NAMIC Wiki - User contributions [en]

2012 Winter Project Week:GBMseg

2012-01-10T17:21:44Z

Mmilch: /* Key Investigators */

==Key Investigators==
* WUSM: Dan Marcus, Misha Milchenko
* Brigham and Women's: Andrey Fedorov, Jan Egger

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

<h3>Objective</h3>
We are looking to segment and visualize GBM's from various MR sequences in Slicer, and create an integrated display for clinician review, both radiologist and non-radiologist.

</div>

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

<h3>Approach, Plan</h3>

The approach is to obtain accurate registration of a number of MR sequences of each tumor case, segment what is thought to be the tumor on T1 post contrast and analyze correlation with pathology data.

</div>

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

<h3>Progress</h3>

Segmented one T2 FLAIR image (W009), voxel size 1x1x5mm using growcut region algorithm. Manual pre-labeling was done on approximately central slice of the tumor in three section planes separately. Two-class tissue model (enhancing and non-enhancing region) was used.
Results: visually, the algorithm picked out most (about 80%) of the enhancing region. Some sharp mass processes were missed, as well as some areas that subjectively might not belong to tumor were also attributed to tumor. Comparing with hi-res T1 post-contrast (1x1x2mm voxel), revealed significant areas that highlight differently on T1 and T2, esp. around tumor boundary. Another accuracy limiting factor was high anisotropy of T2 acquisition, which resulted in ghosted data, particularly observabe in the areas of low signal, such as adjacent to bone.

</div>
</div>

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

==Delivery Mechanism==
GBM MR preprocessing pipeline

==References==
GrowCut segmentation Slicer documentation: http://wiki.slicer.org/slicerWiki/index.php/Modules:GrowCutSegmentation-Documentation-3.6

V. Vezhnevets and V. Konouchine, "GrowCut - Interactive multi-label N-D image segmentation," in Proc. Graphicon, 2005. pp. 150--156.

Mark Jenkinson, Stephen Smith. "Optimisation in Robust Linear Registration of Brain Images." FMRIB Technical Report TR00MJ2, http://www.fmrib.ox.ac.uk/analysis/techrep/tr00mj2/tr00mj2/

</div>

2012 Winter Project Week:GBMseg

2012-01-10T17:00:17Z

Mmilch: /* Delivery Mechanism */

2012 Winter Project Week:GBMseg

2012-01-10T16:59:16Z

Mmilch: /* Delivery Mechanism */

2012 Winter Project Week:GBMseg

2012-01-10T16:00:16Z

Mmilch: /* References */

2012 Winter Project Week

2012-01-09T18:50:44Z

Mmilch: /* Head and Neck Cancer */

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)
* [[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===
* [[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]] (Gene Payne, 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:PatchBased|A patch-based approach to the segmentation of organs of risk]] (Christian Wachinger, Polina Golland)
* [[2012_Winter_Project_Week:PairwiseLF|Label fusion with pairwise interactions]] (Ramesh Sridharan, 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)
*[[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]] (Mehdi Moradi, Isaiah Norton, Tamas Ungi)
*[[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: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: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: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)

===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)

===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)]]
* 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)
*[[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...

2012 Winter Project Week

2012-01-09T18:49:55Z

Mmilch: /* Head and Neck Cancer */

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)
* [[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===
* [[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]] (Gene Payne, 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:PatchBased|A patch-based approach to the segmentation of organs of risk]] (Christian Wachinger, Polina Golland)
* [[2012_Winter_Project_Week:PairwiseLF|Label fusion with pairwise interactions]] (Ramesh Sridharan, 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)

===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)
*[[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]] (Mehdi Moradi, Isaiah Norton, Tamas Ungi)
*[[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: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: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: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)

===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)

===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)]]
* 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)
*[[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...

2012 Winter Project Week:GBMseg

2012-01-09T15:59:16Z

Mmilch: /* Key Investigators */

2012 Winter Project Week:GBMseg

2012-01-05T16:02:21Z

Mmilch: /* References */

2012 Winter Project Week:GBMseg

2012-01-05T16:02:08Z

Mmilch: /* Delivery Mechanism */

==Key Investigators==
* WUSM: Dan Marcus, Misha Milchenko
* Brigham and Women's: Andrey Fedorov

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

<h3>Objective</h3>
We are looking to segment and visualize GBM's from various MR sequences in Slicer, and create an integrated display for clinisian review, both radiologist and non-radiologist.

</div>

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

<h3>Approach, Plan</h3>

The approach is to obtain accurate registration of a number of MR sequences of each tumor case, and analyze correlation with pathology data.

</div>

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

<h3>Progress</h3>
</div>
</div>

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

==Delivery Mechanism==

==References==
*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.
* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.
* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.
* Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .

</div>

2012 Winter Project Week:GBMseg

2012-01-05T16:00:43Z

Mmilch: /* Key Investigators */

==Key Investigators==
* WUSM: Dan Marcus, Misha Milchenko
* Brigham and Women's: Andrey Fedorov

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

<h3>Objective</h3>
We are looking to segment and visualize GBM's from various MR sequences in Slicer, and create an integrated display for clinisian review, both radiologist and non-radiologist.

</div>

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

<h3>Approach, Plan</h3>

The approach is to obtain accurate registration of a number of MR sequences of each tumor case, and analyze correlation with pathology data.

</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 (please select the appropriate options by noting YES against them below)

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)
==References==
*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.
* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.
* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.
* Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .

</div>

2012 Winter Project Week:GBMseg

2012-01-05T15:27:47Z

Mmilch: /* Instructions for Use of this Template */

==Key Investigators==
* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
* Utah: Tom Fletcher, Ross Whitaker

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

<h3>Objective</h3>
We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.

</div>

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

<h3>Approach, Plan</h3>

Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below. The main challenge to this approach is <foo>.

Our plan for the project week is to first try out <bar>,...

</div>

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

<h3>Progress</h3>
Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.

</div>
</div>

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

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

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)
==References==
*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.
* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.
* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.
* Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .

</div>

2012 Winter Project Week:GBMseg

2012-01-05T15:27:14Z

Mmilch: Created page with '==Instructions for Use of this Template== #Please create a new wiki page with an appropriate title for your project using the convention 2012_Winter_Project_Week:<Project Name> #…'

==Instructions for Use of this Template==
#Please create a new wiki page with an appropriate title for your project using the convention 2012_Winter_Project_Week:<Project Name>
#Copy the entire text of this page into the page created above
#Link the created page into the list of projects for the project event
#Delete this section from the created page
#Send an email to tkapur at bwh.harvard.edu if you are stuck
==Key Investigators==
* UNC: Isabelle Corouge, Casey Goodlett, Guido Gerig
* Utah: Tom Fletcher, Ross Whitaker

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

<h3>Objective</h3>
We are developing methods for analyzing diffusion tensor data along fiber tracts. The goal is to be able to make statistical group comparisons with fiber tracts as a common reference frame for comparison.

</div>

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

<h3>Approach, Plan</h3>

Our approach for analyzing diffusion tensors is summarized in the IPMI 2007 reference below. The main challenge to this approach is <foo>.

Our plan for the project week is to first try out <bar>,...

</div>

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

<h3>Progress</h3>
Software for the fiber tracking and statistical analysis along the tracts has been implemented. The statistical methods for diffusion tensors are implemented as ITK code as part of the [[NA-MIC/Projects/Diffusion_Image_Analysis/DTI_Software_and_Algorithm_Infrastructure|DTI Software Infrastructure]] project. The methods have been validated on a repeated scan of a healthy individual. This work has been published as a conference paper (MICCAI 2005) and a journal version (MEDIA 2006). Our recent IPMI 2007 paper includes a nonparametric regression method for analyzing data along a fiber tract.

</div>
</div>

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

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

#ITK Module
#Slicer Module
##Built-in
##Extension -- commandline
##Extension -- loadable
#Other (Please specify)
==References==
*Fletcher P, Tao R, Jeong W, Whitaker R. [http://www.na-mic.org/publications/item/view/634 A volumetric approach to quantifying region-to-region white matter connectivity in diffusion tensor MRI.] Inf Process Med Imaging. 2007;20:346-358. PMID: 17633712.
* Corouge I, Fletcher P, Joshi S, Gouttard S, Gerig G. [http://www.na-mic.org/publications/item/view/292 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Med Image Anal. 2006 Oct;10(5):786-98. PMID: 16926104.
* Corouge I, Fletcher P, Joshi S, Gilmore J, Gerig G. [http://www.na-mic.org/publications/item/view/1122 Fiber tract-oriented statistics for quantitative diffusion tensor MRI analysis.] Int Conf Med Image Comput Comput Assist Interv. 2005;8(Pt 1):131-9. PMID: 16685838.
* Goodlett C, Corouge I, Jomier M, Gerig G, A Quantitative DTI Fiber Tract Analysis Suite, The Insight Journal, vol. ISC/NAMIC/ MICCAI Workshop on Open-Source Software, 2005, Online publication: http://hdl.handle.net/1926/39 .

</div>

2012 Winter Project Week

2012-01-05T15:22:29Z

Mmilch: /* Head and Neck Cancer */

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 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)
*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===
* [[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]] (Gene Payne, 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:PatchBased|A patch-based approach to the segmentation of organs of risk]] (Christian Wachinger, Polina Golland)
* [[2012_Winter_Project_Week:PairwiseLF|Label fusion with pairwise interactions]] (Ramesh Sridharan, 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)

===IGT for Surgery and Radiation Treatments===
*[[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: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, Stephen Aylward)
*[[2012_Winter_Project_Week:LiveUltrasound|Live ultrasound in Slicer4 using Plus and OpenIGTLink]] (Tamas Ungi, Elvis Chen)
*[[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]] (Mehdi Moradi, Isaiah Norton, PLUS developers?)
*[[2012_Winter_Project_Week:hybridMRS | Generation of a hybrid MR-Spectroscopic (MRS) dataset under 3DSlicer]] (Jan Egger, Isaiah Norton, Bjoern Menze, Daniel Hořínek, Antonín Škoch, Jens Sommer, Christopher Nimsky, 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)]]
* [[2012_Winter_Project_Week:FastInterpolation|Fast Image Interpolation Given Parameterized Deformations For Image Registration (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)]]

===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)

===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)]]
* 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)
*[[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...

2011 Summer Project Week FetchMI: Slicer integration with XNAT

2011-06-21T18:49:34Z

Mmilch: /* Code reivew */

==Key Investigators==
* Brigham and Women's Hospital: Wendy Plesniak
* Washington University: Misha Milchenko

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

<h3>Objective</h3>

#:Produce a working code for exchanging MRML scenes with XNAT via REST API

</div>

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

<h3>Approach, Plan</h3>
#:Reviewing new Misha's code for XNAT client in FetchMI classes;
#:Compiling, running and testing against XNAT Sandbox;
#:Refining the development plan;
#:User testing.

</div>

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

<h3>Progress</h3>



</div>
</div>

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

==Code reivew==
[[File:2011_Summer_Project_Week_FetchMI-_Slicer_integration_with_XNAT_diagram.png|840px]]

==References==
[http://docs.xnat.org/XNAT+REST+API+Usage XNAT 1.5 REST API]<br>
[[2011_Winter_Project_Week:FetchMIAPI | 2011 Winter Project Week: FetchMI API]]

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a built-in Slicer module (FetchMI).

2011 Summer Project Week FetchMI: Slicer integration with XNAT

2011-06-21T18:46:56Z

Mmilch: /* Code reivew */

==Key Investigators==
* Brigham and Women's Hospital: Wendy Plesniak
* Washington University: Misha Milchenko

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

<h3>Objective</h3>

#:Produce a working code for exchanging MRML scenes with XNAT via REST API

</div>

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

<h3>Approach, Plan</h3>
#:Reviewing new Misha's code for XNAT client in FetchMI classes;
#:Compiling, running and testing against XNAT Sandbox;
#:Refining the development plan;
#:User testing.

</div>

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

<h3>Progress</h3>



</div>
</div>

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

==Code reivew==
[[File:2011_Summer_Project_Week_FetchMI-_Slicer_integration_with_XNAT_diagram.png]]

==References==
[http://docs.xnat.org/XNAT+REST+API+Usage XNAT 1.5 REST API]<br>
[[2011_Winter_Project_Week:FetchMIAPI | 2011 Winter Project Week: FetchMI API]]

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a built-in Slicer module (FetchMI).

File:2011 Summer Project Week FetchMI- Slicer integration with XNAT diagram.png

2011-06-21T18:46:32Z

Mmilch:

2011 Summer Project Week FetchMI: Slicer integration with XNAT

2011-06-20T18:28:17Z

Mmilch: /* References */

==Key Investigators==
* Brigham and Women's Hospital: Wendy Plesniak
* Washington University: Misha Milchenko

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

<h3>Objective</h3>

#:Produce a working code for exchanging MRML scenes with XNAT via REST API

</div>

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

<h3>Approach, Plan</h3>
#:Reviewing new Misha's code for XNAT client in FetchMI classes;
#:Compiling, running and testing against XNAT Sandbox;
#:Refining the development plan;
#:User testing.

</div>

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

<h3>Progress</h3>



</div>
</div>

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

==Code reivew==
Files

==References==
[http://docs.xnat.org/XNAT+REST+API+Usage XNAT 1.5 REST API]<br>
[[2011_Winter_Project_Week:FetchMIAPI | 2011 Winter Project Week: FetchMI API]]

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a built-in Slicer module (FetchMI).

2011 Summer Project Week FetchMI: Slicer integration with XNAT

2011-06-20T18:27:23Z

Mmilch: /* References */

==Key Investigators==
* Brigham and Women's Hospital: Wendy Plesniak
* Washington University: Misha Milchenko

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

<h3>Objective</h3>

#:Produce a working code for exchanging MRML scenes with XNAT via REST API

</div>

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

<h3>Approach, Plan</h3>
#:Reviewing new Misha's code for XNAT client in FetchMI classes;
#:Compiling, running and testing against XNAT Sandbox;
#:Refining the development plan;
#:User testing.

</div>

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

<h3>Progress</h3>



</div>
</div>

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

==References==
[http://docs.xnat.org/XNAT+REST+API+Usage XNAT 1.5 REST API]<br>
[[2011_Winter_Project_Week:FetchMIAPI | 2011 Winter Project Week: FetchMI API]]

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a built-in Slicer module (FetchMI).

2011 Summer Project Week FetchMI: Slicer integration with XNAT

2011-06-20T18:27:09Z

Mmilch: /* References */

==Key Investigators==
* Brigham and Women's Hospital: Wendy Plesniak
* Washington University: Misha Milchenko

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

<h3>Objective</h3>

#:Produce a working code for exchanging MRML scenes with XNAT via REST API

</div>

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

<h3>Approach, Plan</h3>
#:Reviewing new Misha's code for XNAT client in FetchMI classes;
#:Compiling, running and testing against XNAT Sandbox;
#:Refining the development plan;
#:User testing.

</div>

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

<h3>Progress</h3>



</div>
</div>

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

==References==
[http://docs.xnat.org/XNAT+REST+API+Usage XNAT 1.5 REST API]<br>
[[2011_Winter_Project_Week:FetchMIAPI | 2011 Winter Project Week: FetchMI API]]

Code review.

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a built-in Slicer module (FetchMI).

2011 Summer Project Week FetchMI: Slicer integration with XNAT

2011-06-15T17:39:42Z

Mmilch: /* Key Investigators */

==Key Investigators==
* Brigham and Women's Hospital: Wendy Plesniak
* Washington University: Misha Milchenko

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

<h3>Objective</h3>

#:Produce a working code for exchanging MRML scenes with XNAT via REST API

</div>

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

<h3>Approach, Plan</h3>
#:Reviewing new Misha's code for XNAT client in FetchMI classes;
#:Compiling, running and testing against XNAT Sandbox;
#:Refining the development plan;
#:User testing.

</div>

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

<h3>Progress</h3>



</div>
</div>

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

==References==
[http://docs.xnat.org/XNAT+REST+API+Usage XNAT 1.5 REST API]<br>
[[2011_Winter_Project_Week:FetchMIAPI | 2011 Winter Project Week: FetchMI API]]

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a built-in Slicer module (FetchMI).

2011 Summer Project Week

2011-06-14T16:10:21Z

Mmilch: /* Projects */

Back to [[Events]]

[[image:PW-MIT2011.png|right|200px]]

*'''Dates:''' June 20-24, 2011
*'''Location:''' MIT

==Preliminary Agenda==
==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 20
!style="width:18%" |Tuesday, June 21
!style="width:18%" |Wednesday, June 22
!style="width:18%" |Thursday, June 23
!style="width:18%" |Friday, June 24
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''9am-11am:''' [[2011 Project Week Breakout Session: Slicer4|Slicer 4 Core Modules Usability Review]]''' [[MIT_Project_Week_Rooms#Star|Star Room]]
<br>----------------------------------------<br>
'''11-12pm: <font color="#4020ff">Breakout Session:'''</font> [[2011 Summer Project Week Breakout Session Slicer4 Annotation|Slicer4 Annotations]] (Nicole Aucoin)<br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''9am-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-5:00pm: NA-MIC Kit Update''' Slicer4 Developers Guided Tour (Pieper) ([[media:2011 Summer-Slicer4.ppt|Draft Slides]]), Slicer4 Extension Writing Tutorial (Finet, Fillion-Robin)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:MultiVolumeContainer#Summer_2011_Project_Week_Breakout_Session Slicer4 MultiVolume Containers] (Nicole Aucoin)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
<br>----------------------------------------<br>
'''3-4pm:''' [[Summer_2011_Tutorial_Contest|Tutorial Contest Presentations]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' [[2011 Summer Project Week Breakout Session VTKCharts|VTK Charts]] (Marcus Hanwell)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2011|Tutorial Contest Winner Announcement]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2011_Summer_Project_Week_Breakout_Session_EMRegistration|Inter-subject Registration for EM segmenter]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''1-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Projects==

* Please make a link for your project to a new page based on the [[2011_Summer_Project_Week_Template| 2011 Summer Project Page Template]]

#valuate the applicability of DICOM RT I/O facility in Slicer (via Plastimatch Extension) for Brachytherapy Planning (Tina Kapur, Greg Sharp, Robert Cormack?)
#Visualization of b-spline and vector fields (Steve, Danielle, Dominik)
#[[2011_Summer_Project_Week_Annotation_Module|Annotation Module in Slicer4]] (Nicole Aucoin, Daniel Haehn)
#[[2011_Summer_Project_Week_RECIST|RECIST Slicer4 module]] (Nicole Aucoin)
#DicomToNrrdConverter refactoring ( Xiaodong Tao, Mark Scully)
#[[2011_Summer_Project_Week_normal_consistency_particles|Normal consistency in particle correspondence computation using great circles in principal spheres - Huntington's Disease]], (Beatriz Paniagua, Martin Styner, Sungkyu Jung, Mark Scully)
#Group-wise Automatic Mesh-Based analysis of CortIcal Thickness (GAMBIT) - TBI (Clement Vachet, Martin Styner, Randi Gollub?)
#[[2011_Summer_Project__Week_Shape_Analysis_UNC |SPHARM & particles shape analysis - Huntington's Disease]] - Lucile Bompard, Clement Vachet, Beatriz Paniagua, Martin Styner
#Non-rigid, inter-patient registration of bone masks derived from CT for Head and Neck Cancer Radiation Therapy (Ivan Kolesov, Yi Gao, Gregory Sharp, and Allen Tannenbaum)
#[[2011_Summer_Project_Week_RSS_for_AFib_Ablation|Robust Statistical Segmentation (RSS) for the Atrial Fibrillation Ablation Therapy]] (Yi Gao, Kedar Patwardhan, Wassim Haddad, and Allen Tannenbaum, Rob MacLeod, Josh Blauer, and Josh Cates)
#Mass Spectrometry for Brain Tumor Therapy (Behnood Gholami, Nathalie Agar)
#Multimodality Image Registration for TBI? (Yifei Lou, Danielle Pace, Jack Van Horn?, Marcel Prastawa?)
#[[2011_Summer_Project_Week_Segmentation_TBI|Segmentation of Longitudinal TBI data]] (Bo Wang, Jack Van Horn, Andrei Irimia, Marcel Prastawa, Guido Gerig)
#Longitudinal Shape Regression - Huntington's Disease (James Fishbaugh, Guido Gerig)
#[[2011_Summer_Project__Week_DVH|Dose volume histograms in Slicer]] (Greg Sharp, Nadya Shusharina, Steve Pieper, Csaba Pinter, Tina Kapur)
#[[2011_Summer_Project__Week_DICOM_RT|Synthetic images, vector fields, RT structures and RT doses in Slicer and ITK]]. (Nadya Shusharina, Greg Sharp, Luis Ibanez, Steve Pieper)
#[[2011_Summer_Project_Week_Watersheds|Interactive Watersheds Segmentation Module for Slicer for Atrial Fibrillation and HN Cancer]] (Josh Cates, Ross Whitaker, Steve Pieper, Jim Miller, Nadya)
#Segmentation of Nerve and Nerve Ganglia in the Spine (Adrian Dalca, Giovanna Danagoulian, Ron Kikinis, Ehud Schmidt, Polina Golland)
#Image Manifold Learning with Spectral Embedding and Laplacian Eigenmaps (Ramesh Sridharan, Polina Golland)
#Shapeworks Shape Analysis for Atrial Fibrilliation and HD (Manasi Datar, Beatriz UNC, Mark Scully)
#Explore the applicability of RSS and Shapeworks for Ventricular Segmentation(Chiara Carminati, ?, ?)
#[[2011_Summer_Project_Week_Integrate_BRAINSCut_into_Slicer3]](Regina Kim, ... )
#The Vascular Modeling Toolkit in 3D Slicer 4 (Daniel Haehn, Luca Antiga, Steve Pieper)
#[[2011_Summer_Project_Week__LANDWARP_integration|Integration of LANDWARP into interactive registration module]] (Andrey Fedorov, Greg Sharp, Nadya Shusharina)
#[[2011_Summer_Project_Week_Registration_of_mouse_brains|Registration of mouse brains]] (Francois Budin)
#ShapeWorks Applications (Manasi Datar, Beatriz Paniagua, Martin Styner, Ross Whitaker, ?)
#[[2011_Summer_Project__Week_Wireless_Joystick|Wireless joystick controlling medical devices and software (e.g. Slicer4) in the operating room]] (Szymon Kostrzewski)
#Live Tracked Ultrasound in 3D Slicer 4 (Tamas Heffter)
#[http://wiki.na-mic.org/Wiki/index.php/Survey_stealthlink_openigtlink Surveying research teams interested in Open IGT Link support of Stealth Station (Nobuhiko Hata, Ron Kikinis)]
#DTIPrep - "Study-specific Protocol" based automatic DWI/DTI quality control and preparation - Huntington's Disease (Mashid Farzinfar, Clement Vachet, Joy Matsui, Martin Styner)
#DTIProcessing - Huntington's Disease (Clement Vachet, Joy Matsui, Martin Styner)
#Volumetric DTI into Slicer for HD for Tract based roi segmentation (Steve Callahan, Mark Scully, Jim Miller)
#Nifti Support for Diffusion Tensor Images (Demian)
#Finishing details on the workflows: DICOM->Full brain tractography / peritumoral (Demian)
#Refactoring of the tractography display widget (Isaiah)
#Laterality (Lauren)
#Selection for models and bundles post-clustering (Lauren)
#ROI-based / picking selection of fiber bundles (Maybe one of Sylvain's interns)
#Adding streamlined tractography to the Finsler front propagation tractography toolkit (Antonio)
#Add ODF estimation / visualization (Antonio)
#Workflows and Service Oriented Architecture Modules for Slicer4 as Extensions (Alexander Zaitsev, Wendy Plesniak, Ron Kikinis)
#[[2011_Summer_Project__Week_DICOM_Networking|DICOM Networking interface for Slicer4]] (Steve Pieper, Nicole Aucoin, Noby Hata)
#Stenosis Detector in 3D Slicer 4 (Suares Tamekue, Daniel Haehn, Luca Antiga)
#[[2011_Summer_Project_Week_Spine_Segmentation_And_Osteoporosis_Screening_CT|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)
#Slicer module for building an average population HARDI Atlas (Ryan Eckbo)
#4D Ultrasound (Laurent Chauvin, Noby Hata, Atsushi Yamada)
#EM Segmentation in 3D Slicer 4 (Daniel Haehn, Dominique Belhachemi, Kilian Pohl)
#[[NonRigidRegistrationThatAccommodatesResection|Demons Based Non-Rigid Registration that Accommodates Resection in 3D Slicer]] (Petter Risholm, Sandy Wells)
#[[2011_Summer_Project_Week_re-parameterize_fiber|Re-parameterize fiber tracts for fiber statistics analysis]]
#[[2011_Summer_Project_Week_Automated_GUI_Testing| Automated GUI Testing (Sonia Pujol, Steve Pieper, Dave Partyka, Jean-Christophe Fillion-Robin, Xiaodong Tao)]]
#[[2011_Summer_Project_Week_Plastimatch_for_EMSegmenter | Integrating Plastimatch into the EMSegmenter]] (Dominique Belhachemi, Kilian Pohl, Greg Sharp)
#[[2011_Summer_Project_Week_Customizing_EMSegmenter_pipelines_for_brain_lesions | Customizing EMSegmenter pipelines for brain lesions]] (Dominique Belhachemi, Alexander Zaitsev, Kilian Pohl)
#[[2011_Summer_Project_Week_Slicer_Extension_for_GLISTR | Slicer extension for GLiome Image SegmenTation and Registration (GLISTR)]] (Andreas Schuh, Daniel Haehn, Kilian Pohl)
#[[2011_Summer_Project_Week_WMGeometry_Slicer4 | White matter geometry measures in Slicer 4]] (Peter Savadjiev)
#Internationalization of Slicer (Luping Fang, Steve Pieper, Daniel Haehn, Suares Tamekue, Jean-Christophe Fillion-Robin, Jean-Christophe, Julien Finet, Yiming Ge, Ping Cao)
#[[2011_Summer_Project_Week__BRAINSFit_new_features_integration|Integrate new features into BRAINSFit]] (Andrey Fedorov, Hans Johnson, Mark Scully)
#[[2011_Summer_Project_Week_FetchMI:_Slicer_integration_with_XNAT |FetchMI: Slicer integration with XNAT 1.5]] (Misha Milchenko, Wendy Plesniak)

==Background==

We are pleased to announce the 13th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 28th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

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

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

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

== Logistics ==
*'''Dates:''' June 20-24, 2011
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please register [http://guest.cvent.com/d/sdqy0l/4W here]. Payment must be made by credit card.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' Boston Marriott Cambridge, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. Group rate is $199/night plus tax. Book [http://www.marriott.com/hotels/travel/boscb?groupCode=jrbjrba&app=resvlink&fromDate=6/19/11&toDate=6/24/11 here] or call 1-617-494-6600 and mention that you are booking in the MIT Room Block. '''All reservations must be made by May 29, 2011 to receive the discounted rate.'''

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 28, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 12, all participants to add a one line title of their project to #Projects
#By 3pm ET on Thursday June 9, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 16: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## 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...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

==Registrants==

Do not add your name to this list- it is maintaining by the organizers based on your paid registration (see Logistics for link)
# Nicole Aucoin , Brigham and Women's Hospital
# Dominique Belhachemi , University of Pennsylvania
# Anthony Blumfiled , Radnostics
# Lucile Bompard , UNC NIRAL
# Sylvain Bouix , Brigham and Women's Hospital
# Francois Budin , UNC NIRAL
# Steve Callahan , University of Utah
# Joshua Cates , University of Utah
# Laurent Chauvin , Brigham and Women's Hospital
# Adrian Dalca , MIT CSAIL
# Manasi Datar , University of Utah
# Colin Davey ,
# Ryan Eckbo , Brigham and Women's Hospital
# Jan Egger , University Hospital of Marburg
# Luping Fang , Zhejiang University of Technology, China
# mahshid farzinfar , UNC
# Andriy Fedorov , Brigham and Women's Hospital
# Julien Finet , Kitware Inc.
# James Fishbaugh , University of Utah
# Greg Gardner , University of Utah
# Ronen Globinsky , Yale University
# Maged Goubran , Robarts Research Institute
# Daniel Haehn , University of Pennsylvania
# Mike Halle , Brigham and Women's Hospital
# Noby Hata , Brigham and Women's Hospital
# Tamas Heffter , Queen's University
# Andrei Irimia , University of California, Los Angeles
# Hans Johnson , University of Iowa
# Ilknur Kabul , Kitware
# Tina Kapur , Brigham and Women's Hospital
# Ron Kikinis , Brigham and Women's Hospital; Harvard Medical School
# Regina Kim , University of Iowa
# Szymon Kostrzewski , Ecole Polytechnique Federale de Lausanne EPFL
# Dillon Lee , University of Utah
# Yinpeng Li , UNC-NIRAL
# Yifei Lou , Georgia Institute of Technology
# mohsen mahvash , Harvard Medical School (BWH and VA)
# Katie Mastrogiacomo , Brigham and Women's Hospital
# Joy Matsui , University of Iowa
# Dominik Meier , BWH
# Mikhail Milchenko , Washington University in St. Louis
# James Miller , GE Research
# Isaiah Norton , Brigham and Women's Hospital
# Danielle Pace , Kitware
# Beatriz Paniagua , University of North Carolina at Chapel Hill
# Xenophon Papademetris , Yale University
# Kedar Patwardhan , GE Global Research
# Steve Pieper , Isomics, Inc.
# Csaba Pinter , Queen's University
# Wendy Plesniak , Brigham and Women's Hospital
# Kilian Pohl , UPenn
# Marcel Prastawa , University of Utah
# Sonia Pujol , Brigham and Women's Hospital
# Martin Rajchl , Robarts Research Institute
# Petter Risholm , Brigham and Women's Hospital
# Peter Savadjiev , Brigham and Women's Hospital
# Andreas Schuh , University of Pennsylvania
# Mark Scully , University of Iowa
# Gregory Sharp , MGH
# Yundi Shi , UNC-Chapel Hill
# Nadya Shusharina , MGH
# Ramesh Sridharan , MIT CSAIL
# Hao Su , WPI
# Suarez Tamekue , Brigham and Women's Hospital
# Xiaodong Tao , GE Research
# Clement Vachet , UNC Chapel Hill
# Antonio Vega , Brigham and Women's Hospital
# Gopal Veni , University of Utah
# Bo Wang , University of Utah
# Demian Wasserman , Brigham and Women's Hospital
# Sandy Wells , Brigham and Women's Hospital
# Jason White , Brigham and Women's Hospital
# Atsushi Yamada , Brigham and Women's Hospital
# Alexander Yarmarkovich , Isomics
# Alexander Zaitsev , Brigham and Women's Hospital

2011 Summer Project Week FetchMI: Slicer integration with XNAT

2011-06-14T16:09:14Z

Mmilch: /* References */

==Key Investigators==
* Harvard Medical School: Wendy Plesniak
* Washington University: Misha Milchenko

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

<h3>Objective</h3>

#:Produce a working code for exchanging MRML scenes with XNAT via REST API

</div>

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

<h3>Approach, Plan</h3>
#:Reviewing new Misha's code for XNAT client in FetchMI classes;
#:Compiling, running and testing against XNAT Sandbox;
#:Refining the development plan;
#:User testing.

</div>

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

<h3>Progress</h3>



</div>
</div>

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

==References==
[http://docs.xnat.org/XNAT+REST+API+Usage XNAT 1.5 REST API]<br>
[[2011_Winter_Project_Week:FetchMIAPI | 2011 Winter Project Week: FetchMI API]]

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a built-in Slicer module (FetchMI).

2011 Summer Project Week FetchMI: Slicer integration with XNAT

2011-06-14T16:07:03Z

Mmilch: moved FetchMI: Slicer integration with XNAT to 2011 Summer Project Week FetchMI: Slicer integration with XNAT

==Key Investigators==
* Harvard Medical School: Wendy Plesniak
* Washington University: Misha Milchenko

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

<h3>Objective</h3>

#:Produce a working code for exchanging MRML scenes with XNAT via REST API

</div>

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

<h3>Approach, Plan</h3>
#:Reviewing new Misha's code for XNAT client in FetchMI classes;
#:Compiling, running and testing against XNAT Sandbox;
#:Refining the development plan;
#:User testing.

</div>

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

<h3>Progress</h3>



</div>
</div>

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

==References==
XNAT REST API [http://docs.xnat.org/XNAT+REST+API+Usage]<br>
[[2011_Winter_Project_Week:FetchMIAPI]]

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a built-in Slicer module (FetchMI).

FetchMI: Slicer integration with XNAT

2011-06-14T16:07:03Z

Mmilch: moved FetchMI: Slicer integration with XNAT to 2011 Summer Project Week FetchMI: Slicer integration with XNAT

#REDIRECT [[2011 Summer Project Week FetchMI: Slicer integration with XNAT]]

2011 Summer Project Week

2011-06-14T16:05:28Z

Mmilch: /* Projects */

Back to [[Events]]

[[image:PW-MIT2011.png|right|200px]]

*'''Dates:''' June 20-24, 2011
*'''Location:''' MIT

==Preliminary Agenda==
==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 20
!style="width:18%" |Tuesday, June 21
!style="width:18%" |Wednesday, June 22
!style="width:18%" |Thursday, June 23
!style="width:18%" |Friday, June 24
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''9am-11am:''' [[2011 Project Week Breakout Session: Slicer4|Slicer 4 Core Modules Usability Review]]''' [[MIT_Project_Week_Rooms#Star|Star Room]]
<br>----------------------------------------<br>
'''11-12pm: <font color="#4020ff">Breakout Session:'''</font> [[2011 Summer Project Week Breakout Session Slicer4 Annotation|Slicer4 Annotations]] (Nicole Aucoin)<br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''9am-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-5:00pm: NA-MIC Kit Update''' Slicer4 Developers Guided Tour (Pieper) ([[media:2011 Summer-Slicer4.ppt|Draft Slides]]), Slicer4 Extension Writing Tutorial (Finet, Fillion-Robin)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:MultiVolumeContainer#Summer_2011_Project_Week_Breakout_Session Slicer4 MultiVolume Containers] (Nicole Aucoin)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
<br>----------------------------------------<br>
'''3-4pm:''' [[Summer_2011_Tutorial_Contest|Tutorial Contest Presentations]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' [[2011 Summer Project Week Breakout Session VTKCharts|VTK Charts]] (Marcus Hanwell)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2011|Tutorial Contest Winner Announcement]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2011_Summer_Project_Week_Breakout_Session_EMRegistration|Inter-subject Registration for EM segmenter]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''1-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Projects==

* Please make a link for your project to a new page based on the [[2011_Summer_Project_Week_Template| 2011 Summer Project Page Template]]

#valuate the applicability of DICOM RT I/O facility in Slicer (via Plastimatch Extension) for Brachytherapy Planning (Tina Kapur, Greg Sharp, Robert Cormack?)
#Visualization of b-spline and vector fields (Steve, Danielle, Dominik)
#[[2011_Summer_Project_Week_Annotation_Module|Annotation Module in Slicer4]] (Nicole Aucoin, Daniel Haehn)
#[[2011_Summer_Project_Week_RECIST|RECIST Slicer4 module]] (Nicole Aucoin)
#DicomToNrrdConverter refactoring ( Xiaodong Tao, Mark Scully)
#[[2011_Summer_Project_Week_normal_consistency_particles|Normal consistency in particle correspondence computation using great circles in principal spheres - Huntington's Disease]], (Beatriz Paniagua, Martin Styner, Sungkyu Jung, Mark Scully)
#Group-wise Automatic Mesh-Based analysis of CortIcal Thickness (GAMBIT) - TBI (Clement Vachet, Martin Styner, Randi Gollub?)
#[[2011_Summer_Project__Week_Shape_Analysis_UNC |SPHARM & particles shape analysis - Huntington's Disease]] - Lucile Bompard, Clement Vachet, Beatriz Paniagua, Martin Styner
#Non-rigid, inter-patient registration of bone masks derived from CT for Head and Neck Cancer Radiation Therapy (Ivan Kolesov, Yi Gao, Gregory Sharp, and Allen Tannenbaum)
#[[2011_Summer_Project_Week_RSS_for_AFib_Ablation|Robust Statistical Segmentation (RSS) for the Atrial Fibrillation Ablation Therapy]] (Yi Gao, Kedar Patwardhan, Wassim Haddad, and Allen Tannenbaum, Rob MacLeod, Josh Blauer, and Josh Cates)
#Mass Spectrometry for Brain Tumor Therapy (Behnood Gholami, Nathalie Agar)
#Multimodality Image Registration for TBI? (Yifei Lou, Danielle Pace, Jack Van Horn?, Marcel Prastawa?)
#[[2011_Summer_Project_Week_Segmentation_TBI|Segmentation of Longitudinal TBI data]] (Bo Wang, Jack Van Horn, Andrei Irimia, Marcel Prastawa, Guido Gerig)
#Longitudinal Shape Regression - Huntington's Disease (James Fishbaugh, Guido Gerig)
#[[2011_Summer_Project__Week_DVH|Dose volume histograms in Slicer]] (Greg Sharp, Nadya Shusharina, Steve Pieper, Csaba Pinter, Tina Kapur)
#[[2011_Summer_Project__Week_DICOM_RT|Synthetic images, vector fields, RT structures and RT doses in Slicer and ITK]]. (Nadya Shusharina, Greg Sharp, Luis Ibanez, Steve Pieper)
#[[2011_Summer_Project_Week_Watersheds|Interactive Watersheds Segmentation Module for Slicer for Atrial Fibrillation and HN Cancer]] (Josh Cates, Ross Whitaker, Steve Pieper, Jim Miller, Nadya)
#Segmentation of Nerve and Nerve Ganglia in the Spine (Adrian Dalca, Giovanna Danagoulian, Ron Kikinis, Ehud Schmidt, Polina Golland)
#Image Manifold Learning with Spectral Embedding and Laplacian Eigenmaps (Ramesh Sridharan, Polina Golland)
#Shapeworks Shape Analysis for Atrial Fibrilliation and HD (Manasi Datar, Beatriz UNC, Mark Scully)
#Explore the applicability of RSS and Shapeworks for Ventricular Segmentation(Chiara Carminati, ?, ?)
#[[2011_Summer_Project_Week_Integrate_BRAINSCut_into_Slicer3]](Regina Kim, ... )
#The Vascular Modeling Toolkit in 3D Slicer 4 (Daniel Haehn, Luca Antiga, Steve Pieper)
#[[2011_Summer_Project_Week__LANDWARP_integration|Integration of LANDWARP into interactive registration module]] (Andrey Fedorov, Greg Sharp, Nadya Shusharina)
#[[2011_Summer_Project_Week_Registration_of_mouse_brains|Registration of mouse brains]] (Francois Budin)
#ShapeWorks Applications (Manasi Datar, Beatriz Paniagua, Martin Styner, Ross Whitaker, ?)
#[[2011_Summer_Project__Week_Wireless_Joystick|Wireless joystick controlling medical devices and software (e.g. Slicer4) in the operating room]] (Szymon Kostrzewski)
#Live Tracked Ultrasound in 3D Slicer 4 (Tamas Heffter)
#[http://wiki.na-mic.org/Wiki/index.php/Survey_stealthlink_openigtlink Surveying research teams interested in Open IGT Link support of Stealth Station (Nobuhiko Hata, Ron Kikinis)]
#DTIPrep - "Study-specific Protocol" based automatic DWI/DTI quality control and preparation - Huntington's Disease (Mashid Farzinfar, Clement Vachet, Joy Matsui, Martin Styner)
#DTIProcessing - Huntington's Disease (Clement Vachet, Joy Matsui, Martin Styner)
#Volumetric DTI into Slicer for HD for Tract based roi segmentation (Steve Callahan, Mark Scully, Jim Miller)
#Nifti Support for Diffusion Tensor Images (Demian)
#Finishing details on the workflows: DICOM->Full brain tractography / peritumoral (Demian)
#Refactoring of the tractography display widget (Isaiah)
#Laterality (Lauren)
#Selection for models and bundles post-clustering (Lauren)
#ROI-based / picking selection of fiber bundles (Maybe one of Sylvain's interns)
#Adding streamlined tractography to the Finsler front propagation tractography toolkit (Antonio)
#Add ODF estimation / visualization (Antonio)
#Workflows and Service Oriented Architecture Modules for Slicer4 as Extensions (Alexander Zaitsev, Wendy Plesniak, Ron Kikinis)
#[[2011_Summer_Project__Week_DICOM_Networking|DICOM Networking interface for Slicer4]] (Steve Pieper, Nicole Aucoin, Noby Hata)
#Stenosis Detector in 3D Slicer 4 (Suares Tamekue, Daniel Haehn, Luca Antiga)
#[[2011_Summer_Project_Week_Spine_Segmentation_And_Osteoporosis_Screening_CT|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)
#Slicer module for building an average population HARDI Atlas (Ryan Eckbo)
#4D Ultrasound (Laurent Chauvin, Noby Hata, Atsushi Yamada)
#EM Segmentation in 3D Slicer 4 (Daniel Haehn, Dominique Belhachemi, Kilian Pohl)
#[[NonRigidRegistrationThatAccommodatesResection|Demons Based Non-Rigid Registration that Accommodates Resection in 3D Slicer]] (Petter Risholm, Sandy Wells)
#[[2011_Summer_Project_Week_re-parameterize_fiber|Re-parameterize fiber tracts for fiber statistics analysis]]
#[[2011_Summer_Project_Week_Automated_GUI_Testing| Automated GUI Testing (Sonia Pujol, Steve Pieper, Dave Partyka, Jean-Christophe Fillion-Robin, Xiaodong Tao)]]
#[[2011_Summer_Project_Week_Plastimatch_for_EMSegmenter | Integrating Plastimatch into the EMSegmenter]] (Dominique Belhachemi, Kilian Pohl, Greg Sharp)
#[[2011_Summer_Project_Week_Customizing_EMSegmenter_pipelines_for_brain_lesions | Customizing EMSegmenter pipelines for brain lesions]] (Dominique Belhachemi, Alexander Zaitsev, Kilian Pohl)
#[[2011_Summer_Project_Week_Slicer_Extension_for_GLISTR | Slicer extension for GLiome Image SegmenTation and Registration (GLISTR)]] (Andreas Schuh, Daniel Haehn, Kilian Pohl)
#[[2011_Summer_Project_Week_WMGeometry_Slicer4 | White matter geometry measures in Slicer 4]] (Peter Savadjiev)
#Internationalization of Slicer (Luping Fang, Steve Pieper, Daniel Haehn, Suares Tamekue, Jean-Christophe Fillion-Robin, Jean-Christophe, Julien Finet, Yiming Ge, Ping Cao)
#[[2011_Summer_Project_Week__BRAINSFit_new_features_integration|Integrate new features into BRAINSFit]] (Andrey Fedorov, Hans Johnson, Mark Scully)
#[[FetchMI:_Slicer_integration_with_XNAT | FetchMI: Slicer integration with XNAT 1.5]] (Misha Milchenko, Wendy Plesniak)

==Background==

We are pleased to announce the 13th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 28th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

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

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

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

== Logistics ==
*'''Dates:''' June 20-24, 2011
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please register [http://guest.cvent.com/d/sdqy0l/4W here]. Payment must be made by credit card.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' Boston Marriott Cambridge, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. Group rate is $199/night plus tax. Book [http://www.marriott.com/hotels/travel/boscb?groupCode=jrbjrba&app=resvlink&fromDate=6/19/11&toDate=6/24/11 here] or call 1-617-494-6600 and mention that you are booking in the MIT Room Block. '''All reservations must be made by May 29, 2011 to receive the discounted rate.'''

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 28, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 12, all participants to add a one line title of their project to #Projects
#By 3pm ET on Thursday June 9, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 16: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## 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...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

==Registrants==

Do not add your name to this list- it is maintaining by the organizers based on your paid registration (see Logistics for link)
# Nicole Aucoin , Brigham and Women's Hospital
# Dominique Belhachemi , University of Pennsylvania
# Anthony Blumfiled , Radnostics
# Lucile Bompard , UNC NIRAL
# Sylvain Bouix , Brigham and Women's Hospital
# Francois Budin , UNC NIRAL
# Steve Callahan , University of Utah
# Joshua Cates , University of Utah
# Laurent Chauvin , Brigham and Women's Hospital
# Adrian Dalca , MIT CSAIL
# Manasi Datar , University of Utah
# Colin Davey ,
# Ryan Eckbo , Brigham and Women's Hospital
# Jan Egger , University Hospital of Marburg
# Luping Fang , Zhejiang University of Technology, China
# mahshid farzinfar , UNC
# Andriy Fedorov , Brigham and Women's Hospital
# Julien Finet , Kitware Inc.
# James Fishbaugh , University of Utah
# Greg Gardner , University of Utah
# Ronen Globinsky , Yale University
# Maged Goubran , Robarts Research Institute
# Daniel Haehn , University of Pennsylvania
# Mike Halle , Brigham and Women's Hospital
# Noby Hata , Brigham and Women's Hospital
# Tamas Heffter , Queen's University
# Andrei Irimia , University of California, Los Angeles
# Hans Johnson , University of Iowa
# Ilknur Kabul , Kitware
# Tina Kapur , Brigham and Women's Hospital
# Ron Kikinis , Brigham and Women's Hospital; Harvard Medical School
# Regina Kim , University of Iowa
# Szymon Kostrzewski , Ecole Polytechnique Federale de Lausanne EPFL
# Dillon Lee , University of Utah
# Yinpeng Li , UNC-NIRAL
# Yifei Lou , Georgia Institute of Technology
# mohsen mahvash , Harvard Medical School (BWH and VA)
# Katie Mastrogiacomo , Brigham and Women's Hospital
# Joy Matsui , University of Iowa
# Dominik Meier , BWH
# Mikhail Milchenko , Washington University in St. Louis
# James Miller , GE Research
# Isaiah Norton , Brigham and Women's Hospital
# Danielle Pace , Kitware
# Beatriz Paniagua , University of North Carolina at Chapel Hill
# Xenophon Papademetris , Yale University
# Kedar Patwardhan , GE Global Research
# Steve Pieper , Isomics, Inc.
# Csaba Pinter , Queen's University
# Wendy Plesniak , Brigham and Women's Hospital
# Kilian Pohl , UPenn
# Marcel Prastawa , University of Utah
# Sonia Pujol , Brigham and Women's Hospital
# Martin Rajchl , Robarts Research Institute
# Petter Risholm , Brigham and Women's Hospital
# Peter Savadjiev , Brigham and Women's Hospital
# Andreas Schuh , University of Pennsylvania
# Mark Scully , University of Iowa
# Gregory Sharp , MGH
# Yundi Shi , UNC-Chapel Hill
# Nadya Shusharina , MGH
# Ramesh Sridharan , MIT CSAIL
# Hao Su , WPI
# Suarez Tamekue , Brigham and Women's Hospital
# Xiaodong Tao , GE Research
# Clement Vachet , UNC Chapel Hill
# Antonio Vega , Brigham and Women's Hospital
# Gopal Veni , University of Utah
# Bo Wang , University of Utah
# Demian Wasserman , Brigham and Women's Hospital
# Sandy Wells , Brigham and Women's Hospital
# Jason White , Brigham and Women's Hospital
# Atsushi Yamada , Brigham and Women's Hospital
# Alexander Yarmarkovich , Isomics
# Alexander Zaitsev , Brigham and Women's Hospital

2011 Summer Project Week

2011-06-14T16:04:35Z

Mmilch: /* Projects */

Back to [[Events]]

[[image:PW-MIT2011.png|right|200px]]

*'''Dates:''' June 20-24, 2011
*'''Location:''' MIT

==Preliminary Agenda==
==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 20
!style="width:18%" |Tuesday, June 21
!style="width:18%" |Wednesday, June 22
!style="width:18%" |Thursday, June 23
!style="width:18%" |Friday, June 24
|-
|
|bgcolor="#dbdbdb"|'''Project Presentations'''
|bgcolor="#6494ec"|'''NA-MIC Update Day'''
|
|bgcolor="#88aaae"|'''IGT Day'''
|bgcolor="#faedb6"|'''Reporting Day'''
|-
|bgcolor="#ffffdd"|'''8:30am'''
|
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|bgcolor="#ffffaa"|Breakfast
|-
|bgcolor="#ffffdd"|'''9am-12pm'''
|
|'''9am-11am:''' [[2011 Project Week Breakout Session: Slicer4|Slicer 4 Core Modules Usability Review]]''' [[MIT_Project_Week_Rooms#Star|Star Room]]
<br>----------------------------------------<br>
'''11-12pm: <font color="#4020ff">Breakout Session:'''</font> [[2011 Summer Project Week Breakout Session Slicer4 Annotation|Slicer4 Annotations]] (Nicole Aucoin)<br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Project Week Breakout Session: ITK|ITK]] (Luis Ibanez)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''9am-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-5:00pm: NA-MIC Kit Update''' Slicer4 Developers Guided Tour (Pieper) ([[media:2011 Summer-Slicer4.ppt|Draft Slides]]), Slicer4 Extension Writing Tutorial (Finet, Fillion-Robin)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:MultiVolumeContainer#Summer_2011_Project_Week_Breakout_Session Slicer4 MultiVolume Containers] (Nicole Aucoin)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
<br>----------------------------------------<br>
'''3-4pm:''' [[Summer_2011_Tutorial_Contest|Tutorial Contest Presentations]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' [[2011 Summer Project Week Breakout Session VTKCharts|VTK Charts]] (Marcus Hanwell)
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2011|Tutorial Contest Winner Announcement]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3-4pm: <font color="#4020ff">Breakout Session:'''</font><br>[[2011_Summer_Project_Week_Breakout_Session_EMRegistration|Inter-subject Registration for EM segmenter]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''1-4pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2011 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]]
<br>[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Projects==

* Please make a link for your project to a new page based on the [[2011_Summer_Project_Week_Template| 2011 Summer Project Page Template]]

#valuate the applicability of DICOM RT I/O facility in Slicer (via Plastimatch Extension) for Brachytherapy Planning (Tina Kapur, Greg Sharp, Robert Cormack?)
#Visualization of b-spline and vector fields (Steve, Danielle, Dominik)
#[[2011_Summer_Project_Week_Annotation_Module|Annotation Module in Slicer4]] (Nicole Aucoin, Daniel Haehn)
#[[2011_Summer_Project_Week_RECIST|RECIST Slicer4 module]] (Nicole Aucoin)
#DicomToNrrdConverter refactoring ( Xiaodong Tao, Mark Scully)
#[[2011_Summer_Project_Week_normal_consistency_particles|Normal consistency in particle correspondence computation using great circles in principal spheres - Huntington's Disease]], (Beatriz Paniagua, Martin Styner, Sungkyu Jung, Mark Scully)
#Group-wise Automatic Mesh-Based analysis of CortIcal Thickness (GAMBIT) - TBI (Clement Vachet, Martin Styner, Randi Gollub?)
#[[2011_Summer_Project__Week_Shape_Analysis_UNC |SPHARM & particles shape analysis - Huntington's Disease]] - Lucile Bompard, Clement Vachet, Beatriz Paniagua, Martin Styner
#Non-rigid, inter-patient registration of bone masks derived from CT for Head and Neck Cancer Radiation Therapy (Ivan Kolesov, Yi Gao, Gregory Sharp, and Allen Tannenbaum)
#[[2011_Summer_Project_Week_RSS_for_AFib_Ablation|Robust Statistical Segmentation (RSS) for the Atrial Fibrillation Ablation Therapy]] (Yi Gao, Kedar Patwardhan, Wassim Haddad, and Allen Tannenbaum, Rob MacLeod, Josh Blauer, and Josh Cates)
#Mass Spectrometry for Brain Tumor Therapy (Behnood Gholami, Nathalie Agar)
#Multimodality Image Registration for TBI? (Yifei Lou, Danielle Pace, Jack Van Horn?, Marcel Prastawa?)
#[[2011_Summer_Project_Week_Segmentation_TBI|Segmentation of Longitudinal TBI data]] (Bo Wang, Jack Van Horn, Andrei Irimia, Marcel Prastawa, Guido Gerig)
#Longitudinal Shape Regression - Huntington's Disease (James Fishbaugh, Guido Gerig)
#[[2011_Summer_Project__Week_DVH|Dose volume histograms in Slicer]] (Greg Sharp, Nadya Shusharina, Steve Pieper, Csaba Pinter, Tina Kapur)
#[[2011_Summer_Project__Week_DICOM_RT|Synthetic images, vector fields, RT structures and RT doses in Slicer and ITK]]. (Nadya Shusharina, Greg Sharp, Luis Ibanez, Steve Pieper)
#[[2011_Summer_Project_Week_Watersheds|Interactive Watersheds Segmentation Module for Slicer for Atrial Fibrillation and HN Cancer]] (Josh Cates, Ross Whitaker, Steve Pieper, Jim Miller, Nadya)
#Segmentation of Nerve and Nerve Ganglia in the Spine (Adrian Dalca, Giovanna Danagoulian, Ron Kikinis, Ehud Schmidt, Polina Golland)
#Image Manifold Learning with Spectral Embedding and Laplacian Eigenmaps (Ramesh Sridharan, Polina Golland)
#Shapeworks Shape Analysis for Atrial Fibrilliation and HD (Manasi Datar, Beatriz UNC, Mark Scully)
#Explore the applicability of RSS and Shapeworks for Ventricular Segmentation(Chiara Carminati, ?, ?)
#[[2011_Summer_Project_Week_Integrate_BRAINSCut_into_Slicer3]](Regina Kim, ... )
#The Vascular Modeling Toolkit in 3D Slicer 4 (Daniel Haehn, Luca Antiga, Steve Pieper)
#[[2011_Summer_Project_Week__LANDWARP_integration|Integration of LANDWARP into interactive registration module]] (Andrey Fedorov, Greg Sharp, Nadya Shusharina)
#[[2011_Summer_Project_Week_Registration_of_mouse_brains|Registration of mouse brains]] (Francois Budin)
#ShapeWorks Applications (Manasi Datar, Beatriz Paniagua, Martin Styner, Ross Whitaker, ?)
#[[2011_Summer_Project__Week_Wireless_Joystick|Wireless joystick controlling medical devices and software (e.g. Slicer4) in the operating room]] (Szymon Kostrzewski)
#Live Tracked Ultrasound in 3D Slicer 4 (Tamas Heffter)
#[http://wiki.na-mic.org/Wiki/index.php/Survey_stealthlink_openigtlink Surveying research teams interested in Open IGT Link support of Stealth Station (Nobuhiko Hata, Ron Kikinis)]
#DTIPrep - "Study-specific Protocol" based automatic DWI/DTI quality control and preparation - Huntington's Disease (Mashid Farzinfar, Clement Vachet, Joy Matsui, Martin Styner)
#DTIProcessing - Huntington's Disease (Clement Vachet, Joy Matsui, Martin Styner)
#Volumetric DTI into Slicer for HD for Tract based roi segmentation (Steve Callahan, Mark Scully, Jim Miller)
#Nifti Support for Diffusion Tensor Images (Demian)
#Finishing details on the workflows: DICOM->Full brain tractography / peritumoral (Demian)
#Refactoring of the tractography display widget (Isaiah)
#Laterality (Lauren)
#Selection for models and bundles post-clustering (Lauren)
#ROI-based / picking selection of fiber bundles (Maybe one of Sylvain's interns)
#Adding streamlined tractography to the Finsler front propagation tractography toolkit (Antonio)
#Add ODF estimation / visualization (Antonio)
#Workflows and Service Oriented Architecture Modules for Slicer4 as Extensions (Alexander Zaitsev, Wendy Plesniak, Ron Kikinis)
#[[2011_Summer_Project__Week_DICOM_Networking|DICOM Networking interface for Slicer4]] (Steve Pieper, Nicole Aucoin, Noby Hata)
#Stenosis Detector in 3D Slicer 4 (Suares Tamekue, Daniel Haehn, Luca Antiga)
#[[2011_Summer_Project_Week_Spine_Segmentation_And_Osteoporosis_Screening_CT|Spine Segmentation & Osteoporosis Screening In CT Imaging Studies]] (Anthony Blumfield)
#Slicer module for building an average population HARDI Atlas (Ryan Eckbo)
#4D Ultrasound (Laurent Chauvin, Noby Hata, Atsushi Yamada)
#EM Segmentation in 3D Slicer 4 (Daniel Haehn, Dominique Belhachemi, Kilian Pohl)
#[[NonRigidRegistrationThatAccommodatesResection|Demons Based Non-Rigid Registration that Accommodates Resection in 3D Slicer]] (Petter Risholm, Sandy Wells)
#[[2011_Summer_Project_Week_re-parameterize_fiber|Re-parameterize fiber tracts for fiber statistics analysis]]
#[[2011_Summer_Project_Week_Automated_GUI_Testing| Automated GUI Testing (Sonia Pujol, Steve Pieper, Dave Partyka, Jean-Christophe Fillion-Robin, Xiaodong Tao)]]
#[[2011_Summer_Project_Week_Plastimatch_for_EMSegmenter | Integrating Plastimatch into the EMSegmenter]] (Dominique Belhachemi, Kilian Pohl, Greg Sharp)
#[[2011_Summer_Project_Week_Customizing_EMSegmenter_pipelines_for_brain_lesions | Customizing EMSegmenter pipelines for brain lesions]] (Dominique Belhachemi, Alexander Zaitsev, Kilian Pohl)
#[[2011_Summer_Project_Week_Slicer_Extension_for_GLISTR | Slicer extension for GLiome Image SegmenTation and Registration (GLISTR)]] (Andreas Schuh, Daniel Haehn, Kilian Pohl)
#[[2011_Summer_Project_Week_WMGeometry_Slicer4 | White matter geometry measures in Slicer 4]] (Peter Savadjiev)
#Internationalization of Slicer (Luping Fang, Steve Pieper, Daniel Haehn, Suares Tamekue, Jean-Christophe Fillion-Robin, Jean-Christophe, Julien Finet, Yiming Ge, Ping Cao)
#[[2011_Summer_Project_Week__BRAINSFit_new_features_integration|Integrate new features into BRAINSFit]] (Andrey Fedorov, Hans Johnson, Mark Scully)
#[[FetchMI:_Slicer_integration_with_XNAT]] (Misha Milchenko, Wendy Plesniak)

==Background==

We are pleased to announce the 13th PROJECT WEEK of hands-on research and development activity for applications in Image-Guided Therapy, Neuroscience, and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 28th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

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

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

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

== Logistics ==
*'''Dates:''' June 20-24, 2011
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please register [http://guest.cvent.com/d/sdqy0l/4W here]. Payment must be made by credit card.
*'''Registration Fee:''' $260 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' Boston Marriott Cambridge, Two Cambridge Center, 50 Broadway, Cambridge, MA 02142. Group rate is $199/night plus tax. Book [http://www.marriott.com/hotels/travel/boscb?groupCode=jrbjrba&app=resvlink&fromDate=6/19/11&toDate=6/24/11 here] or call 1-617-494-6600 and mention that you are booking in the MIT Room Block. '''All reservations must be made by May 29, 2011 to receive the discounted rate.'''

== Preparation ==

# Please make sure that you are on the http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week mailing list
# The NA-MIC engineering team will be discussing infrastructure projects in a kickoff TCON on April 28, 3pm ET. In the weeks following, new and old participants from the above mailing list will be invited to join to discuss their projects, so please make sure you are on it!
# By 3pm ET on Thursday May 12, all participants to add a one line title of their project to #Projects
#By 3pm ET on Thursday June 9, all project leads to complete [[Project_Week/Template|Complete a templated wiki page for your project]]. Please do not edit the template page itself, but create a new page for your project and cut-and-paste the text from this template page. If you have questions, please send an email to tkapur at bwh.harvard.edu.
# By 3pm on June 16: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Zack)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## 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...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## Projects to develop extension modules should work with the [http://viewvc.slicer.org/viewcvs.cgi/branches/Slicer-3-6/#dirlist Slicer-3-6 branch] (new code should not be checked into the branch).
## Projects to modify core behavior of slicer should be done on the [http://viewvc.slicer.org/viewcvs.cgi/trunk/ trunk].

==Registrants==

Do not add your name to this list- it is maintaining by the organizers based on your paid registration (see Logistics for link)
# Nicole Aucoin , Brigham and Women's Hospital
# Dominique Belhachemi , University of Pennsylvania
# Anthony Blumfiled , Radnostics
# Lucile Bompard , UNC NIRAL
# Sylvain Bouix , Brigham and Women's Hospital
# Francois Budin , UNC NIRAL
# Steve Callahan , University of Utah
# Joshua Cates , University of Utah
# Laurent Chauvin , Brigham and Women's Hospital
# Adrian Dalca , MIT CSAIL
# Manasi Datar , University of Utah
# Colin Davey ,
# Ryan Eckbo , Brigham and Women's Hospital
# Jan Egger , University Hospital of Marburg
# Luping Fang , Zhejiang University of Technology, China
# mahshid farzinfar , UNC
# Andriy Fedorov , Brigham and Women's Hospital
# Julien Finet , Kitware Inc.
# James Fishbaugh , University of Utah
# Greg Gardner , University of Utah
# Ronen Globinsky , Yale University
# Maged Goubran , Robarts Research Institute
# Daniel Haehn , University of Pennsylvania
# Mike Halle , Brigham and Women's Hospital
# Noby Hata , Brigham and Women's Hospital
# Tamas Heffter , Queen's University
# Andrei Irimia , University of California, Los Angeles
# Hans Johnson , University of Iowa
# Ilknur Kabul , Kitware
# Tina Kapur , Brigham and Women's Hospital
# Ron Kikinis , Brigham and Women's Hospital; Harvard Medical School
# Regina Kim , University of Iowa
# Szymon Kostrzewski , Ecole Polytechnique Federale de Lausanne EPFL
# Dillon Lee , University of Utah
# Yinpeng Li , UNC-NIRAL
# Yifei Lou , Georgia Institute of Technology
# mohsen mahvash , Harvard Medical School (BWH and VA)
# Katie Mastrogiacomo , Brigham and Women's Hospital
# Joy Matsui , University of Iowa
# Dominik Meier , BWH
# Mikhail Milchenko , Washington University in St. Louis
# James Miller , GE Research
# Isaiah Norton , Brigham and Women's Hospital
# Danielle Pace , Kitware
# Beatriz Paniagua , University of North Carolina at Chapel Hill
# Xenophon Papademetris , Yale University
# Kedar Patwardhan , GE Global Research
# Steve Pieper , Isomics, Inc.
# Csaba Pinter , Queen's University
# Wendy Plesniak , Brigham and Women's Hospital
# Kilian Pohl , UPenn
# Marcel Prastawa , University of Utah
# Sonia Pujol , Brigham and Women's Hospital
# Martin Rajchl , Robarts Research Institute
# Petter Risholm , Brigham and Women's Hospital
# Peter Savadjiev , Brigham and Women's Hospital
# Andreas Schuh , University of Pennsylvania
# Mark Scully , University of Iowa
# Gregory Sharp , MGH
# Yundi Shi , UNC-Chapel Hill
# Nadya Shusharina , MGH
# Ramesh Sridharan , MIT CSAIL
# Hao Su , WPI
# Suarez Tamekue , Brigham and Women's Hospital
# Xiaodong Tao , GE Research
# Clement Vachet , UNC Chapel Hill
# Antonio Vega , Brigham and Women's Hospital
# Gopal Veni , University of Utah
# Bo Wang , University of Utah
# Demian Wasserman , Brigham and Women's Hospital
# Sandy Wells , Brigham and Women's Hospital
# Jason White , Brigham and Women's Hospital
# Atsushi Yamada , Brigham and Women's Hospital
# Alexander Yarmarkovich , Isomics
# Alexander Zaitsev , Brigham and Women's Hospital

2011 Summer Project Week FetchMI: Slicer integration with XNAT

2011-06-14T16:02:13Z

Mmilch: /* Key Investigators */

==Key Investigators==
* Harvard Medical School: Wendy Plesniak
* Washington University: Misha Milchenko

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

<h3>Objective</h3>

#:Produce a working code for exchanging MRML scenes with XNAT via REST API

</div>

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

<h3>Approach, Plan</h3>
#:Reviewing new Misha's code for XNAT client in FetchMI classes;
#:Compiling, running and testing against XNAT Sandbox;
#:Refining the development plan;
#:User testing.

</div>

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

<h3>Progress</h3>



</div>
</div>

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

==References==
XNAT REST API [http://docs.xnat.org/XNAT+REST+API+Usage]<br>
[[2011_Winter_Project_Week:FetchMIAPI]]

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a built-in Slicer module (FetchMI).

2011 Summer Project Week FetchMI: Slicer integration with XNAT

2011-06-14T16:01:54Z

Mmilch: /* Key Investigators */

==Key Investigators==
* Harvard Medical School: Wendy Plesniak
* Washington University: Misha Milchenko

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

<h3>Objective</h3>

#:Produce a working code for exchanging MRML scenes with XNAT via REST API

</div>

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

<h3>Approach, Plan</h3>
#:Reviewing new Misha's code for XNAT client in FetchMI classes;
#:Compiling, running and testing against XNAT Sandbox;
#:Refining the development plan;
#:User testing;

</div>

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

<h3>Progress</h3>



</div>
</div>

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

==References==
XNAT REST API [http://docs.xnat.org/XNAT+REST+API+Usage]<br>
[[2011_Winter_Project_Week:FetchMIAPI]]

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a built-in Slicer module (FetchMI).

2011 Summer Project Week FetchMI: Slicer integration with XNAT

2011-06-14T16:01:29Z

Mmilch: /* Key Investigators */

==Key Investigators==
* Harvard Medical School: Wendy Plesniak
* Washington University: Misha Milchenko

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

<h3>Objective</h3>

#:Produce a working code for exchanging MRML scenes with XNAT via REST API

</div>

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

<h3>Approach, Plan</h3>
#:Reviewing new Misha's code for XNAT client in FetchMI classes.<br>
#:Compiling, running and testing against XNAT Sandbox.<br>
#:Refining the development plan<br>
#:User testing<br>

</div>

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

<h3>Progress</h3>



</div>
</div>

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

==References==
XNAT REST API [http://docs.xnat.org/XNAT+REST+API+Usage]<br>
[[2011_Winter_Project_Week:FetchMIAPI]]

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a built-in Slicer module (FetchMI).

2011 Summer Project Week FetchMI: Slicer integration with XNAT

2011-06-14T15:59:39Z

Mmilch: /* Delivery Mechanism */

==Key Investigators==
* Harvard Medical School: Wendy Plesniak
* Washington University: Misha Milchenko

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

<h3>Objective</h3>

#:Produce a working code for exchanging MRML scenes with XNAT via REST API

</div>

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

<h3>Approach, Plan</h3>
#:Reviewing new Misha's code for XNAT client in FetchMI classes.
#:Compiling, running and testing against XNAT Sandbox.
#:Refining the development plan
#:User testing

</div>

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

<h3>Progress</h3>



</div>
</div>

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

==References==
XNAT REST API [http://docs.xnat.org/XNAT+REST+API+Usage]<br>
[[2011_Winter_Project_Week:FetchMIAPI]]

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a built-in Slicer module (FetchMI).

2011 Summer Project Week FetchMI: Slicer integration with XNAT

2011-06-14T15:58:49Z

Mmilch: /* References */

==Key Investigators==
* Harvard Medical School: Wendy Plesniak
* Washington University: Misha Milchenko

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

<h3>Objective</h3>

#:Produce a working code for exchanging MRML scenes with XNAT via REST API

</div>

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

<h3>Approach, Plan</h3>
#:Reviewing new Misha's code for XNAT client in FetchMI classes.
#:Compiling, running and testing against XNAT Sandbox.
#:Refining the development plan
#:User testing

</div>

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

<h3>Progress</h3>



</div>
</div>

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

==References==
XNAT REST API [http://docs.xnat.org/XNAT+REST+API+Usage]<br>
[[2011_Winter_Project_Week:FetchMIAPI]]

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a

#NITRIC distribution
#Slicer Module
##Built-in:
##Extension -- commandline:
##Extension -- loadable:

2011 Summer Project Week FetchMI: Slicer integration with XNAT

2011-06-14T15:49:21Z

Mmilch: /* Key Investigators */

==Key Investigators==
* Harvard Medical School: Wendy Plesniak
* Washington University: Misha Milchenko

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

<h3>Objective</h3>

#:Produce a working code for exchanging MRML scenes with XNAT via REST API

</div>

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

<h3>Approach, Plan</h3>
#:Reviewing new Misha's code for XNAT client in FetchMI classes.
#:Compiling, running and testing against XNAT Sandbox.
#:Refining the development plan
#:User testing

</div>

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

<h3>Progress</h3>



</div>
</div>

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

==References==
D’Avila A, Scanavacca M, Sosa E, Riskin JN, Reddy VY. Pericardial anatomy for the Interventional Electrophysiologist. J Cardiovasc Electrophysiol 2003;14:422-430

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a

#NITRIC distribution
#Slicer Module
##Built-in:
##Extension -- commandline:
##Extension -- loadable:

2011 Summer Project Week FetchMI: Slicer integration with XNAT

2011-06-14T15:43:47Z

Mmilch: moved User:Mmilch to FetchMI: Slicer integration with XNAT

==Key Investigators==
* Harvard Medical School: Mohsen Mahvash

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

<h3>Objective</h3>

#:Segmentaion and 3d
#:reconstruction of pericardial sac
#: (a thin tissue layer that covers the heart)

</div>

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

<h3>Approach, Plan</h3>
#:Trying 3dslicer modules
#:for segmentation
#:and 3d reconstruction

</div>

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

<h3>Progress</h3>



</div>
</div>

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

==References==
D’Avila A, Scanavacca M, Sosa E, Riskin JN, Reddy VY. Pericardial anatomy for the Interventional Electrophysiologist. J Cardiovasc Electrophysiol 2003;14:422-430

==Delivery Mechanism==



This work will be delivered to the NAMIC Kit as a

#NITRIC distribution
#Slicer Module
##Built-in:
##Extension -- commandline:
##Extension -- loadable:

User:Mmilch

2011-06-14T15:43:47Z

Mmilch: moved User:Mmilch to FetchMI: Slicer integration with XNAT

#REDIRECT [[FetchMI: Slicer integration with XNAT]]

2011 Summer Project Week FetchMI: Slicer integration with XNAT

2011-06-14T15:36:17Z

Mmilch: Created page with '==Key Investigators== * Harvard Medical School: Mohsen Mahvash <div style="margin: 20px;"> <div style="width: 27%; float: left; padding-right: 3%;"> <h3>Objective</h3> #:Segm…'

2011 Winter Project Week:FetchMIAPI

2011-01-18T18:57:26Z

Mmilch: /* NOTES */

==Key Investigators==
* Wash U: Dan Marcus, Misha Milchenko

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

<h3>Objective</h3>
Recode the FetchMI interface to work with the XNAT 1.5 REST API

</div>

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

<h3>Approach, Plan</h3>
FetchMI was originally coded to work with the XNAT Desktop API which is now being updated to look like the XNAT 1.5 API. So updating FetchMI will allow Slicer to exchange data with both Desktop and Enterprise systems.

'''Short term plan:''' Implement for workflow for '''Slicer3.6''' like this:
* The user will go to the XNAT web interface to navigate to the data they want.
* They will download these data (probably DICOM) locally and load into Slicer.
* In Slicer, the user will construct a scene file and then upload that scene file to the XNAT through the FetchMI upload interface.
* Only scenes will be downloadable from XNATE into Slicer via FetchMI.
* Once a scene has been uploaded to XNAT, it will be accessible, along with all of the required data files, from FetchMI’s download interface.
* The scene files will be posted to the project-level resources and will need to have some basic slicer metadata added to the format and/or content tags to allow the (for short term) implicit filtering for .mrml files through the query interface.
* FetchMI's existing query interface will display *only* project tags for search to user initially (this eliminates the need to modify GUI to do hierarchical queries for short term) and will only look for files with format=MRML. So all Scenes will be uploaded at the project level, and will be searched at the project level.
* There may be a need to add additional tags as well.

'''Long term plan:'''
* All refined work will go into Slicer 4.
* And extensions to query, parsing, tagging, upload and download LOGIC to accommodate moving individual (non-mrml) datasets to the XNE repository.
* This will include substantial GUI revisions.</div>

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

<h3>Progress</h3>
The FetchMI code has been reviewed and relevant replacement code has been identified.

Classes to be added:
* vtkFetchMIWebServicesClientXNE <-- vtkFetchMIWebServicesClient (generates queries, performs queries, UL, DL, etc. via curl.) (is an existing vtkFetchMIWebServicesClientXND)
* vtkFetchMIParserXNE <-- vtkFetchMIParser (parsers server responses) (is an existing vtkFetchMIParserXND)
* vtkFetchMIWriterXNE <-- vtkFetchMIWriter (writes required XML for upload) (is an existing vtkFetchMIWriterXND)
* vtkMRMLXNEHandler <-- vtkMRMLHTTPHandler (both in RemoteIO Lib) (is an existing vtkMRMLXNDHandler)

Places in code to be touched (wendy can help with these):
* vtkMRMLFetchMINode
* vtkFetchMILogic
* vtkFetchMIServer
* vtkFetchMIServerCollection

</div>
</div>

==NOTES==
<b>QUERY</b>

1. Query for all projects:<br>
GET REST/projects/<br>
(returns a list of all accessible projects.)<br>
2. Query for all scenes in project proj1:<br>
GET REST/projects/proj1/resources/scenes/files<br>

<b>UPLOAD SCENE</b>

Conventions: test project will be named <i>proj1</i>; resource for all the scenes will be named <i>scenes</i>.

* suppose we have a scene file scene1.mrml
* create a unique catalog resource under projects/proj1/resources, (can be one or two REST calls, to ensure uniqueness, should be verified. Say the resource is labeled scene1_files.
* check whether the scene file with name scene1.mrml already exists:
GET REST/projects/proj1/resources/scenes/files/scene1.mrml
If yes, prompt the user to change the file name or overwrite.
* upload all parts of the scene1.mrml to scene1_files (supposing there are N files in the scene)
PUT REST/projects/proj1/resources/scene1_files/files/scene_file1.ext1
...
PUT REST/projects/proj1/resources/scene1_files/files/scene_fileN.extN
or
PUT REST/projects/proj1/resources/scene1_files/files/all_scene_files.zip?unzip=true
* put URI's for all the resources for the scene into the scene1.mrml:
http://xnatserver/projects/proj1/resources/scene1_files/files/file1.ext1 ... fileN.extN
* upload scene1.mrml
PUT /REST/projects/proj1/resources/scenes/files/scene1.mrml
* configure the format tag on resource and any other metadata we might want.

<b>DOWNLOAD SCENE</b>
* list all the scene files for a selected project:
GET /REST/projects/proj1/resources/scenes/files?format=xml
* let the user select the scene (scene1.mrml as in previous example) and then download it:
GET /REST/projects/proj1/resources/scenes/files/scene1.mrml
* Parse the scene file and download resources for this scene:
GET http://xnatserver/projects/proj1/resources/scene1_files/files/file1.ext1 ... fileN.extN

==References==

2011 Winter Project Week:FetchMIAPI

2011-01-18T18:57:11Z

Mmilch: /* NOTES */

==Key Investigators==
* Wash U: Dan Marcus, Misha Milchenko

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

<h3>Objective</h3>
Recode the FetchMI interface to work with the XNAT 1.5 REST API

</div>

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

<h3>Approach, Plan</h3>
FetchMI was originally coded to work with the XNAT Desktop API which is now being updated to look like the XNAT 1.5 API. So updating FetchMI will allow Slicer to exchange data with both Desktop and Enterprise systems.

'''Short term plan:''' Implement for workflow for '''Slicer3.6''' like this:
* The user will go to the XNAT web interface to navigate to the data they want.
* They will download these data (probably DICOM) locally and load into Slicer.
* In Slicer, the user will construct a scene file and then upload that scene file to the XNAT through the FetchMI upload interface.
* Only scenes will be downloadable from XNATE into Slicer via FetchMI.
* Once a scene has been uploaded to XNAT, it will be accessible, along with all of the required data files, from FetchMI’s download interface.
* The scene files will be posted to the project-level resources and will need to have some basic slicer metadata added to the format and/or content tags to allow the (for short term) implicit filtering for .mrml files through the query interface.
* FetchMI's existing query interface will display *only* project tags for search to user initially (this eliminates the need to modify GUI to do hierarchical queries for short term) and will only look for files with format=MRML. So all Scenes will be uploaded at the project level, and will be searched at the project level.
* There may be a need to add additional tags as well.

'''Long term plan:'''
* All refined work will go into Slicer 4.
* And extensions to query, parsing, tagging, upload and download LOGIC to accommodate moving individual (non-mrml) datasets to the XNE repository.
* This will include substantial GUI revisions.</div>

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

<h3>Progress</h3>
The FetchMI code has been reviewed and relevant replacement code has been identified.

Classes to be added:
* vtkFetchMIWebServicesClientXNE <-- vtkFetchMIWebServicesClient (generates queries, performs queries, UL, DL, etc. via curl.) (is an existing vtkFetchMIWebServicesClientXND)
* vtkFetchMIParserXNE <-- vtkFetchMIParser (parsers server responses) (is an existing vtkFetchMIParserXND)
* vtkFetchMIWriterXNE <-- vtkFetchMIWriter (writes required XML for upload) (is an existing vtkFetchMIWriterXND)
* vtkMRMLXNEHandler <-- vtkMRMLHTTPHandler (both in RemoteIO Lib) (is an existing vtkMRMLXNDHandler)

Places in code to be touched (wendy can help with these):
* vtkMRMLFetchMINode
* vtkFetchMILogic
* vtkFetchMIServer
* vtkFetchMIServerCollection

</div>
</div>

==NOTES==
<b>QUERY</b>

1. Query for all projects:<br>
GET REST/projects/<br>
(returns a list of all accessible projects.)
2. Query for all scenes in project proj1:<br>
GET REST/projects/proj1/resources/scenes/files<br>

<b>UPLOAD SCENE</b>

Conventions: test project will be named <i>proj1</i>; resource for all the scenes will be named <i>scenes</i>.

* suppose we have a scene file scene1.mrml
* create a unique catalog resource under projects/proj1/resources, (can be one or two REST calls, to ensure uniqueness, should be verified. Say the resource is labeled scene1_files.
* check whether the scene file with name scene1.mrml already exists:
GET REST/projects/proj1/resources/scenes/files/scene1.mrml
If yes, prompt the user to change the file name or overwrite.
* upload all parts of the scene1.mrml to scene1_files (supposing there are N files in the scene)
PUT REST/projects/proj1/resources/scene1_files/files/scene_file1.ext1
...
PUT REST/projects/proj1/resources/scene1_files/files/scene_fileN.extN
or
PUT REST/projects/proj1/resources/scene1_files/files/all_scene_files.zip?unzip=true
* put URI's for all the resources for the scene into the scene1.mrml:
http://xnatserver/projects/proj1/resources/scene1_files/files/file1.ext1 ... fileN.extN
* upload scene1.mrml
PUT /REST/projects/proj1/resources/scenes/files/scene1.mrml
* configure the format tag on resource and any other metadata we might want.

<b>DOWNLOAD SCENE</b>
* list all the scene files for a selected project:
GET /REST/projects/proj1/resources/scenes/files?format=xml
* let the user select the scene (scene1.mrml as in previous example) and then download it:
GET /REST/projects/proj1/resources/scenes/files/scene1.mrml
* Parse the scene file and download resources for this scene:
GET http://xnatserver/projects/proj1/resources/scene1_files/files/file1.ext1 ... fileN.extN

==References==

2011 Winter Project Week:FetchMIAPI

2011-01-18T18:56:29Z

Mmilch: /* NOTES */

==Key Investigators==
* Wash U: Dan Marcus, Misha Milchenko

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

<h3>Objective</h3>
Recode the FetchMI interface to work with the XNAT 1.5 REST API

</div>

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

<h3>Approach, Plan</h3>
FetchMI was originally coded to work with the XNAT Desktop API which is now being updated to look like the XNAT 1.5 API. So updating FetchMI will allow Slicer to exchange data with both Desktop and Enterprise systems.

'''Short term plan:''' Implement for workflow for '''Slicer3.6''' like this:
* The user will go to the XNAT web interface to navigate to the data they want.
* They will download these data (probably DICOM) locally and load into Slicer.
* In Slicer, the user will construct a scene file and then upload that scene file to the XNAT through the FetchMI upload interface.
* Only scenes will be downloadable from XNATE into Slicer via FetchMI.
* Once a scene has been uploaded to XNAT, it will be accessible, along with all of the required data files, from FetchMI’s download interface.
* The scene files will be posted to the project-level resources and will need to have some basic slicer metadata added to the format and/or content tags to allow the (for short term) implicit filtering for .mrml files through the query interface.
* FetchMI's existing query interface will display *only* project tags for search to user initially (this eliminates the need to modify GUI to do hierarchical queries for short term) and will only look for files with format=MRML. So all Scenes will be uploaded at the project level, and will be searched at the project level.
* There may be a need to add additional tags as well.

'''Long term plan:'''
* All refined work will go into Slicer 4.
* And extensions to query, parsing, tagging, upload and download LOGIC to accommodate moving individual (non-mrml) datasets to the XNE repository.
* This will include substantial GUI revisions.</div>

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

<h3>Progress</h3>
The FetchMI code has been reviewed and relevant replacement code has been identified.

Classes to be added:
* vtkFetchMIWebServicesClientXNE <-- vtkFetchMIWebServicesClient (generates queries, performs queries, UL, DL, etc. via curl.) (is an existing vtkFetchMIWebServicesClientXND)
* vtkFetchMIParserXNE <-- vtkFetchMIParser (parsers server responses) (is an existing vtkFetchMIParserXND)
* vtkFetchMIWriterXNE <-- vtkFetchMIWriter (writes required XML for upload) (is an existing vtkFetchMIWriterXND)
* vtkMRMLXNEHandler <-- vtkMRMLHTTPHandler (both in RemoteIO Lib) (is an existing vtkMRMLXNDHandler)

Places in code to be touched (wendy can help with these):
* vtkMRMLFetchMINode
* vtkFetchMILogic
* vtkFetchMIServer
* vtkFetchMIServerCollection

</div>
</div>

==NOTES==
<b>QUERY</b>

1. Query for all projects:
GET REST/projects/
(returns a list of all accessible projects.)
2. Query for all scenes in project proj1:
GET REST/projects/proj1/resources/scenes/files

<b>UPLOAD SCENE</b>

Conventions: test project will be named <i>proj1</i>; resource for all the scenes will be named <i>scenes</i>.

* suppose we have a scene file scene1.mrml
* create a unique catalog resource under projects/proj1/resources, (can be one or two REST calls, to ensure uniqueness, should be verified. Say the resource is labeled scene1_files.
* check whether the scene file with name scene1.mrml already exists:
GET REST/projects/proj1/resources/scenes/files/scene1.mrml
If yes, prompt the user to change the file name or overwrite.
* upload all parts of the scene1.mrml to scene1_files (supposing there are N files in the scene)
PUT REST/projects/proj1/resources/scene1_files/files/scene_file1.ext1
...
PUT REST/projects/proj1/resources/scene1_files/files/scene_fileN.extN
or
PUT REST/projects/proj1/resources/scene1_files/files/all_scene_files.zip?unzip=true
* put URI's for all the resources for the scene into the scene1.mrml:
http://xnatserver/projects/proj1/resources/scene1_files/files/file1.ext1 ... fileN.extN
* upload scene1.mrml
PUT /REST/projects/proj1/resources/scenes/files/scene1.mrml
* configure the format tag on resource and any other metadata we might want.

<b>DOWNLOAD SCENE</b>
* list all the scene files for a selected project:
GET /REST/projects/proj1/resources/scenes/files?format=xml
* let the user select the scene (scene1.mrml as in previous example) and then download it:
GET /REST/projects/proj1/resources/scenes/files/scene1.mrml
* Parse the scene file and download resources for this scene:
GET http://xnatserver/projects/proj1/resources/scene1_files/files/file1.ext1 ... fileN.extN

==References==

2011 Winter Project Week:FetchMIAPI

2011-01-18T15:24:13Z

Mmilch: /* NOTES */

==Key Investigators==
* Wash U: Dan Marcus, Misha Milchenko

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

<h3>Objective</h3>
Recode the FetchMI interface to work with the XNAT 1.5 REST API

</div>

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

<h3>Approach, Plan</h3>
FetchMI was originally coded to work with the XNAT Desktop API which is now being updated to look like the XNAT 1.5 API. So updating FetchMI will allow Slicer to exchange data with both Desktop and Enterprise systems.

'''Short term plan:''' Implement for workflow for '''Slicer3.6''' like this:
* The user will go to the XNAT web interface to navigate to the data they want.
* They will download these data (probably DICOM) locally and load into Slicer.
* In Slicer, the user will construct a scene file and then upload that scene file to the XNAT through the FetchMI upload interface.
* Only scenes will be downloadable from XNATE into Slicer via FetchMI.
* Once a scene has been uploaded to XNAT, it will be accessible, along with all of the required data files, from FetchMI’s download interface.
* The scene files will be posted to the project-level resources and will need to have some basic slicer metadata added to the format and/or content tags to allow the (for short term) implicit filtering for .mrml files through the query interface.
* FetchMI's existing query interface will display *only* project tags for search to user initially (this eliminates the need to modify GUI to do hierarchical queries for short term) and will only look for files with format=MRML. So all Scenes will be uploaded at the project level, and will be searched at the project level.
* There may be a need to add additional tags as well.

'''Long term plan:'''
* All refined work will go into Slicer 4.
* And extensions to query, parsing, tagging, upload and download LOGIC to accommodate moving individual (non-mrml) datasets to the XNE repository.
* This will include substantial GUI revisions.</div>

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

<h3>Progress</h3>
The FetchMI code has been reviewed and relevant replacement code has been identified.

Classes to be added:
* vtkFetchMIWebServicesClientXNE <-- vtkFetchMIWebServicesClient (generates queries, performs queries, UL, DL, etc. via curl.) (is an existing vtkFetchMIWebServicesClientXND)
* vtkFetchMIParserXNE <-- vtkFetchMIParser (parsers server responses) (is an existing vtkFetchMIParserXND)
* vtkFetchMIWriterXNE <-- vtkFetchMIWriter (writes required XML for upload) (is an existing vtkFetchMIWriterXND)
* vtkMRMLXNEHandler <-- vtkMRMLHTTPHandler (both in RemoteIO Lib) (is an existing vtkMRMLXNDHandler)

Places in code to be touched (wendy can help with these):
* vtkMRMLFetchMINode
* vtkFetchMILogic
* vtkFetchMIServer
* vtkFetchMIServerCollection

</div>
</div>

==NOTES==
<b>UPLOAD SCENE</b>

Conventions: test project will be named <i>proj1</i>; resource for all the scenes will be named <i>scenes</i>.

* suppose we have a scene file scene1.mrml
* create a unique catalog resource under projects/proj1/resources, (can be one or two REST calls, to ensure uniqueness, should be verified. Say the resource is labeled scene1_files.
* check whether the scene file with name scene1.mrml already exists:
GET REST/projects/proj1/resources/scenes/files/scene1.mrml
If yes, prompt the user to change the file name or overwrite.
* upload all parts of the scene1.mrml to scene1_files (supposing there are N files in the scene)
PUT REST/projects/proj1/resources/scene1_files/files/scene_file1.ext1
...
PUT REST/projects/proj1/resources/scene1_files/files/scene_fileN.extN
or
PUT REST/projects/proj1/resources/scene1_files/files/all_scene_files.zip?unzip=true
* put URI's for all the resources for the scene into the scene1.mrml:
http://xnatserver/projects/proj1/resources/scene1_files/files/file1.ext1 ... fileN.extN
* upload scene1.mrml
PUT /REST/projects/proj1/resources/scenes/files/scene1.mrml
* configure the format tag on resource and any other metadata we might want.

<b>DOWNLOAD SCENE</b>
* list all the scene files for a selected project:
GET /REST/projects/proj1/resources/scenes/files?format=xml
* let the user select the scene (scene1.mrml as in previous example) and then download it:
GET /REST/projects/proj1/resources/scenes/files/scene1.mrml
* Parse the scene file and download resources for this scene:
GET http://xnatserver/projects/proj1/resources/scene1_files/files/file1.ext1 ... fileN.extN

==References==

2011 Winter Project Week:FetchMIAPI

2011-01-12T18:45:35Z

Mmilch: /* NOTES */

==Key Investigators==
* Wash U: Dan Marcus, Misha Milchenko

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

<h3>Objective</h3>
Recode the FetchMI interface to work with the XNAT 1.5 REST API

</div>

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

<h3>Approach, Plan</h3>
FetchMI was originally coded to work with the XNAT Desktop API which is now being updated to look like the XNAT 1.5 API. So updating FetchMI will allow Slicer to exchange data with both Desktop and Enterprise systems.

'''Short term plan:''' Implement for workflow for '''Slicer3.6''' like this:
* The user will go to the XNAT web interface to navigate to the data they want.
* They will download these data (probably DICOM) locally and load into Slicer.
* In Slicer, the user will construct a scene file and then upload that scene file to the XNAT through the FetchMI upload interface.
* Only scenes will be downloadable from XNATE into Slicer via FetchMI.
* Once a scene has been uploaded to XNAT, it will be accessible, along with all of the required data files, from FetchMI’s download interface.
* The scene files will be posted to the project-level resources and will need to have some basic slicer metadata added to the format and/or content tags to allow the (for short term) implicit filtering for .mrml files through the query interface.
* FetchMI's existing query interface will display *only* project tags for search to user initially (this eliminates the need to modify GUI to do hierarchical queries for short term) and will only look for files with format=MRML. So all Scenes will be uploaded at the project level, and will be searched at the project level.
* There may be a need to add additional tags as well.

'''Long term plan:'''
* All refined work will go into Slicer 4.
* And extensions to query, parsing, tagging, upload and download LOGIC to accommodate moving individual (non-mrml) datasets to the XNE repository.
* This will include substantial GUI revisions.</div>

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

<h3>Progress</h3>
The FetchMI code has been reviewed and relevant replacement code has been identified.

Classes to be added:
* vtkFetchMIWebServicesClientXNE <-- vtkFetchMIWebServicesClient (generates queries, performs queries, UL, DL, etc. via curl.) (is an existing vtkFetchMIWebServicesClientXND)
* vtkFetchMIParserXNE <-- vtkFetchMIParser (parsers server responses) (is an existing vtkFetchMIParserXND)
* vtkFetchMIWriterXNE <-- vtkFetchMIWriter (writes required XML for upload) (is an existing vtkFetchMIWriterXND)
* vtkMRMLXNEHandler <-- vtkMRMLHTTPHandler (both in RemoteIO Lib) (is an existing vtkMRMLXNDHandler)

Places in code to be touched:
* vtkMRMLFetchMINode
* vtkFetchMILogic

</div>
</div>

==NOTES==
<b>UPLOAD SCENE</b>
Conventions: test project will be named <i>proj1</i>; resource for all the scenes will be named <i>scenes</i>.

* suppose we have a scene file scene1.mrml
* create a unique catalog resource under projects/proj1/resources, (can be one or two REST calls, to ensure uniqueness, should be verified. Say the resource is labeled scene1_files.
* check whether the scene file with name scene1.mrml already exists:
GET REST/projects/proj1/resources/scenes/files/scene1.mrml
If yes, prompt the user to change the file name or overwrite.
* upload all parts of the scene1.mrml to scene1_files (supposing there are N files in the scene)
PUT REST/projects/proj1/resources/scene1_files/files/scene_file1.ext1
...
PUT REST/projects/proj1/resources/scene1_files/files/scene_fileN.extN
or
PUT REST/projects/proj1/resources/scene1_files/files/all_scene_files.zip?unzip=true
* put URI's for all the resources for the scene into the scene1.mrml:
http://xnatserver/projects/proj1/resources/scene1_files/files/file1.ext1 ... fileN.extN
* upload scene1.mrml
PUT /REST/projects/proj1/resources/scenes/files/scene1.mrml
* configure the format tag on resource and any other metadata we might want.

<b>DOWNLOAD SCENE</b>
* list all the scene files for a selected project:
GET /REST/projects/proj1/resources/scenes/files?format=xml
* let the user select the scene (scene1.mrml as in previous example) and then download it:
GET /REST/projects/proj1/resources/scenes/files/scene1.mrml
* Parse the scene file and download resources for this scene:
GET http://xnatserver/projects/proj1/resources/scene1_files/files/file1.ext1 ... fileN.extN

==References==

2011 Winter Project Week:FetchMIAPI

2011-01-12T18:35:58Z

Mmilch: /* NOTES */

==Key Investigators==
* Wash U: Dan Marcus, Misha Milchenko

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

<h3>Objective</h3>
Recode the FetchMI interface to work with the XNAT 1.5 REST API

</div>

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

<h3>Approach, Plan</h3>
FetchMI was originally coded to work with the XNAT Desktop API which is now being updated to look like the XNAT 1.5 API. So updating FetchMI will allow Slicer to exchange data with both Desktop and Enterprise systems.

'''Short term plan:''' Implement for workflow for '''Slicer3.6''' like this:
* The user will go to the XNAT web interface to navigate to the data they want.
* They will download these data (probably DICOM) locally and load into Slicer.
* In Slicer, the user will construct a scene file and then upload that scene file to the XNAT through the FetchMI upload interface.
* Only scenes will be downloadable from XNATE into Slicer via FetchMI.
* Once a scene has been uploaded to XNAT, it will be accessible, along with all of the required data files, from FetchMI’s download interface.
* The scene files will be posted to the project-level resources and will need to have some basic slicer metadata added to the format and/or content tags to allow the (for short term) implicit filtering for .mrml files through the query interface.
* FetchMI's existing query interface will display *only* project tags for search to user initially (this eliminates the need to modify GUI to do hierarchical queries for short term) and will only look for files with format=MRML. So all Scenes will be uploaded at the project level, and will be searched at the project level.
* There may be a need to add additional tags as well.

'''Long term plan:'''
* All refined work will go into Slicer 4.
* And extensions to query, parsing, tagging, upload and download LOGIC to accommodate moving individual (non-mrml) datasets to the XNE repository.
* This will include substantial GUI revisions.</div>

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

<h3>Progress</h3>
The FetchMI code has been reviewed and relevant replacement code has been identified.

Classes to be added:
* vtkFetchMIWebServicesClientXNE <-- vtkFetchMIWebServicesClient (generates queries, performs queries, UL, DL, etc. via curl.) (is an existing vtkFetchMIWebServicesClientXND)
* vtkFetchMIParserXNE <-- vtkFetchMIParser (parsers server responses) (is an existing vtkFetchMIParserXND)
* vtkFetchMIWriterXNE <-- vtkFetchMIWriter (writes required XML for upload) (is an existing vtkFetchMIWriterXND)
* vtkMRMLXNEHandler <-- vtkMRMLHTTPHandler (both in RemoteIO Lib) (is an existing vtkMRMLXNDHandler)

Places in code to be touched:
* vtkMRMLFetchMINode
* vtkFetchMILogic

</div>
</div>

==NOTES==
<b>UPLOAD SCENE</b>
Conventions: test project will be named <i>proj1</i>; resource for all the scenes will be named <i>scenes</i>.

* suppose we have a scene file scene1.mrml
* create a unique catalog resource under projects/proj1/resources, (can be one or two REST calls, to ensure uniqueness, should be verified. Say the resource is labeled scene1_files.
* check whether the scene file with name scene1.mrml already exists:
GET REST/projects/proj1/resources/scenes/scene1.mrml
If yes, prompt the user to change the file name or overwrite.
* upload all parts of the scene1.mrml to scene1_files (supposing there are N files in the scene)
PUT REST/projects/proj1/resources/scene1_files/scene_file1.ext1
...
PUT REST/projects/proj1/resources/scene1_files/scene_fileN.extN
or
PUT REST/projects/proj1/resources/scene1_files/all_scene_files.zip?unzip=true
* put URI's for all the resources for the scene into the scene1.mrml:
http://xnatserver/projects/proj1/resources/scene1_files/file1.ext1 ... fileN.extN
* upload scene1.mrml
PUT /REST/projects/proj1/resources/scenes/scene1.mrml
* configure the format tag on resource and any other metadata we might want.

<b>DOWNLOAD SCENE</b>
* list all the scene files for a selected project:
GET /REST/projects/proj1/resources/scenes?format=xml
* let the user select the scene (scene1.mrml as in previous example) and then download it:
GET /REST/projects/proj1/resources/scenes/scene1.mrml
* Parse the scene file and download resources for this scene:
GET http://xnatserver/projects/proj1/resources/scene1_files/file1.ext1 ... fileN.extN

==References==

2011 Winter Project Week:FetchMIAPI

2011-01-12T18:33:17Z

Mmilch: /* NOTES */

==Key Investigators==
* Wash U: Dan Marcus, Misha Milchenko

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

<h3>Objective</h3>
Recode the FetchMI interface to work with the XNAT 1.5 REST API

</div>

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

<h3>Approach, Plan</h3>
FetchMI was originally coded to work with the XNAT Desktop API which is now being updated to look like the XNAT 1.5 API. So updating FetchMI will allow Slicer to exchange data with both Desktop and Enterprise systems.

'''Short term plan:''' Implement for workflow for '''Slicer3.6''' like this:
* The user will go to the XNAT web interface to navigate to the data they want.
* They will download these data (probably DICOM) locally and load into Slicer.
* In Slicer, the user will construct a scene file and then upload that scene file to the XNAT through the FetchMI upload interface.
* Only scenes will be downloadable from XNATE into Slicer via FetchMI.
* Once a scene has been uploaded to XNAT, it will be accessible, along with all of the required data files, from FetchMI’s download interface.
* The scene files will be posted to the project-level resources and will need to have some basic slicer metadata added to the format and/or content tags to allow the (for short term) implicit filtering for .mrml files through the query interface.
* FetchMI's existing query interface will display *only* project tags for search to user initially (this eliminates the need to modify GUI to do hierarchical queries for short term) and will only look for files with format=MRML. So all Scenes will be uploaded at the project level, and will be searched at the project level.
* There may be a need to add additional tags as well.

'''Long term plan:'''
* All refined work will go into Slicer 4.
* And extensions to query, parsing, tagging, upload and download LOGIC to accommodate moving individual (non-mrml) datasets to the XNE repository.
* This will include substantial GUI revisions.</div>

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

<h3>Progress</h3>
The FetchMI code has been reviewed and relevant replacement code has been identified.

Classes to be added:
* vtkFetchMIWebServicesClientXNE <-- vtkFetchMIWebServicesClient (generates queries, performs queries, UL, DL, etc. via curl.) (is an existing vtkFetchMIWebServicesClientXND)
* vtkFetchMIParserXNE <-- vtkFetchMIParser (parsers server responses) (is an existing vtkFetchMIParserXND)
* vtkFetchMIWriterXNE <-- vtkFetchMIWriter (writes required XML for upload) (is an existing vtkFetchMIWriterXND)
* vtkMRMLXNEHandler <-- vtkMRMLHTTPHandler (both in RemoteIO Lib) (is an existing vtkMRMLXNDHandler)

Places in code to be touched:
* vtkMRMLFetchMINode
* vtkFetchMILogic

</div>
</div>

==NOTES==
UPLOAD SCENE
Conventions: test project will be named <b>proj1</b>; resource for all the scenes will be named <b>scenes</b>.

* suppose we have a scene file scene1.mrml
* create a unique catalog resource under projects/proj1/resources, (can be one or two REST calls, to ensure uniqueness, should be verified. Say the resource is labeled scene1_files.
* check whether the scene file with name scene1.mrml already exists:
GET REST/projects/proj1/resources/scenes/scene1.mrml
If yes, prompt the user to change the file name or overwrite.
* upload all parts of the scene1.mrml to scene1_files (supposing there are N files in the scene)
PUT REST/projects/proj1/resources/scene1_files/scene_file1.ext1
...
PUT REST/projects/proj1/resources/scene1_files/scene_fileN.extN
or
PUT REST/projects/proj1/resources/scene1_files/all_scene_files.zip?unzip=true
* put URI's for all the resources for the scene into the scene1.mrml:
http://xnatserver/projects/proj1/resources/scene1_files/file1.ext1 ... fileN.extN
* upload scene1.mrml
PUT /REST/projects/proj1/resources/scenes/scene1.mrml
* configure the format tag on resource and any other metadata we might want.

DOWNLOAD SCENE
* list all the scene files for a selected project:
GET /REST/projects/proj1/resources/scenes?format=xml
* let the user select the scene (scene1.mrml as in previous example) and then download it:
GET /REST/projects/proj1/resources/scenes/scene1.mrml
* Parse the scene file and download resources for this scene:
GET http://xnatserver/projects/proj1/resources/scene1_files/file1.ext1 ... fileN.extN

==References==

2011 Winter Project Week:FetchMIAPI

2011-01-12T18:26:29Z

Mmilch: /* NOTES */

==Key Investigators==
* Wash U: Dan Marcus, Misha Milchenko

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

<h3>Objective</h3>
Recode the FetchMI interface to work with the XNAT 1.5 REST API

</div>

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

<h3>Approach, Plan</h3>
FetchMI was originally coded to work with the XNAT Desktop API which is now being updated to look like the XNAT 1.5 API. So updating FetchMI will allow Slicer to exchange data with both Desktop and Enterprise systems.

'''Short term plan:''' Implement for workflow for '''Slicer3.6''' like this:
* The user will go to the XNAT web interface to navigate to the data they want.
* They will download these data (probably DICOM) locally and load into Slicer.
* In Slicer, the user will construct a scene file and then upload that scene file to the XNAT through the FetchMI upload interface.
* Only scenes will be downloadable from XNATE into Slicer via FetchMI.
* Once a scene has been uploaded to XNAT, it will be accessible, along with all of the required data files, from FetchMI’s download interface.
* The scene files will be posted to the project-level resources and will need to have some basic slicer metadata added to the format and/or content tags to allow the (for short term) implicit filtering for .mrml files through the query interface.
* FetchMI's existing query interface will display *only* project tags for search to user initially (this eliminates the need to modify GUI to do hierarchical queries for short term) and will only look for files with format=MRML. So all Scenes will be uploaded at the project level, and will be searched at the project level.
* There may be a need to add additional tags as well.

'''Long term plan:'''
* All refined work will go into Slicer 4.
* And extensions to query, parsing, tagging, upload and download LOGIC to accommodate moving individual (non-mrml) datasets to the XNE repository.
* This will include substantial GUI revisions.</div>

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

<h3>Progress</h3>
The FetchMI code has been reviewed and relevant replacement code has been identified.

Classes to be added:
* vtkFetchMIWebServicesClientXNE <-- vtkFetchMIWebServicesClient (generates queries, performs queries, UL, DL, etc. via curl.) (is an existing vtkFetchMIWebServicesClientXND)
* vtkFetchMIParserXNE <-- vtkFetchMIParser (parsers server responses) (is an existing vtkFetchMIParserXND)
* vtkFetchMIWriterXNE <-- vtkFetchMIWriter (writes required XML for upload) (is an existing vtkFetchMIWriterXND)
* vtkMRMLXNEHandler <-- vtkMRMLHTTPHandler (both in RemoteIO Lib) (is an existing vtkMRMLXNDHandler)

Places in code to be touched:
* vtkMRMLFetchMINode
* vtkFetchMILogic

</div>
</div>

==NOTES==
upload scene.

Notation: test project will be named <b>proj1</b>; resource for all the scenes will be named <b>scenes</b>.

* suppose we have a scene file scene1.mrml
* create a unique catalog resource under projects/proj1/resources, (can be one or two REST calls, to ensure uniqueness, should be verified. Say the resource is labeled scene1_files.
* check whether the scene file with name scene1.mrml already exists:
GET REST/projects/proj1/resources/scenes/scene1.mrml
If yes, prompt the user to change the file name or overwrite.
* upload all parts of the scene1.mrml to scene1_files
PUT REST/projects/proj1/resources/scene1_files/all_scene_files.zip?unzip=true
* put URI's for all the resources for the scene into the scene1.mrml:
http://xnatserver/projects/proj1/resources/scene1_files/file1.ext1 ... fileN.extN
* upload scene1.mrml
PUT /REST/projects/proj1/resources/scenes/scene1.mrml
* configure the format tag on resource and any other metadata we might want.

==References==

Events:August2008XNATDesktop

2008-08-22T18:38:18Z

Mmilch: /* TO-DO items for XND side */

Plans for the Integration of XNAT desktop and Slicer
=Visit of XNAT team to Boston=
*Tentative Date: August 21-22nd
*Location: 1249 Boylston Street, 2nd floor demo room [http://www.spl.harvard.edu/pages/Directions#Getting_to_1249_Boylston_Street. Directions to 1249 Boylston]
*Agenda/Goals
** Attempt to get base use case worked through
*** upload files to XND
*** query for them
*** download them as a group
*** modify them in slicer
*** re-upload new files with tags
** Thursday 10am Eastern discussion with Dan Blezek about intersection with XCEDE web services implementation.
** Thursday 11pm Eastern XND Demo and discussion of local use case (C-F, Johanna, Monika)

** XND User Interface Review with Wendy
* People: Misha, Kevin, Wendy, Nicole, Steve, Ron (Thursday)

== Plan for supporting initial use case ==

[[image:NeurosurgeryUsecase.png ]]

Step1. Subject is scanned and data is pushed to a networked disk (and referenced by a PACS system) automatically.

Step2. Researcher1 uses an XND client (on a laptop or a desktop system) to mark up subject data and to upload it (via drag and drop) to the central XND repository xnd.bwh.harvard.edu.

Step3. Researcher2 opens slicer and queries XND webservices on svr = http://xnd.bwh.harvard.edu:8081 for a list of subjects.

Query for all subjects on system...
'''send:''' curl GET $srv/search??subject
'''response:''' xml for all subjects in xnd.bwh.harvard.edu

Choose a subject, query for available data...
'''send:''' curl GET $srv/search?subject=$subj
'''response:''' xml containing URIs of all resources for the individual subject $subj

Slicer parses XML and presents list of all resources; researcher2 queries for for only DICOM data for a particular subject...
'''send:''' curl GET $srv/search?subject=$subj&fileType=DICOM
'''response:''' xml containing URIs of all DICOM resources for subject $subj

Slicer parses XML and presents list of URIs, researcher2 requests to download uris of interest...
'''send:''' curl GET $uri
'''response:

Step4. Completed neurosurgical planning analysis and upload results.

Create metadatadocument (XML) for individual data file, or for scene + selected data. First, post each dataset, and assemble MRML file using returned uris. Then, post or put mrml file.
'''send:''' curl -T POST contentType= .... (please flesh this out!)
'''response:''' uri of posted file (xml or just uri?)
'''send:''' curl -T PUT with filename?
'''response:''' (?)

Step5. In IGT, download scene for patient (subject) into slicer.

Query for a subject and query for available scene files...
'''send:''' curl GET $srv/search?subject=$subj&fileType=MRML
'''response:''' xml containing URIs of all MRML files

Slicer parses XML and presents list of MRML files, and clinican selects one with $uri.
'''send:''' curl GET $uri
'''response:''' (?)

Clinician cuts link to remote repository.

== TO-DO items for XND side==
* Send example metadata XML file (and script that writes it?) to Slicer dev.
* Provide some info on webservices API as it develops
* Add credentialing on XND before a server is set up in a public place (consistent with XNAT E)
* Establish public (read-only?) access to source code of XND web services and visual client, in version control system;
* command-line server style version of file server repository
* command-line script for using XND rules for importing data in XND database?
* turn on multiple remote repositories in the client interface, and more convenient/automated upload/download with XND client
* More automated way to manage directories with changing content, and options for routing to other repositories
* Client interface usability improvements (as suggested by Wendy)

== TO-DO items for Slicer side==
* download data from XND to slicer
** Done, from localhost
* put data to XND from Slicer
** Working on slicer "Publish to XND" test
* post data to XND from Slicer
** Work on slicer "Post to XND" test
* better integrate remote/local load&save options in Slicer.

== Questions ==
* vision for XNAT enterprise and XNAT desktop (longterm, how do they relate, how tightly are they coupled, and what should we use and when?)

== Questions ==
* not sure how to regard XND (and or versus) XNATenterprise with our use cases -- where to focus development on Slicer & XNATenterprise, or Slicer & XND, etc. We would like to develop a clean implementation that meets our basic use cases, and that scales reasonably well.

=== Other Topics ===

Misha to meet with Bernhard about deidentification algorithms for full body CT scans.

=Use-case scenarios=
==Use scenario 0: (things about some external examples we like)==
<gallery perrow="2" widths="640px" heights="400px">
Image:Osirix_with_thumbnails.png| The available images are displayed as small icons with annotation. User drags images to the display port.
Image:DICOMViewer_Layouts.png| Available date is displayed in an hierarchical text and icon representation
</gallery>

==Use Scenario 1: fluid use of XND with Slicer ==
*I am using Slicer on my laptop and would like to use XNAT desktop to keep data organized on my hard disk
Capabilities needed
**how to set up when I download slicer?
**I am upgrading Slicer do I need to upgrade xnat as well?
**I worked today on a case. I would like to add my derived data and new mrml file to the existing stuff.
**I would like to upload stuff that is currently in Slicer
**I would like to download a mrml file and all associated data files.

== Use scenario 3: saving MRML files to hosted repository ==

[http://www.slicer.org/slicerWiki/index.php/Slicer3:XCEDE_use_cases#Slicer_use-case_.230:_Demo_we_would_like_to_show_for_BIRN described here] (similar to above).

=== notes ===
* StoreXAR doesn't currently have the functionality in the the use case described (getting xnat's uri back once a file is uploaded).
* Tim's suggested workaround for now: separately request a catalog of all files for a given session id. This is similar to what would be returned by StoreXAR as described in the use case.
* [http://central.xnat.org/archive/catalogs/xnat:imageSessionData/BC_CT_TOR_1_1 log into central.xnat.org and click this link to see catalog]
* There's not currently a commandline executable -- we will have to write this.
* The HTTP Session ID needs to be attached to the HTTP Request.
* what if a MRML scene contains data from multiple subjects, or multiple experiments, or multiple projects? How to upload this?

(Link to XNAT Desktop [http://www.slicer.org/slicerWiki/index.php/Slicer3:XND tutorial] for Slicer.)

= some design & usability stuff: =

[[media:XNAT.doc | word doc with XND and some xnat central design notes]]

=technical questions:=

* What are preferred ways to access web services – such as e.g. shell scripts calling cURL, some preferred C++ web client, Python or Java programs?
* What are requirements for XNAT File Repository web services security model?
* What would be a typical workload for various types of queries to XND (XNAT Desktop) repository - including seach, file put and file get?
* Currently, XNAT Desktop supports single file manipulation. Should it, (and if it should, then to what extent?) support treating a set of files as a single 'bundle' (for instance, "MRML file and all associated files")? What criteria should it support to automatically identify a set of files as belonging to one bundle?
* Will XNAT Desktop have to use Slicer ontology for basic tags (Project, Subject, Experiment, Scan) or will Slicer adopt, to some extent, XNAT ontology? (XNAT ontology is required to be used by Desktop when interacting with hosted XNAT Enterprise server).

=Advantage Windows experience=

=Reference=
http://slicer.spl.harvard.edu/slicerWiki/index.php/Slicer3:XCEDE_use_cases#XCEDE_REST_Interface

=Comments from Misha=
from Aug 18 2008
==What do we have to show, from the time of last demo:==
*XNAT File repository server supporting newly developed file repository REST-style Web Services, and (finally) integrated with client-server visual interface (XNAT Desktop a.k.a. XND).
*Kevin will demonstrate types of queries currently supported by Web Services, File Repository database structure and provide detail on requirements for development of Web Services clients;
*Within this scope, I can also demonstrate ontology generation approaches used by XND (which were mentioned before, DICOM rule and
regular expression rule) - most importantly, these rules are used to generate XNAT ontology from arbitrary hierarchy of files and folders.
*Go over the upload to XNAT Central, using last release of XND visual interface with improved upload capability.

==Points of discussion==
*We’d like to see a detailed use case for the Slicer integration, so that we could go over missing pieces in more detail. Some of the missing/unclear pieces are listed below, but it will be crucial to have a list of possible pitfalls, as complete as possible.
*Typical use of XNAT File Repository: will it be used as a local repository for Slicer projects, a hosted research data archive, a remote/back-up/secondary repository for cross-institutional data sharing, anything else?
*Prefedded way of accessing web services – such as e.g. shell scripts calling cURL, some preferred C++ web client, Python or Java programs – to test against most probable client platforms.
*Scaling: anticipated density of Web Services requests of each type (i.e. various types of search (file search, metadata search), file put / file get), from a typical Slicer client;
*Resource access control (resource-based) / session based user authentication model, other sequrity issues? Preferred security model (or at least requirements to the security model)?
*Use scenarios for XND client: standalone tool for tagging data and transferring between centralized repository and/or local users; PACS worklist-like interface for navigating DICOM data/launching viewing tools for clinical radiologists; anything else?
*Most desired features of the XND client: metadata organization/control, search/filtering features, interface organization from user perspective
*Support for Slicer ontologies, ontology conversion, ontology migration issues which will arise as soon as existing data archive will need to be converted to XNAT file repository;
*other suggestions/critiques/clarifications?

Events:August2008XNATDesktop

2008-08-18T21:10:19Z

Mmilch: /* notes: */