphosis for TBI (Danielle Pace, Marc Niethammer, Marcel Prastawa, Andrei Irimia, Jack van Horn, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Multimodal Deformable Registration of Traumatic Brain Injury MR Volumes using Graphics Processing Units]] (Yifei Lou, Andrei Irimia, Patricio Vela, Allen Tannenbaum, Micah C. Chambers, Jack Van Horn and Paul M. Vespa, Danielle Pace, Stephen Aylward)
* [[2012_Winter_Project_Week:TBIRegistration|Integration of unscented Kalman filter (UKF) based multi-tensor tractography in Slicer]] (Christian Baumgartner, Yogesh Rathi, Carl-Fredrik Westin)

===Predict Huntington's Disease DBP===
* [[2012_Winter_Project_Week:SPIEWorkshop|SPIE DTI Workshop Preparation: Perform DTI Quality Control]] (Jean-Baptiste Berger, Sonia Pujol, Guido Gerig, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DWIPhantom|DTI tractography phantom: a software for evaluating tractography algorithms]] (Gwendoline Roger,Yundi Shi, Clement Vachet, Martin Styner, Sylvain Gouttard)
* [[2012_Winter_Project_Week:FVLight|FiberViewerLight: a fiber bundle visualization and clustering tool]] (Jean-Baptiste Berger, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:DTIAFA|DTIAtlasFiberAnalyzer]] (Jean-Baptiste Berger, Yundi Shi, Clement Vachet, Martin Styner)
* [[2012_Winter_Project_Week:PairWiseDTIRegistration|Pairwise DTI registration: DTI-Reg]] (Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:ShapeAnalysisSubcorticalStructuresHD|Morphometric analysis in subcortical structures in HD]] (Beatriz Paniagua, Clement Vachet, Hans Johnson, Martin Styner)
* [[2012_Winter_Project_Week:DTI pipeline|Applying our DTI pipeline to analyse HD data]] (Gopalkrishna Veni, Hans Johnson, Martin Styner, Ross Whitaker)
* [[2012_Winter_Project_Week: DTI Change Modeling | Longitudinal change modeling of fiber tracts in serial HD DTI data]] (Anuja Sharma, Hans Johnson, Guido Gerig)
* [[2012_Winter_Project_Week: Continuous 4D shapes | Continuous 4d shape models from time-discrete data: Subcortical structures in HD]] (James Fishbaugh, Hans Johnson, Guido Gerig)

===Atrial fibrillation DBP===
* [[2012_Winter_Project_Week:EndoSeg|Endocardial Segmentation in DE-MRI for AFib]] (Yi Gao, Liang-Jia Zhu, Josh Cates, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:LAWallRegistration|Longitudinal Alignment and Visualization of Left-Atrial Wall from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:PVRegistration|Longitudinal Alignment and Visualization of Pulmonary Veins from DEMRI and MRA]] (Josh Cates, Yi Gao, Liang-Jia Zhu, Greg Gardner, Alan Morris, Danny Perry, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
* [[2012_Winter_Project_Week:RealTime|OpenIGT for realtime MRI-guided RF ablation]] (Gene Payne, Rob MacLeod, and Junichi Tokuda)

===Head and Neck Cancer DBP===
* A patch-based approach to the segmentation of organs of risk (Christian Wachinger, Polina Golland)
* RT dose comparison tool for Slicer (Nadya Shusharina, Greg Sharp)
* [[2012_Winter_Project_Week:InteractiveSegmentation|Interactive editing tools for segmentation]] (Greg Sharp, Steve Pieper)

===IGT for Surgery and Radiation Treatments===
*[[2012_Winter_Project_Week:PelvicRegistration|Pelvic Registration]] (Mehdi Moradi UBC/BWH, Jan Egger, Andrey Fedorov)
*iGyne (Jan Egger, Xiaojun Chen, Radhika Tibrewal, Mehdi Moradi)
*[[2012_Winter_Project_Week:OpenIGTLink_Interface_for_Slicer4| OpenIGTLink interface for Slicer4]] (Junichi Tokuda, Clif Burdette/Jack Blevins, Tamas Ungi, Andras Lasso)
*[[2012_Winter_Project_Week:Needle Detection in MR Images for Brachytherapy in AMIGO|Needle Detection in MR Images for Brahytherapy in AMIGO]] (Radhika Tibrewal, Jan Egger, Xiaojun Chen)
*[[2012_Winter_Project_Week:LiveUltrasound|Live ultrasound in Slicer4 using Plus and OpenIGTLink]] (Tamas Ungi, Elvis Chen)
*[[2012_Winter_Project_Week:OsteoPlan|Surgical Planning for facial osteotomy (OsteoPlan)]] (Laurent, Noby)
*Generating a hybrid MR Spectroscopic Dataset under Slicer (Isaiah Norton, Jan Egger, Tina Kapur)
* [[2012_Winter_Project_Week:RTTools|RT tools for Slicer4]] (Csaba Pinter, Kevin Wang, Andras Lasso, Greg Sharp)
* [[2012_Winter_Project_Week:RTSS|RT structure set data representation]] (Greg Sharp, Andras Lasso, Steve Pieper, etc.)

===Musculoskeletal System===
* [[2012_Winter_Project_Week:Radnostics|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)

===Registration===
* [[2012_Winter_Project_Week:CMFreg|Framework for Cranio-Maxillo Facial registration in Slicer3]] (Beatriz Paniagua, Lucia Cevidanes, Martin Styner)
* [[2012_Winter_Project_Week:SlidingOrgans|Registration in the presence of sliding between organs (Danielle Pace, Marc Neithammer, Stephen Aylward)]]
* [[2012_Winter_Project_Week:GeometricMetamorphosis|Estimating the infiltration / recession of pathologies independent of background deformations (Danielle Pace, Stephen Aylward, Marc Niethammer)]]

===Shape Analysis===
* [[2012_Winter_Project_Week:PNSnormals|Principal Nested Spheres Normal Consistency in ShapeWorks]] (Beatriz Paniagua, Josh Cates, Manasi Datar, Ross Whitaker, Martin Styner)
* [[2012_Winter_Project_Week:GeomIndicesSlicer4|Porting of White Matter Geometric Indices Module to Slicer4]] (Peter Savadjiev)

===NA-MIC Kit Internals===
*Slicer4 release (Jean-Christophe Fillion-Robin (JC), and Julien Finet (J2))
*Slicer4 extensions (JC)
*Slicer4 documentation (JC)
*Slicer4 GUI Testing (Benjamin Long, J2, JC)
*Slicer4 data on MIDAS (Josh Cates, Patrick Reynolds)
*Slicer4 extension: Slicer4 Scene Views Module (Nicole Aucoin)
*Slicer4 Annotations Module
** File format refactor (Nicole Aucoin)
** QT 3D Text rendering proof of concept (Julien Finet, Steve Pieper, Nicole Aucoin)
*[[2012_Project_Week:DICOM|DICOM Networking, Database, and Slicer Integration]] (Steve, Andrey, Andras)
*[[2012_Project_Week:EditorExtensions|Editor Extension Examples and Debugging]] (Steve, Andrey, Jc, Hans, Satra)
*[[2012_Project_Week:ViewerControls|Redesign of the slice viewer control panels]] (Julien Finet, Ron Kikinis, Hans Johnson, Greg Sharp)
* [[2012_Project_Week:AutomatedTesting |Automated Testing (Sonia Pujol, Steve Pieper, Jc, Benjamin)]]
* Remove legacy code from slicer4 (itk, modules, build scripts) (Hans, Jim, Steve, J2, JC)
*[[2012_Project_Week:BatchProcessing|Batch Processing with Slicer Modules]] (Steve, Andrey, JC, Hans, Satra)
*[[2012_Project_Week:4DImageSlicer4|Support for 4D Images in Slicer4]] (Andrey, Steve, Junichi, Alex)
* AIM, DICOM SR and Slicer annotations (Andrey, Steve, Nicole, Jayashree)

=== Preparation ===

#Please make sure that you are on the [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week na-mic-project-week mailing list]
#Starting Thursday, October 27th, part of the weekly Thursday 3pm NA-MIC Engineering TCON will be used to prepare for this meeting. The schedule for these preparatory calls is as follows:
#*October 27: MGH DBP
#*November 3: Iowa DBP Huntingtons, Engineering Infrastructure Topics
#*November 10: Utah Atrial Fibrillation DBP
#*November 17: UCLA TBI DBP
#*November 24: No call. thanksgiving.
#*December 1:
#*December 8:
#*December 15:Finalize Projects
#*January 5: Loose Ends
#By December 15: [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
#By December 15: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
##[https://www.kitware.com/Admin/SendPassword.cgi Ask Zack for a Sandbox account]
##Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
##Gather test images in any of the Data sharing resources we have (e.g. MIDAS, xNAT). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
##Setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Zack)
#Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...

NAMIC Wiki:Users

2011-12-14T19:29:45Z

Moradi: Blanked the page

2012 Winter Project Week:PelvicRegistration

2011-12-14T19:29:40Z

Moradi: Created page with '==Key Investigators at Brigham and Women's == * Computational core: Mehdi Moradi, Andriy Fedorov, Firdaus Janoos, Tina Kapur, Jan Egger, Sandy Wells * Clinical core: Clare Tempan…'

NAMIC Wiki:Users

2011-12-14T19:28:03Z

Moradi:

NAMIC Wiki:Users

2011-12-14T19:26:26Z

Moradi: /* Key Investigators at Brigham and Women's */

==Key Investigators at Brigham and Women's ==
* Computational core: Mehdi Moradi, Andriy Fedorov, Firdaus Janoos, Jan Egger, Sandy Wells
* Clinical core: Clare Tempany, Kemal Tuncali

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
We will implement a basic surface-based deformable registration solution to register prostate 3D ultrasound data to MRI. This is to enable clinical integration of the diagnostic MRI data with ultrasound during prostate brachytherapy with dynamic intraoperative dose planning.
</div>

</div>

NAMIC Wiki:Users

2011-12-14T19:23:07Z

Moradi:

NAMIC Wiki:Users

2011-12-14T19:21:51Z

Moradi: Created page with ' ==Key Investigators== * Brigham and Women's Hospital: Computational core: Mehdi Moradi, Andriy Fedorov, Firdaus Janoos, Jan Egger, Sandy Wells Clinical core: Clare Tempany, Kem…'

==Key Investigators==
* Brigham and Women's Hospital:
Computational core: Mehdi Moradi, Andriy Fedorov, Firdaus Janoos, Jan Egger, Sandy Wells
Clinical core: Clare Tempany, Kemal Tuncali

<div style="margin: 20px;">

<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
We will implement a basic surface-based deformable registration solution to register prostate 3D ultrasound data to MRI
</div>

</div>