NAMIC Wiki - User contributions [en]

2013 Project Week:WebbasedAnatomicalTeachingFrameworkSummer2013

2013-06-17T15:31:02Z

Haehn: /* Project Description */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:PediBrainAtlas.jpg|Screenshot of the prototype
</gallery>

==Key Investigators==

* Daniel Haehn, Nicolas Rannou, Rudolph Pienaar, Ellen Grant (Boston Children's Hospital)
* Steve Pieper (Isomics Inc.)
* Randy Gollub, Lilla Zollei, Nathaniel Reynolds (MGH)

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Over the last several years, an [[CTSC:ARRA_supplement | infrastructure has been developed to integrate health records and PACS image archives]] to support research on large collections of data collected during delivery of healthcare (as contrasted with data collected as part of clinical trials). This resulted in the availability of [http://www.mi2b2.org the mi2b2 system]. An application enabled by this technology is supported by an [http://projectreporter.nih.gov/project_info_description.cfm?aid=8272742&icde=13552329&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC R01 to use clinical scans of children aged zero to six years old to build a teaching atlas].
* One goal of the [http://www.mi2b2.org mi2b2] collaborative effort is to create a web-based teaching tool for fetal and neonatal anatomy as well as a browser for quantified information. A basic prototype has been created: [http://fnndsc.github.io/babybrain/ http://fnndsc.github.io/babybrain/]. The purpose of this project is to construct a 4D MRI dataset as a concatenation of multiple 3D MRI datasets (pediatric MRI scans at different stages of development), and to develop the functionality within [https://github.com/xtk/X#readme XTK] to visualize and navigate this 4D dataset in a web browser.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
Right now, the multiple volumes of the training data get loaded one-by-one on demand. We want to load either everything at the beginning (maybe from a 4D dataset or separate 3D ones) or leverage webworkers to load the rest odf the data in the background while the user interacts with the page.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* A prototype was created: http://fnndsc.github.com/babybrain

</div>
</div>

== Draft Development Plans ==

=== Phase I: Developer Mockups ===
During the first half of 2013:
* ...

=== Phase II: Limited Beta ===
During second half of 2013:
* ...

=== Phase III: Authoring Tools ===
During 2014:
* ...

2013 Project Week:WebbasedAnatomicalTeachingFrameworkSummer2013

2013-06-17T15:29:41Z

Haehn: /* Project Description */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:PediBrainAtlas.jpg|Screenshot of the prototype
</gallery>

==Key Investigators==

* Daniel Haehn, Nicolas Rannou, Rudolph Pienaar, Ellen Grant (Boston Children's Hospital)
* Steve Pieper (Isomics Inc.)
* Randy Gollub, Lilla Zollei, Nathaniel Reynolds (MGH)

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Over the last several years, an [[CTSC:ARRA_supplement | infrastructure has been developed to integrate health records and PACS image archives]] to support research on large collections of data collected during delivery of healthcare (as contrasted with data collected as part of clinical trials). This resulted in the availability of [http://www.mi2b2.org the mi2b2 system]. An application enabled by this technology is supported by an [http://projectreporter.nih.gov/project_info_description.cfm?aid=8272742&icde=13552329&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC R01 to use clinical scans of children aged zero to six years old to build a teaching atlas].
* One goal of the [http://www.mi2b2.org mi2b2] collaborative effort is to create a web-based teaching tool for fetal and neonatal anatomy as well as a browser for quantified information. A basic prototype has been created: [http://fnndsc.github.io/babybrain/ http://fnndsc.github.io/babybrain/]. The purpose of this project is to construct a 4D MRI dataset as a concatenation of multiple 3D MRI datasets (pediatric MRI scans at different stages of development), and to develop the functionality within [https://github.com/xtk/X#readme XTK] to visualize and navigate this 4D dataset in a web browser.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
We propose the following steps to create a high-level didactic content creation tool.
* ...
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* A prototype was created: http://fnndsc.github.com/babybrain

</div>
</div>

== Draft Development Plans ==

=== Phase I: Developer Mockups ===
During the first half of 2013:
* ...

=== Phase II: Limited Beta ===
During second half of 2013:
* ...

=== Phase III: Authoring Tools ===
During 2014:
* ...

2013 Project Week:WebbasedAnatomicalTeachingFrameworkSummer2013

2013-06-17T15:29:07Z

Haehn:

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:PediBrainAtlas.jpg|Screenshot of the prototype
</gallery>

==Key Investigators==

* Daniel Haehn, Nicolas Rannou, Rudolph Pienaar, Ellen Grant (Boston Children's Hospital)
* Steve Pieper (Isomics Inc.)
* Randy Gollub, Lilla Zollei, Nathaniel Reynolds (MGH)

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Over the last several years, an [[CTSC:ARRA_supplement | infrastructure has been developed to integrate health records and PACS image archives]] to support research on large collections of data collected during delivery of healthcare (as contrasted with data collected as part of clinical trials). This resulted in the availability of [http://www.mi2b2.org the mi2b2 system]. An application enabled by this technology is supported by an [http://projectreporter.nih.gov/project_info_description.cfm?aid=8272742&icde=13552329&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC R01 to use clinical scans of children aged zero to six years old to build a teaching atlas].
* One goal of the [http://www.mi2b2.org mi2b2] collaborative effort is to create a web-based teaching tool for fetal and neonatal anatomy as well as a browser for quantified information. A basic prototype has been created: [http://fnndsc.github.io/babybrain/ http://fnndsc.github.io/babybrain/]. The purpose of this project is to construct a 4D MRI dataset as a concatenation of multiple 3D MRI datasets (pediatric MRI scans at different stages of development), and to develop the functionality within [https://github.com/xtk/X#readme XTK] to visualize and navigate this 4D dataset in a web browser.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
We propose the following steps to create a high-level didactic content creation tool.
* ...
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* ...

</div>
</div>

== Draft Development Plans ==

=== Phase I: Developer Mockups ===
During the first half of 2013:
* ...

=== Phase II: Limited Beta ===
During second half of 2013:
* ...

=== Phase III: Authoring Tools ===
During 2014:
* ...

2013 Summer Project Week

2013-06-17T15:28:52Z

Haehn: /* Additional Collaborations */

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

Dates: June 17-21, 2013.

Location: MIT, Cambridge, MA.

==Agenda==

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

== '''Projects''' ==

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

==Some Stats==
68 Projects, 95 Attendees. First time attendees? 5+ time attendees?

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

===Traumatic Brain Injury===
* [[Visualization and quantification of peri-contusional white matter bundles in traumatic brain injury using diffusion tensor imaging]] (Andrei Irimia, Micah Chambers, Ron Kikinis, Jack van Horn)
* [[Clinically oriented assessment of local changes in the properties of white matter affected by intra-cranial hemorrhage]] (Andrei Irimia, Micah Chambers, Ron Kikinis, Jack van Horn)
* [[Validation and testing of 3D Slicer modules implementing the Utah segmentation algorithm for traumatic brain injury]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Guido Gerig, Jack van Horn)
* [[Exploring multi-modal registration for improved longitudinal modeling of patient-specific 4D DTI data]] (Anuja Sharma, Bo Wang, Andrei Irimia, Micah Chambers, Guido Gerig, Jack van Horn)
* [[2013_Summer_Project_Week: A Portable Ultrasound Device for Intracranial Hemorrhage Detection|A Portable Ultrasound Device for Intracranial Hemorrhage Detection]] (Jason White, Vicki Noble, Kirby Vosburgh)

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

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

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

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

=== '''Additional Collaborations'''===
* [[2013_Summer_Project_Week:Radnostics |Spine Segmentation & Osteoporosis Detection In CT Imaging Studies]] (Anthony Blumfield, Ron Kikinis)
* [[2013_Summer_Project_Week: Computer Assisted Surgery| Computer Assisted Reconstruction of Complex Bone Fractures]] (Karl Fritscher, Peter Karasev, Ivan Kolesov, Allen Tannenbaum, Ron Kikinis)
* [[2013_Summer_Project_Week:XNAT 3D Viewer| XNAT 3D Viewer]] (Amanda Hartung, Steve Pieper, Daniel Haehn)
* [[2013_Summer_Project_Week:kukarobot| Interface for the integration of a KUKA robot using OpenIGTLink]] (Sebastian Tauscher, Thomas Neff, Junichi Tokuda, Nobuhiko Hata)
* [[2013_Summer_Project_Week:Application of Statistical Shape Modeling to Robot Assisted Spine Surgery | Application of Statistical Shape Modeling to Robot Assisted Spine Surgery]] (Marine Clogenson)
* [[2013_Summer_Project_Week:Robot_Control| Robot Control]] (A.Vilchis, J-C. Avila-Vilchis, S.Pujol)
* [[2013_Summer_Project_Week:Epilepsy_Surgery|Identification of MRI Blurring in Temporal Lobe Epilepsy Surgery]] (Luiz Murta)
* [[2013_Summer_Project_Week:_Is_Neurosurgical_Rigid_Registration_Really_Rigid%3F| Is Neurosurgical Rigid Registration Really Rigid?]] (Athena)
* [[2013_Summer_Project_Week: Individualized Neuroimaging Content Analysis using 3D Slicer in Alzheimer's Disease| Individualized Neuroimaging Content Analysis using 3D Slicer]] (Sidong Liu, Weidong Cai, Sonia Pujol, Ron Kikinis)
* [[2013_Summer_Project_Week:CMFReg | Cranio-Maxillofacial Registration]] (Vinicius Boen)
* [[2013_Summer_Project_Week:DTIPipelineExtensions | DTI Analysis Pipeline as Slicer4 Extensions]] (Francois Budin)
*[[2013_Project_Week:WebbasedAnatomicalTeachingFrameworkSummer2013|Web-based anatomical teaching framework]] (Nathaniel Reynolds, Daniel Haehn, Nicolas Rannou, Steve Pieper, Rudolph Pienaar, Lilla Zollei)
* [[2013_Summer_Project_Week:Biomedical_Image_Computing_Teaching_Modules|3D Slicer based Biomedical image computing teaching modules]] (A. Vilchis, J-C. Avila-Vilchis, S. Pujol)
* [[2013_Summer_Project_Week:Analyzing Breast Tumor Heterogeneity Using 3D Slicer|Analyzing Breast Tumor Heterogeneity Using 3D Slicer]] (Sneha Durgapal, Jayender Jagadeesan, Tobias Penzkofer, Vivek Narayan)
* [[2013_Summer_Project_Week:WMH Segmentation for Stroke|WMH Segmentation for Stroke]] (Adrian Dalca, Ramesh Sridharan, Polina Golland)
* [[2013_Summer_Project_Week:WMQL Integration in Slicer|White Matter Query Language (WMQL) Integration in Slicer]] (Demian Wassermann, Carl-Fredrik Westin)

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

== '''Background''' ==

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

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

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

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

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

== '''Logistics''' ==

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

== '''Preparation''' ==

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

== '''Registrants''' ==

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

#Parth Amin, WIT, aminp@wit.edu
#Charles Anderson, BWH, canderson26@partners.org
#Peter Anderson, retired, traneus@verizon.net
#Nicole Aucoin, BWH, nicole@bwh.harvard.edu
#Juan Carlos Avila Vilchis, Univ del Estado de Mexico, jc.avila.vilchis@hotmail.com
#Salma Bengali, Univ UT, salma.bengali@carma.utah.edu
#Anthony Blumfield, Radnostics, Anthony.Blumfield@Radnostics.com
#Vinicius Boen, Univ Michigan, vboen@umich.edu
#Matthew Brennan, MIT, brennanm@mit.edu
#Francois Budin, NIRAL-UNC, fbudin@unc.edu
#Ivan Buzurovic, BWH/HMS, ibuzurovic@lroc.harvard.edu
#Josh Cates, Univ UT, cates@sci.utah.edu
#Micah Chambers, UCLA, micahcc@ucla.edu
#Laurent Chauvin, BWH - SPL, lchauvin@bwh.harvard.edu
#Marine Clogenson, Ecole Polytechnique Federale de Lausanne (Switzerland), marine.clogenson@epfl.ch
#Adrian Dalca, MIT, adalca@MIT.EDU
#Matthew D'Artista, BWH - SPL, mdartista7@gmail.com
#Manasi Datar, Univ UT-SCI Institute, datar@sci.utah.edu
#Sneha Durgapal, BWH, durgapalsneha@gmail.com
#Luping Fang, Zhejiang Univ of Technology (China), flp@zjut.edu.cn
#Andriy Fedorov, BWH, fedorov@bwh.harvard.edu
#Jean-Christophe Fillion-Robin, Kitware, jchris.fillionr@kitware.com
#Gregory Fischer, WPI, gfischer@wpi.edu
#Barton Fiske, zSpace Inc, bfiske@zspace.com
#Matthew Flynn, WIT, flynnm3@wit.edu
#Karl Fritscher, MGH, kfritscher@gmail.com
#Yi Gao, Univ AL Birmingham, gaoyi.cn@gmail.com
#Maria Gonzalez-Puente, WIT, gonzalezpuentem@wit.edu
#Daniel Haehn, Boston Childrens Hospital, daniel.haehn@childrens.harvard.edu
#Michael Halle, BWH-SPL, mhalle@bwh.harvard.edu
#Rola Harmouche, BWH, rharmo@bwh.harvard.edu
#Amanda Hartung, Rochester Inst of Tech, amh1646@rit.edu
#Nobuhiko Hata, BWH, hata@bwh.harvard.edu
#Nicholas Herlambang, AZE Technology Inc, nicholas.herlambang@azetech.com
#Matthew Holden, Queen's Univ (Canada), mholden8@cs.queensu.ca
#Andrei Irimia, UCLA, andrei.irimia@loni.ucla.edu
#Jayender Jagadeesan, BWH-SPL, jayender@bwh.harvard.edu
#Hans Johnson, Univ Iowa, hans-johnson@uiowa.edu
#Tina Kapur, BWH/HMS, tkapur@bwh.harvard.edu
#Alex Kikinis, BWH, alexkikinis@gmail.com
#Ron Kikinis, HMS, kikinis@bwh.harvard.edu
#Nils Klarlund, IEEE, klarlund@ieee.org
#Daniel Kostro, BWH, dkostro@bwh.harvard.edu
#Andras Lasso, Queen's Univ (Canada), lasso@cs.queensu.ca
#Rui Li, GE Global Research, li.rui@ge.com
#Xu Li, BWH, lixu0103@gmail.com
#Lichen Liang, MGH, lichenl@nmr.mgh.harvard.edu
#Sidong Liu, Univ Sydney (Australia), sliu7418@uni.sydney.edu.au
#William Lorensen, Bill's Basement, bill.lorensen@gmail.com
#Bradley Lowekamp, Medical Science & Computing Inc, bradley.lowekamp@nih.gov
#Athena Lyons, Univ Western Australia, 20359511@student.uwa.edu.au
#Nikos Makris, MGH, nikos@nmr.mgh.harvard.edu
#Katie Mastrogiacomo, BWH - SPL, kmast@bwh.harvard.edu
#Alireza Mehrtash, BWH - SPL, mehrtash@bwh.harvard.edu
#Hans Meine, Fraunhofer MEVIS (Germany), hans.meine@mevis.fraunhofer.de
#Jim Miller, GE Global Research, millerjv@ge.com
#Luis Murta, Univ Sao Paulo (Brazil), lomurta@gmail.com
#Arie Nakhmani, Univ AL Birmingham, anry@uab.edu
#Isaiah Norton, BWH, inorton@bwh.harvard.edu
#Lauren O'Donnell, BWH, odonnell@bwh.harvard.edu
#Dirk Padfield, GE Global Research, padfield@research.ge.com
#Jian Pan, Zhejiang Univ of Technology (China), pj@zjut.edu.cn
#George Papadimitriou, MGH, georgep@nmr.mgh.harvard.edu
#Tobias Penzkofer, BWH - SPL, pt@bwh.harvard.edu
#Rudolph Pienaar, Boston Childrens Hospital, Rudolph.Pienaar@childrens.harvard.edu
#Steve Pieper, Isomics Inc, pieper@isomics.com
#Csaba Pinter, Queen's Univ (Canada), pinter@cs.queensu.ca
#Sonia Pujol, HMS, spujol@bwh.harvard.edu
#Adam Rankin, Queen's Univ (Canada), rankin@cs.queensu.ca
#Nathaniel Reynolds, MGH, reynolds@nmr.mgh.harvard.edu
#Raul San Jose, BWH, rjosest@bwh.harvard.edu
#Peter Savadjiev, BWH, petersv@bwh.harvard.edu
#Anuja Sharma, Univ UT-SCI Institute, anuja@cs.utah.edu
#Greg Sharp, MGH, gcsharp@partners.org
#Nadya Shusharina, MGH, nshusharina@partners.org
#Sebastian Tauscher, Leibniz Univ Hannover (Germany), sebastian.tauscher@imes.uni-hannover.de
#Clare Tempany, BWH, ctempanyafdhal@partners.org
#Cyrill von Tiesenhausen, KUKA Laboratories (Germany), cyrill.tiesenhausen@kuka.com
#Gaurie Tilak, BWH, gaurie_tilak@hms.harvard.edu
#Matthew Toews, BWH/HMS, mt@bwh.harvard.edu
#Junichi Tokuda, BWH, tokuda@bwh.harvard.edu
#Tamas Ungi, Queen's Univ (Canada), ungi@cs.queensu.ca
#Adriana Vilchis González, Univ del Estado de Mexico, hvigady@hotmail.com
#Kirby Vosburgh, BWH, kirby@bwh.harvard.edu
#Christian Wachinger, MIT, wachinge@mit.edu
#Bo Wang, Univ UT-SCI Institute, bowang@sci.utah.edu
#Demian Wassermann, BWH, demian@bwh.harvard.edu
#David Welch, Univ Iowa, david-welch@uiowa.edu
#William Wells, BWH/HMS, sw@bwh.harvard.edu
#Phillip White, BWH/HMS, white@bwh.harvard.edu
#Alex Yarmarkovich, Isomics Inc, alexy@bwh.harvard.edu
#Kitaro Yoshimitsu, BWH, kitarof1@bwh.harvard.edu
#Yang Yu, Rutgers Univ, yyu@cs.rutgers.edu
#Paolo Zaffino, Univ Magna Graecia of Catanzaro (Italy), p.zaffino@unicz.it
#Lilla Zollei, MGH, lzollei@nmr.mgh.harvard.edu

Imaging in Neuroscience

2013-04-04T17:59:34Z

Haehn: /* Course Materials */

The 3D Slicer software platform will be presented as part of the Harvard Catalyst course "Advanced Imaging: Imaging in Neuroscience" course organized by Dr. Randy Gollub

==Course Faculty==
*Junichi Tokuda, Brigham and Women's Hospital, Harvard Medical School (Presenter)
*Nicole Aucoin, Brigham and Women's Hospital, Harvard Medical School
*Sonia Pujol, Brigham and Women's Hospital, Harvard Medical School
*Randy L. Gollub, Massachusetts General Hospital, Harvard Medical School
*P. Ellen Grant, Boston Children's Hospital, Harvard Medical School
*Daniel Haehn, Boston Children's Hospital, Harvard Medical School
*Nicolas Rannou, Boston Children's Hospital, Harvard Medical School
*Nathaniel A Reynolds, Massachusetts General Hospital, Harvard Medical School

==Course Logistics==
Date: April 8, 2013, 11:30-12:00
Location: Sheraton Commander Hotel, Boston, MA

==Agenda==
*11:30-12:00: The 3D Slicer open-source platform for image analysis and 3D visualization of medical image data (lecture)
*12:00-1:00: Slicer4 minute tutorial (hands-on session) and Diffusion tractography (demo)

[[Media:ImagingInNeuroscience_April8-3DSlicer_SoniaPujol.pdf | 3D Slicer course - Imaging in Neuroscience]]

== Course Materials ==
In preparation for the hands-on session, please download the 3D Slicer version 4.2.1 and the Slicer4 minute datasets.

[http://download.slicer.org 3D Slicer 4.x]

[http://www.slicer.org/slicerWiki/index.php/File:Slicer4minute.zip Slicer4minute dataset (hands-on)]

[[media:Dti.zip |DTI dataset (demo)]]

Additional materials for learning more about 3D Slicer are available on the Slicer 101 page.

User:Haehn

2013-03-14T14:31:18Z

Haehn: /* Daniel Haehn's Page */

== Daniel Haehn's Page ==

{| class="wikitable" style="text-align:left; width:90%; height:200px"
|- style="height:20px"
! Info ||
|- style="vertical-align:top"
|'''Daniel Haehn'''

http://danielhaehn.com

|| <center>[[Image:haehn.jpg]]</center>
|}

=== VMTK in 3D Slicer ===

The Vascular Modeling Toolkit ([http://vmtk.org VMTK]) is a collection of libraries and tools for 3D reconstruction, geometric analysis, mesh generation and surface data analysis for image-based modeling of blood vessels. It should be very interesting to offer such techniques in 3D Slicer.

The official project page:
http://www.vmtk.org/Main/VmtkIn3DSlicer

More recent news on this project: <br>

http://www.na-mic.org/Wiki/index.php/2009_Winter_Project_Week_Slicer_VMTK<br>
http://www.na-mic.org/Wiki/index.php/Summer2009:The_Vascular_Modeling_Toolkit_in_3D_Slicer<br>
http://www.na-mic.org/Wiki/index.php/2010_Winter_Project_Week_The_Vascular_Modeling_Toolkit_in_3D_Slicer
http://www.na-mic.org/Wiki/index.php/2010_Summer_Project_Week/The_Vascular_Modeling_Toolkit_in_3D_Slicer
http://www.na-mic.org/Wiki/index.php/2011_Winter_Project_Week:The_Vascular_Modeling_Toolkit_in_3D_Slicer
http://www.na-mic.org/Wiki/index.php/2011_Winter_Project_Week:StenosisDetector

This work is done in conjunction with Luca Antiga (Medical Imaging Unit, Bioengineering Department, Mario Negri Institute, Bergamo, Italy).

==== VMKT in Slicer4 ====

The VMTK integration in 3D Slicer will be transitioned to Slicer4.

Some developer notes:
<pre>
# clone the fork
git clone git@github.com:haehn/vmtk.git

# check the status
git status

# switch to branch superbuild
git checkout superbuild

# include upstream by editing .git/config
# 17 [remote "upstream"]
# 18 url = https://github.com/lantiga/vmtk.git
# 19 fetch = +refs/heads/*:refs/remotes/upstream/*

# get the upstream
git fetch upstream

# merge the latest changes to local
git merge upstream/superbuild

# push the latest changes from upstream to fork
git push

</pre>

Now, somebody forked the repo, made some changes we want in the master:

<pre>
# add the remote repo
git remote add jcfr https://github.com/jcfr/EMSegment4.git

# fetch it
git fetch jcfr

# see diff
git log -p master jcfr/master

# now merge the remote with our master
git merge jcfr/master
Updating f5d1b39..dd72623
error: Your local changes to 'CMakeLists.txt' would be overwritten by merge. Aborting.
Please, commit your changes or stash them before you can merge.

# let's revert our local changes
git checkout CMakeLists.txt

# merge again
git merge jcfr/master

# and push it to the master
git push
</pre>

<pre>
# use cherry-pick to merge a commit from another branch into the current branch
git cherry-pick COMMITHASH

# now push
git push
</pre>

=== Images ===
{|
|[[File:Becky.png|thumb|400px]]||[[File:Becky2.png|thumb|400px]]||[[File:Beck3.png|thumb|400px]]
|}

2013 Project Week:WebbasedAnatomicalTeachingFramework

2013-01-11T00:22:29Z

Haehn:

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:Mi2b2_1.png|Screenshot of the prototype
Image:Mi2b2_2.png|Screenshot of the prototype
</gallery>

==Key Investigators==

* Daniel Haehn, Rudolph Pienaar, Ellen Grant (Boston Children's Hospital)
* Steve Pieper (Isomics Inc.)
* Sonia Pujol (BWH)
* Randy Gollub (MGH)

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Over the last several years, an [[CTSC:ARRA_supplement | infrastructure has been developed to integrate health records and PACS image archives]] to support research on large collections of data collected during delivery of healthcare (as contrasted with data collected as part of clinical trials). This resulted in the availability of [http://www.mi2b2.org the mi2b2 system]. An application enabled by this technology is supported by an [http://projectreporter.nih.gov/project_info_description.cfm?aid=8272742&icde=13552329&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC R01 to use clinical scans of children aged zero to six years old to build a teaching atlas].
* One goal of the [http://www.mi2b2.org mi2b2] collaborative effort is to create a web-based teaching tool for fetal and neonatal anatomy as well as a browser for quantified information. The goal of this project is to create a prototype application for this purpose which can be easily extended to other testing scenarios.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
We propose the following steps to create a high-level didactic content creation tool.
* Enable switching between different testing scenarios (fetal brains, liver etc.)
* Start with the existing [http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/Training#Slicer4_3D_Visualization_of_DICOM_images_for_Radiology_Applications Liver tutorial dataset and slides] from the NA-MIC training core which includes a limited number of questions and answers
* Load a visual scene linked to a question catalog from a defined file format (XML?)
* The visualization and the questions are linked so answers can be provided in a fully interactive fashion (picking of a 3D mesh.. etc.)
* Track user-specified answers and provide statistics after testing mode
* Use 3D Slicer to generate content for training and testing
* Prototype will be built on top of existing visualization infrastructure ([http://goXTK.com XTK] and [http://fetalmri.org web-based fetal atlas tool])
* We envision a system somewhat like existing online quiz systems ([http://www.surveymonkey.com], [http://www.classmarker.com/], [http://dontshake.org/lms/lms_information/lms_quiz.php], [http://www.proprofs.com/quiz-school/]) but with interactive 3D content drawn from the clinical use cases.
* May use a helper library like [https://github.com/jewlofthelotus/SlickQuiz SlickQuiz] [http://www.jewlofthelotus.com/2011/12/23/slickquiz-jquery-plugin-now-on-github/comment-page-1/]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* User interface mockups are being prepared
* Development repository: https://github.com/FNNDSC/mi2b2_aim3
* Problems/ToDo:
** <strike>Update WebGLExport module to new XTK version</strike>
** <strike>Fix XTK with Liver CT volume (right now scalar range messes things up) or convert (normalize) the volume</strike>
* First working prototype is online!
** http://fnndsc.github.com/mi2b2_aim3/

</div>
</div>

== Draft Development Plans ==

=== Phase I: Developer Mockups ===
During the first half of 2013:
* Hand-coded (html, javascript) mockups using to create content from existing content
** Liver tutorial from Sonia
** Fetal brain atlas
* Identify best practices and experiment with different Question and Answer modes
* Identify best practices and experiment with user interaction
* Getting feedback on mi2b2 team and refining the mockups

=== Phase II: Limited Beta ===
During second half of 2013:
* Identify first set of training content suitable for wider trial
* Set up a site to host training materials
** Set up back end system to record test results?
** Review [http://en.wikipedia.org/wiki/Redcap_(Research_Electronic_Data_Capture) RedCap] as a back end ([http://www.project-redcap.org/ home page], [https://redcap.vanderbilt.edu/surveys/index.php?hash=40008b9a5380fcacce3976bf7c08af5b example survey)]
** Consider tie-in to RSNA Audience Response Tool
* Open site to radiology trainees and gather feedback
* Integrate infant brain atlas data as it becomes available

=== Phase III: Authoring Tools ===
During 2014:
* Develop system for clinician-educators to easily create content
** Define images, models, annotations, atlases to display
** Define didactic material
** Export content to hosting site
* Leverage tools like Scene Views and WebGL Export from Slicer

File:Mi2b2 2.png

2013-01-11T00:21:34Z

Haehn:

File:Mi2b2 1.png

2013-01-11T00:20:45Z

Haehn:

2013 Project Week:WebbasedAnatomicalTeachingFramework

2013-01-08T21:40:53Z

Haehn: /* Project Description */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

* Daniel Haehn, Rudolph Pienaar, Ellen Grant (Boston Children's Hospital)
* Steve Pieper (Isomics Inc.)
* Sonia Pujol (BWH)
* Randy Gollub (MGH)

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Over the last several years, an [[CTSC:ARRA_supplement | infrastructure has been developed to integrate health records and PACS image archives]] to support research on large collections of data collected during delivery of healthcare (as contrasted with data collected as part of clinical trials). This resulted in the availability of [http://www.mi2b2.org the mi2b2 system]. An application enabled by this technology is supported by an [http://projectreporter.nih.gov/project_info_description.cfm?aid=8272742&icde=13552329&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC R01 to use clinical scans of children aged zero to six years old to build a teaching atlas].
* One goal of the [http://www.mi2b2.org mi2b2] collaborative effort is to create a web-based teaching tool for fetal and neonatal anatomy as well as a browser for quantified information. The goal of this project is to create a prototype application for this purpose which can be easily extended to other testing scenarios.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
We propose the following steps to create a high-level didactic content creation tool.
* Enable switching between different testing scenarios (fetal brains, liver etc.)
* Start with the existing [http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/Training#Slicer4_3D_Visualization_of_DICOM_images_for_Radiology_Applications Liver tutorial dataset and slides] from the NA-MIC training core which includes a limited number of questions and answers
* Load a visual scene linked to a question catalog from a defined file format (XML?)
* The visualization and the questions are linked so answers can be provided in a fully interactive fashion (picking of a 3D mesh.. etc.)
* Track user-specified answers and provide statistics after testing mode
* Use 3D Slicer to generate content for training and testing
* Prototype will be built on top of existing visualization infrastructure ([http://goXTK.com XTK] and [http://fetalmri.org web-based fetal atlas tool])
* We envision a system somewhat like existing online quiz systems ([http://www.surveymonkey.com], [http://www.classmarker.com/], [http://dontshake.org/lms/lms_information/lms_quiz.php], [http://www.proprofs.com/quiz-school/]) but with interactive 3D content drawn from the clinical use cases.
* May use a helper library like [https://github.com/jewlofthelotus/SlickQuiz SlickQuiz] [http://www.jewlofthelotus.com/2011/12/23/slickquiz-jquery-plugin-now-on-github/comment-page-1/]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* User interface mockups are being prepared
* Development repository: https://github.com/FNNDSC/mi2b2_aim3
* Problems/ToDo:
** <strike>Update WebGLExport module to new XTK version</strike>
** <strike>Fix XTK with Liver CT volume (right now scalar range messes things up) or convert (normalize) the volume</strike>
</div>
</div>

== Draft Development Plans ==

=== Phase I: Developer Mockups ===
During the first half of 2013:
* Hand-coded (html, javascript) mockups using to create content from existing content
** Liver tutorial from Sonia
** Fetal brain atlas
* Identify best practices and experiment with different Question and Answer modes
* Identify best practices and experiment with user interaction
* Getting feedback on mi2b2 team and refining the mockups

=== Phase II: Limited Beta ===
During second half of 2013:
* Identify first set of training content suitable for wider trial
* Set up a site to host training materials
** Set up back end system to record test results?
** Review [http://en.wikipedia.org/wiki/Redcap_(Research_Electronic_Data_Capture) RedCap] as a back end ([http://www.project-redcap.org/ home page], [https://redcap.vanderbilt.edu/surveys/index.php?hash=40008b9a5380fcacce3976bf7c08af5b example survey)]
** Consider tie-in to RSNA Audience Response Tool
* Open site to radiology trainees and gather feedback
* Integrate infant brain atlas data as it becomes available

=== Phase III: Authoring Tools ===
During 2014:
* Develop system for clinician-educators to easily create content
** Define images, models, annotations, atlases to display
** Define didactic material
** Export content to hosting site
* Leverage tools like Scene Views and WebGL Export from Slicer

2013 Project Week:WebbasedAnatomicalTeachingFramework

2013-01-08T13:54:25Z

Haehn: /* Project Description */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

* Daniel Haehn, Rudolph Pienaar, Ellen Grant (Boston Children's Hospital)
* Steve Pieper (Isomics Inc.)
* Sonia Pujol (BWH)
* Randy Gollub (MGH)

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Over the last several years, an [[CTSC:ARRA_supplement | infrastructure has been developed to integrate health records and PACS image archives]] to support research on large collections of data collected during delivery of healthcare (as contrasted with data collected as part of clinical trials). This resulted in the availability of [http://www.mi2b2.org the mi2b2 system]. An application enabled by this technology is supported by an [http://projectreporter.nih.gov/project_info_description.cfm?aid=8272742&icde=13552329&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC R01 to use clinical scans of children aged zero to six years old to build a teaching atlas].
* One goal of the [http://www.mi2b2.org mi2b2] collaborative effort is to create a web-based teaching tool for fetal and neonatal anatomy as well as a browser for quantified information. The goal of this project is to create a prototype application for this purpose which can be easily extended to other testing scenarios.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
We propose the following steps to create a high-level didactic content creation tool.
* Enable switching between different testing scenarios (fetal brains, liver etc.)
* Start with the existing [http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/Training#Slicer4_3D_Visualization_of_DICOM_images_for_Radiology_Applications Liver tutorial dataset and slides] from the NA-MIC training core which includes a limited number of questions and answers
* Load a visual scene linked to a question catalog from a defined file format (XML?)
* The visualization and the questions are linked so answers can be provided in a fully interactive fashion (picking of a 3D mesh.. etc.)
* Track user-specified answers and provide statistics after testing mode
* Use 3D Slicer to generate content for training and testing
* Prototype will be built on top of existing visualization infrastructure ([http://goXTK.com XTK] and [http://fetalmri.org web-based fetal atlas tool])
* We envision a system somewhat like existing online quiz systems ([http://www.surveymonkey.com], [http://www.classmarker.com/], [http://dontshake.org/lms/lms_information/lms_quiz.php], [http://www.proprofs.com/quiz-school/]) but with interactive 3D content drawn from the clinical use cases.
* May use a helper library like [https://github.com/jewlofthelotus/SlickQuiz SlickQuiz] [http://www.jewlofthelotus.com/2011/12/23/slickquiz-jquery-plugin-now-on-github/comment-page-1/]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* User interface mockups are being prepared
* Development repository: https://github.com/FNNDSC/mi2b2_aim3
* Problems/ToDo:
** Update WebGLExport module to new XTK version
** <strike>Fix XTK with Liver CT volume (right now scalar range messes things up) or convert (normalize) the volume</strike>
</div>
</div>

== Draft Development Plans ==

=== Phase I: Developer Mockups ===
During the first half of 2013:
* Hand-coded (html, javascript) mockups using to create content from existing content
** Liver tutorial from Sonia
** Fetal brain atlas
* Identify best practices and experiment with different Question and Answer modes
* Identify best practices and experiment with user interaction
* Getting feedback on mi2b2 team and refining the mockups

=== Phase II: Limited Beta ===
During second half of 2013:
* Identify first set of training content suitable for wider trial
* Set up a site to host training materials
** Set up back end system to record test results?
** Review [http://en.wikipedia.org/wiki/Redcap_(Research_Electronic_Data_Capture) RedCap] as a back end ([http://www.project-redcap.org/ home page], [https://redcap.vanderbilt.edu/surveys/index.php?hash=40008b9a5380fcacce3976bf7c08af5b example survey)]
** Consider tie-in to RSNA Audience Response Tool
* Open site to radiology trainees and gather feedback
* Integrate infant brain atlas data as it becomes available

=== Phase III: Authoring Tools ===
During 2014:
* Develop system for clinician-educators to easily create content
** Define images, models, annotations, atlases to display
** Define didactic material
** Export content to hosting site
* Leverage tools like Scene Views and WebGL Export from Slicer

2013 Project Week:WebbasedAnatomicalTeachingFramework

2013-01-07T23:20:20Z

Haehn: /* Project Description */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

* Daniel Haehn, Rudolph Pienaar, Ellen Grant (Boston Children's Hospital)
* Steve Pieper (Isomics Inc.)
* Sonia Pujol (BWH)
* Randy Gollub (MGH)

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Over the last several years, an [[CTSC:ARRA_supplement | infrastructure has been developed to integrate health records and PACS image archives]] to support research on large collections of data collected during delivery of healthcare (as contrasted with data collected as part of clinical trials). This resulted in the availability of [http://www.mi2b2.org the mi2b2 system]. An application enabled by this technology is supported by an [http://projectreporter.nih.gov/project_info_description.cfm?aid=8272742&icde=13552329&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC R01 to use clinical scans of children aged zero to six years old to build a teaching atlas].
* One goal of the [http://www.mi2b2.org mi2b2] collaborative effort is to create a web-based teaching tool for fetal and neonatal anatomy as well as a browser for quantified information. The goal of this project is to create a prototype application for this purpose which can be easily extended to other testing scenarios.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
We propose the following steps to create a high-level didactic content creation tool.
* Enable switching between different testing scenarios (fetal brains, liver etc.)
* Start with the existing [http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/Training#Slicer4_3D_Visualization_of_DICOM_images_for_Radiology_Applications Liver tutorial dataset and slides] from the NA-MIC training core which includes a limited number of questions and answers
* Load a visual scene linked to a question catalog from a defined file format (XML?)
* The visualization and the questions are linked so answers can be provided in a fully interactive fashion (picking of a 3D mesh.. etc.)
* Track user-specified answers and provide statistics after testing mode
* Use 3D Slicer to generate content for training and testing
* Prototype will be built on top of existing visualization infrastructure ([http://goXTK.com XTK] and [http://fetalmri.org web-based fetal atlas tool])
* We envision a system somewhat like existing online quiz systems ([http://www.surveymonkey.com], [http://www.classmarker.com/], [http://dontshake.org/lms/lms_information/lms_quiz.php], [http://www.proprofs.com/quiz-school/]) but with interactive 3D content drawn from the clinical use cases.
* May use a helper library like [https://github.com/jewlofthelotus/SlickQuiz SlickQuiz] [http://www.jewlofthelotus.com/2011/12/23/slickquiz-jquery-plugin-now-on-github/comment-page-1/]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* User interface mockups are being prepared
* Development repository: https://github.com/FNNDSC/mi2b2_aim3
* Problems/ToDo:
** Update WebGLExport module to new XTK version
** Fix XTK with Liver CT volume (right now scalar range messes things up) or convert (normalize) the volume
</div>
</div>

== Draft Development Plans ==

=== Phase I: Developer Mockups ===
During the first half of 2013:
* Hand-coded (html, javascript) mockups using to create content from existing content
** Liver tutorial from Sonia
** Fetal brain atlas
* Identify best practices and experiment with different Question and Answer modes
* Identify best practices and experiment with user interaction
* Getting feedback on mi2b2 team and refining the mockups

=== Phase II: Limited Beta ===
During second half of 2013:
* Identify first set of training content suitable for wider trial
* Set up a site to host training materials
** Set up back end system to record test results?
** Review [http://en.wikipedia.org/wiki/Redcap_(Research_Electronic_Data_Capture) RedCap] as a back end ([http://www.project-redcap.org/ home page], [https://redcap.vanderbilt.edu/surveys/index.php?hash=40008b9a5380fcacce3976bf7c08af5b example survey)]
** Consider tie-in to RSNA Audience Response Tool
* Open site to radiology trainees and gather feedback
* Integrate infant brain atlas data as it becomes available

=== Phase III: Authoring Tools ===
During 2014:
* Develop system for clinician-educators to easily create content
** Define images, models, annotations, atlases to display
** Define didactic material
** Export content to hosting site
* Leverage tools like Scene Views and WebGL Export from Slicer

2013 Project Week:WebbasedAnatomicalTeachingFramework

2013-01-07T17:13:21Z

Haehn: /* Project Description */

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==

* Daniel Haehn, Rudolph Pienaar, Ellen Grant (Boston Children's Hospital)
* Steve Pieper (Isomics Inc.)
* Sonia Pujol (BWH)
* Randy Gollub (MGH)

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Over the last several years, an [[CTSC:ARRA_supplement | infrastructure has been developed to integrate health records and PACS image archives]] to support research on large collections of data collected during delivery of healthcare (as contrasted with data collected as part of clinical trials). This resulted in the availability of [http://www.mi2b2.org the mi2b2 system]. An application enabled by this technology is supported by an [http://projectreporter.nih.gov/project_info_description.cfm?aid=8272742&icde=13552329&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC R01 to use clinical scans of children aged zero to six years old to build a teaching atlas].
* One goal of the [http://www.mi2b2.org mi2b2] collaborative effort is to create a web-based teaching tool for fetal and neonatal anatomy as well as a browser for quantified information. The goal of this project is to create a prototype application for this purpose which can be easily extended to other testing scenarios.
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
We propose the following steps to create a high-level didactic content creation tool.
* Enable switching between different testing scenarios (fetal brains, liver etc.)
* Start with the existing [http://www.slicer.org/slicerWiki/index.php/Documentation/4.2/Training#Slicer4_3D_Visualization_of_DICOM_images_for_Radiology_Applications Liver tutorial dataset and slides] from the NA-MIC training core which includes a limited number of questions and answers
* Load a visual scene linked to a question catalog from a defined file format (XML?)
* The visualization and the questions are linked so answers can be provided in a fully interactive fashion (picking of a 3D mesh.. etc.)
* Track user-specified answers and provide statistics after testing mode
* Use 3D Slicer to generate content for training and testing
* Prototype will be built on top of existing visualization infrastructure ([http://goXTK.com XTK] and [http://fetalmri.org web-based fetal atlas tool])
* We envision a system somewhat like existing online quiz systems ([http://www.surveymonkey.com], [http://www.classmarker.com/], [http://dontshake.org/lms/lms_information/lms_quiz.php], [http://www.proprofs.com/quiz-school/]) but with interactive 3D content drawn from the clinical use cases.
* May use a helper library like [https://github.com/jewlofthelotus/SlickQuiz SlickQuiz] [http://www.jewlofthelotus.com/2011/12/23/slickquiz-jquery-plugin-now-on-github/comment-page-1/]
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* User interface mockups are being prepared
* Development repository: https://github.com/FNNDSC/mi2b2_aim3
</div>
</div>

== Draft Development Plans ==

=== Phase I: Developer Mockups ===
During the first half of 2013:
* Hand-coded (html, javascript) mockups using to create content from existing content
** Liver tutorial from Sonia
** Fetal brain atlas
* Identify best practices and experiment with different Question and Answer modes
* Identify best practices and experiment with user interaction
* Getting feedback on mi2b2 team and refining the mockups

=== Phase II: Limited Beta ===
During second half of 2013:
* Identify first set of training content suitable for wider trial
* Set up a site to host training materials
** Set up back end system to record test results?
** Review [http://en.wikipedia.org/wiki/Redcap_(Research_Electronic_Data_Capture) RedCap] as a back end ([http://www.project-redcap.org/ home page], [https://redcap.vanderbilt.edu/surveys/index.php?hash=40008b9a5380fcacce3976bf7c08af5b example survey)]
** Consider tie-in to RSNA Audience Response Tool
* Open site to radiology trainees and gather feedback
* Integrate infant brain atlas data as it becomes available

=== Phase III: Authoring Tools ===
During 2014:
* Develop system for clinician-educators to easily create content
** Define images, models, annotations, atlases to display
** Define didactic material
** Export content to hosting site
* Leverage tools like Scene Views and WebGL Export from Slicer

2013 Project Week:WebbasedAnatomicalTeachingFramework

2012-12-17T14:46:18Z

Haehn: /* Project Description */

2013 Project Week:WebbasedAnatomicalTeachingFramework

2012-12-17T14:45:27Z

Haehn: /* Project Description */

2013 Project Week:WebbasedAnatomicalTeachingFramework

2012-12-16T18:37:19Z

Haehn: /* Project Description */

2013 Project Week:WebbasedAnatomicalTeachingFramework

2012-12-16T18:35:18Z

Haehn: /* Project Description */

2013 Winter Project Week

2012-12-16T18:24:06Z

Haehn: /* NA-MIC Kit Internals */

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

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

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

Active preparation begins 6-8 weeks prior to the meeting, when a kick-off teleconference is hosted by the NA-MIC Engineering, Dissemination, and Leadership teams, the primary hosts of this event. Invitations to this call are sent to all na-mic members, past attendees of the event, as well as any parties who have expressed an interest in working with NA-MIC. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient NA-MIC coverage for all. Subsequent teleconferences allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams are asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

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

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

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

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

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

=Background and Preparation=

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

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

=Projects=

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

==TBI==
* [[4D DTI tractography in Slicer for TBI]] (Bo Wang, Andrei Irimia, Micah Chambers, Jack Van Horn, Bo Wang, Marcel Prastawa, Guido Gerig)
* [[Clinically oriented TBI connectivity analysis in Slicer]] (Andrei Irimia, Bo Wang, Micah Chambers, Jack Van Horn, Marcel Prastawa, Guido Gerig)
* [[Geometric metamorphosis for TBI]] (Danielle Pace, Stephen Aylward, Andrei Irimia, Micah Chambers)

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

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

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

==Prostate Interventions==
* BRAINSFit in ITK4: extra functionality and testing for prostate MR registration (Andrey, Hans)
* PkModeling for prostate DCE MRI (Jim, Andrey)

==Neurosurgery==

==General Image Guided Therapy==
* United SlicerIGT extension, repository, website (Tamas Ungi, Junichi Tokuda, Adam Rankin)
* Mobile image overlay augmented reality needle guidance (Adam Rankin, Tamas Ungi)

==Radiation Therapy==
* [[2013_Project_Week:DicomRtExport|SlicerRT: DICOM RT export]] (Kevin Wang, Greg Sharp, Csaba Pinter)
* [[2013_Project_Week:RtBeamGeometry|SlicerRT: Beam geometry widgets]] (Csaba Pinter, Greg Sharp)

==General Image Segmentation==

==General Image Registration==

==NA-MIC Kit Internals==
*[[2013_Project_Week:WebbasedAnatomicalTeachingFramework|Web-based anatomical teaching framework for mi2b2]] (Daniel Haehn, Steve Pieper, Sonia Pujol, Randy Gollub, Rudolph Pienaar, Ellen Grant)
*[[2013_Project_Week:ITKv4Default|ITKv4 Default in Superbuild]] - [http://www.na-mic.org/Bug/search.php?project_id=3&sticky_issues=on&sortby=last_updated&dir=DESC&hide_status_id=80&tag_string=ITKv4 Issues] (Matt McCormick, Luis Ibanez, Hans Johnson, Jc?, Bill Lorensen)
*[[2013_Project_Week:MarkupsModule|Slicer4 Markups Module]] (Nicole Aucoin)
*[[2013_Project_Week:ColorHierarchies|Slicer4 Color Hierarchies]] (Nicole Aucoin)
*[[2013_Project_Week:PatientHierarchy|Slicer4 Patient Hierarchy]] (Csaba Pinter, Andrey Fedorov?, Nicole Aucoin, Steve Pieper)
*[[2013_Project_Week:ScalarBar|Slicer4 Scalar bar improvements]] (Kevin Wang, Steve Pieper?, Csaba Pinter)
*[[2013_Project_Week:CliMatlabInterface|Slicer4 CLI Matlab interface]] (Kevin Wang, Steve Pieper?, Csaba Pinter)
*[[2013_Project_Week:PETStandardUptakeValueComputation| PET/CT SUV Module for Clinicians]] (Sonia Pujol, Markus Van Tol, Nicole Aucoin)
*[[2013_Project_Week:SelfTests|Slicer4 Self Test and [http://slicer-devel.65872.n3.nabble.com/ANN-Oldies-But-Goodies-Volume-Data-tt4026821.html Sample Data Refactor]]] (Steve Pieper, Jim Miller, Jc, Sankhesh Jhaveri)
*[[2013_Project_Week:SimplifyMRMLReference|Simplify MRML References]] - Issue [http://www.na-mic.org/Bug/view.php?id=2727 #2727] (Alex Yarmarkovich, Andras Lasso?, Steve Pieper, Julien Finet ?, Sankhesh Jhaveri ?, Jc ?)
*[[2013_Project_Week:SlicerIPythonIntegration|Integration of IPython]] (Jc, Hans Johnson, Dave Welch, Steve Pieper, Matt McCormick)
*[[2013_Project_Week:SlicerDebianPackage|Slicer Debian package]] (Jc, Dominique Belhachemi ?, Greg Sharp)
*[[2013_Project_Week:SimplifyRendererMouseInteraction|Simplify renderer window mouse interaction]] - Mailing list [http://slicer-devel.65872.n3.nabble.com/Left-mouse-button-changes-window-level-Is-it-good-tt4026815.html thread] (Csaba ?, Greg?, Andriy?, Steve, Jc)
*[[2013_Project_Week:PotentialSolutionForDefiningRoleAttributesForVolumes|Potential solutions for defining roles and/or attributes for volumes that are preserved when the volume is processed.]] - Mailing list [http://slicer-devel.65872.n3.nabble.com/Volume-node-subclass-tt4026807.html thread] (Andras?, Greg?, Andriy?, Steve, Jc)
*[[2013_Project_Week:SteeredRegistration|Interactive Registration for Image Guided Therapy]] (Jim Miller, Steve Pieper, Kunlin Cao)

2013 Project Week:WebbasedAnatomicalTeachingFramework

2012-12-16T18:23:48Z

Haehn: Created page with '__NOTOC__ <gallery> Image:PW-SLC2013.png|Projects List </gallery> ==Key Investigators== * Daniel Haehn, Rudolph Pienaar, Ellen Grant (Bost…'

2013 Winter Project Week

2012-12-13T17:06:33Z

Haehn: /* NA-MIC Kit Internals */

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

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

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

Active preparation begins 6-8 weeks prior to the meeting, when a kick-off teleconference is hosted by the NA-MIC Engineering, Dissemination, and Leadership teams, the primary hosts of this event. Invitations to this call are sent to all na-mic members, past attendees of the event, as well as any parties who have expressed an interest in working with NA-MIC. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient NA-MIC coverage for all. Subsequent teleconferences allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams are asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

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

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

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

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

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

=Background and Preparation=

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

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

=Projects=

==TBI==
* [[4D DTI tractography in Slicer for TBI]] (Bo Wang, Andrei Irimia, Micah Chambers, Jack Van Horn, Bo Wang, Marcel Prastawa, Guido Gerig)
* [[Clinically oriented TBI connectivity analysis in Slicer]] (Andrei Irimia, Bo Wang, Micah Chambers, Jack Van Horn, Marcel Prastawa, Guido Gerig)
* [[Geometric metamorphosis for TBI]] (Danielle Pace, Stephen Aylward, Andrei Irimia, Micah Chambers)

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

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

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

==Prostate Interventions==
* BRAINSFit in ITK4: extra functionality and testing for prostate MR registration (Andrey, Hans)
* PkModeling for prostate DCE MRI (Jim, Andrey)

==Neurosurgery==

==General Image Guided Therapy==
* United SlicerIGT extension, repository, website (Tamas Ungi, Junichi Tokuda, Adam Rankin)
* Mobile image overlay augmented reality needle guidance (Adam Rankin, Tamas Ungi)

==Radiation Therapy==
* [[2013_Project_Week:DicomRtExport|SlicerRT: DICOM RT export]] (Kevin Wang, Greg Sharp, Csaba Pinter)
* [[2013_Project_Week:RtBeamGeometry|SlicerRT: Beam geometry widgets]] (Csaba Pinter, Greg Sharp)

==General Image Segmentation==

==General Image Registration==

==NA-MIC Kit Internals==
*[[2013_Project_Week:WebbasedAnatomicalTeachingFramework|Web-based anatomical teaching framework for mi2b2]] (Daniel Haehn, Steve Pieper, Sonia Puyol, Randy Gollub, Rudolph Pienaar, Ellen Grant)
*[[2013_Project_Week:ITKv4Default|ITKv4 Default in Superbuild]] - [http://www.na-mic.org/Bug/search.php?project_id=3&sticky_issues=on&sortby=last_updated&dir=DESC&hide_status_id=80&tag_string=ITKv4 Issues] (Matt McCormick, Luis Ibanez, Hans Johnson, Jc?, Bill Lorensen)
*[[2013_Project_Week:MarkupsModule|Slicer4 Markups Module]] (Nicole Aucoin)
*[[2013_Project_Week:ColorHierarchies|Slicer4 Color Hierarchies]] (Nicole Aucoin)
*[[2013_Project_Week:PatientHierarchy|Slicer4 Patient Hierarchy]] (Csaba Pinter, Andrey Fedorov?, Nicole Aucoin?, Steve Pieper)
*[[2013_Project_Week:ScalarBar|Slicer4 Scalar bar improvements]] (Kevin Wang, Steve Pieper?, Csaba Pinter)
*[[2013_Project_Week:CliMatlabInterface|Slicer4 CLI Matlab interface]] (Kevin Wang, Steve Pieper?, Csaba Pinter)
*[[2013_Project_Week:PETStandardUptakeValueComputation| PET/CT SUV Module for Clinicians]] (Sonia Pujol, Markus Van Tol, Nicole Aucoin)
*[[2013_Project_Week:SelfTests|Slicer4 Self Test and [http://slicer-devel.65872.n3.nabble.com/ANN-Oldies-But-Goodies-Volume-Data-tt4026821.html Sample Data Refactor]]] (Steve Pieper, Jim Miller, Jc, Sankhesh Jhaveri)
*[[2013_Project_Week:SimplifyMRMLReference|Simplify MRML References]] - Issue [http://www.na-mic.org/Bug/view.php?id=2727 #2727] (Alex Yarmarkovich, Andras Lasso?, Steve Pieper, Nicole Aucoin?, Julien Finet ?, Sankhesh Jhaveri ?, Jc ?)
*[[2013_Project_Week:SlicerIPythonIntegration|Integration of IPython]] (Jc, Hans Johnson, Dave Welch, Steve Pieper, Matt McCormick)
*[[2013_Project_Week:SlicerDebianPackage|Slicer Debian package]] (Jc, Dominique Belhachemi ?, Greg Sharp)
*[[2013_Project_Week:SimplifyRendererMouseInteraction|Simplify renderer window mouse interaction]] - Mailing list [http://slicer-devel.65872.n3.nabble.com/Left-mouse-button-changes-window-level-Is-it-good-tt4026815.html thread] (Csaba ?, Greg?, Andriy?, Steve, Jc)
*[[2013_Project_Week:PotentialSolutionForDefiningRoleAttributesForVolumes|Potential solutions for defining roles and/or attributes for volumes that are preserved when the volume is processed.]] - Mailing list [http://slicer-devel.65872.n3.nabble.com/Volume-node-subclass-tt4026807.html thread] (Andras?, Greg?, Andriy?, Steve, Jc)
*[[2013_Project_Week:SteeredRegistration|Interactive Registration for Image Guided Therapy]] (Jim Miller, Steve Pieper, Kunlin Cao)

2012 Summer Project Week:XTK

2012-06-18T14:03:15Z

Haehn:

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:Xfibers.png|Tractography rendered with XTK in 5 lines of JavaScript code, here the [http://lessons.goxtk.com/06/ live version].
Image:Xvolume.png|MRI volume + label map rendered with XTK, here the [http://lessons.goxtk.com/13/ live version].
Image:Xtkabdom.png|The SPL Abdominal Atlas. ''Left'': In 3D Slicer version 4, ''Right'': In a web browser exported using the '''WebGL Export''' module.
Image:Xtkbrain.png|The NAC Brain Atlas: ''Left'': In Slicer, ''Right'': In a web browser.
Image:Xtkblack.png|An example WebGL export with black background color and a caption tooltip. ''Left'': In Slicer, ''Right'': In a web browser.
</gallery>

==Key Investigators==
* Boston Children's Hospital: Daniel Haehn, Nicolas Rannous, Rudolph Pienaar
* Isomics Inc.: Steve Pieper

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

<h3>Objective</h3>
XTK is a WebGL framework providing an easy-to-use API to visualize scientific data on the web. No background or knowledge in Computer Graphics is required and a [https://github.com/xtk/X/wiki/X:Fileformats variety of file formats] can be natively read and visualized with very little JavaScript code.<br><br>Nevertheless, some researchers want to share their data without writing any code so we propose a '''one-click WebGL export module''' for 3D Slicer 4.

</div>

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

<h3>Approach, Plan</h3>
The '''WebGL Export''' module should enable the export of ''Surface Models'', ''Fiber Tracks'' and ''Volumes in 2D and 3D (including Volume Rendering)'' from 3D Slicer 4 to the web.

First step of further development is to update the currently existing '''WebGL Export''' module to a new XTK version. Additionally, a TrackVis file format (.TRK) writer should be implemented for 3D Slicer 4 since XTK natively supports this format for Tractography.

Also, it should be interesting to investigate if Slicer Data Bundles or Scene Views can be exported.

</div>

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

<h3>Progress</h3>
A first version of the '''WebGL Export''' module is part of the latest 3D Slicer 4 release. Currently, it supports the export of ''Surface Models'' to a website (see [http://www.na-mic.org/Wiki/index.php/File:WebGLExport_TutorialContestSummer2012.pdf tutorial]).

</div>
</div>

==Delivery Mechanism==

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

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

==References==
* [http://goXTK.com The XTK website] including lessons, demos etc.
* [https://github.com/xtk/SlicerWebGLExport Github Project Page] for the 3D Slicer WebGL Export module
* '''WebGL for Baby Brains: Neuroimaging in the Browser''' at the WebGL Camp Orlando 2012, [http://www.youtube.com/watch?v=SQuH-xpdlbc Video]
* '''Science!''' featuring XTK, [http://creativejs.com/2012/04/science/ CreativeJS.com]
* '''The X Toolkit for Scientific Visualization''' on [http://www.webgl.com/2012/03/webgl-demo-the-x-toolkit-for-scientific-visualization/ WebGL.com]
* D. Haehn, N. Rannou, B. Ahtam, E. Grant, R. Pienaar: '''Neuroimaging in the Browser using the X Toolkit''', INCF Neuroinformatics 2012, [http://www.neuroinformatics2012.org/abstracts/neuroimaging-in-the-browser-using-the-x-toolkit Abstract]
* A. Klein, N. Nichols, D. Haehn: '''Mindboggle 2 interface: online visualization of extracted brain features with XTK''', INCF Neuroinformatics 2012, [http://www.neuroinformatics2012.org/abstracts/mindboggle-2-interface-online-visualization-of-extracted-brain-features-with-xtk Abstract]

File:Xvolume.png

2012-06-18T14:03:02Z

Haehn:

File:Xfibers.png

2012-06-18T14:01:34Z

Haehn:

2012 Summer Project Week:XTK

2012-06-15T20:50:43Z

Haehn: /* Delivery Mechanism */

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:Xtkabdom.png|The SPL Abdominal Atlas. ''Left'': In 3D Slicer version 4, ''Right'': In a web browser exported using the '''WebGL Export''' module.
Image:Xtkbrain.png|The NAC Brain Atlas: ''Left'': In Slicer, ''Right'': In a web browser.
Image:Xtkblack.png|An example WebGL export with black background color and a caption tooltip. ''Left'': In Slicer, ''Right'': In a web browser.
</gallery>

==Key Investigators==
* Boston Children's Hospital: Daniel Haehn, Nicolas Rannous, Rudolph Pienaar
* Isomics Inc.: Steve Pieper

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

<h3>Objective</h3>
XTK is a WebGL framework providing an easy-to-use API to visualize scientific data on the web. No background or knowledge in Computer Graphics is required and a [https://github.com/xtk/X/wiki/X:Fileformats variety of file formats] can be natively read and visualized with very little JavaScript code.<br><br>Nevertheless, some researchers want to share their data without writing any code so we propose a '''one-click WebGL export module''' for 3D Slicer 4.

</div>

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

<h3>Approach, Plan</h3>
The '''WebGL Export''' module should enable the export of ''Surface Models'', ''Fiber Tracks'' and ''Volumes in 2D and 3D (including Volume Rendering)'' from 3D Slicer 4 to the web.

First step of further development is to update the currently existing '''WebGL Export''' module to a new XTK version. Additionally, a TrackVis file format (.TRK) writer should be implemented for 3D Slicer 4 since XTK natively supports this format for Tractography.

Also, it should be interesting to investigate if Slicer Data Bundles or Scene Views can be exported.

</div>

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

<h3>Progress</h3>
A first version of the '''WebGL Export''' module is part of the latest 3D Slicer 4 release. Currently, it supports the export of ''Surface Models'' to a website (see [http://www.na-mic.org/Wiki/index.php/File:WebGLExport_TutorialContestSummer2012.pdf tutorial]).

</div>
</div>

==Delivery Mechanism==

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

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

==References==
* [http://goXTK.com The XTK website] including lessons, demos etc.
* [https://github.com/xtk/SlicerWebGLExport Github Project Page] for the 3D Slicer WebGL Export module
* '''WebGL for Baby Brains: Neuroimaging in the Browser''' at the WebGL Camp Orlando 2012, [http://www.youtube.com/watch?v=SQuH-xpdlbc Video]
* '''Science!''' featuring XTK, [http://creativejs.com/2012/04/science/ CreativeJS.com]
* '''The X Toolkit for Scientific Visualization''' on [http://www.webgl.com/2012/03/webgl-demo-the-x-toolkit-for-scientific-visualization/ WebGL.com]
* D. Haehn, N. Rannou, B. Ahtam, E. Grant, R. Pienaar: '''Neuroimaging in the Browser using the X Toolkit''', INCF Neuroinformatics 2012, [http://www.neuroinformatics2012.org/abstracts/neuroimaging-in-the-browser-using-the-x-toolkit Abstract]
* A. Klein, N. Nichols, D. Haehn: '''Mindboggle 2 interface: online visualization of extracted brain features with XTK''', INCF Neuroinformatics 2012, [http://www.neuroinformatics2012.org/abstracts/mindboggle-2-interface-online-visualization-of-extracted-brain-features-with-xtk Abstract]

2012 Summer Project Week:XTK

2012-06-15T20:48:52Z

Haehn:

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:Xtkabdom.png|The SPL Abdominal Atlas. ''Left'': In 3D Slicer version 4, ''Right'': In a web browser exported using the '''WebGL Export''' module.
Image:Xtkbrain.png|The NAC Brain Atlas: ''Left'': In Slicer, ''Right'': In a web browser.
Image:Xtkblack.png|An example WebGL export with black background color and a caption tooltip. ''Left'': In Slicer, ''Right'': In a web browser.
</gallery>

==Key Investigators==
* Boston Children's Hospital: Daniel Haehn, Nicolas Rannous, Rudolph Pienaar
* Isomics Inc.: Steve Pieper

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

<h3>Objective</h3>
XTK is a WebGL framework providing an easy-to-use API to visualize scientific data on the web. No background or knowledge in Computer Graphics is required and a [https://github.com/xtk/X/wiki/X:Fileformats variety of file formats] can be natively read and visualized with very little JavaScript code.<br><br>Nevertheless, some researchers want to share their data without writing any code so we propose a '''one-click WebGL export module''' for 3D Slicer 4.

</div>

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

<h3>Approach, Plan</h3>
The '''WebGL Export''' module should enable the export of ''Surface Models'', ''Fiber Tracks'' and ''Volumes in 2D and 3D (including Volume Rendering)'' from 3D Slicer 4 to the web.

First step of further development is to update the currently existing '''WebGL Export''' module to a new XTK version. Additionally, a TrackVis file format (.TRK) writer should be implemented for 3D Slicer 4 since XTK natively supports this format for Tractography.

Also, it should be interesting to investigate if Slicer Data Bundles or Scene Views can be exported.

</div>

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

<h3>Progress</h3>
A first version of the '''WebGL Export''' module is part of the latest 3D Slicer 4 release. Currently, it supports the export of ''Surface Models'' to a website (see [http://www.na-mic.org/Wiki/index.php/File:WebGLExport_TutorialContestSummer2012.pdf tutorial]).

</div>
</div>

==Delivery Mechanism==

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

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

==References==
* [http://goXTK.com The XTK website] including lessons, demos etc.
* [https://github.com/xtk/SlicerWebGLExport Github Project Page] for the 3D Slicer WebGL Export module
* '''WebGL for Baby Brains: Neuroimaging in the Browser''' at the WebGL Camp Orlando 2012, [http://www.youtube.com/watch?v=SQuH-xpdlbc Video]
* '''Science!''' featuring XTK, [http://creativejs.com/2012/04/science/ CreativeJS.com]
* '''The X Toolkit for Scientific Visualization''' on [http://www.webgl.com/2012/03/webgl-demo-the-x-toolkit-for-scientific-visualization/ WebGL.com]
* D. Haehn, N. Rannou, B. Ahtam, E. Grant, R. Pienaar: '''Neuroimaging in the Browser using the X Toolkit''', INCF Neuroinformatics 2012, [http://www.neuroinformatics2012.org/abstracts/neuroimaging-in-the-browser-using-the-x-toolkit Abstract]
* A. Klein, N. Nichols, D. Haehn: '''Mindboggle 2 interface: online visualization of extracted brain features with XTK''', INCF Neuroinformatics 2012, [http://www.neuroinformatics2012.org/abstracts/mindboggle-2-interface-online-visualization-of-extracted-brain-features-with-xtk Abstract]

File:Xtkbrain.png

2012-06-15T20:06:33Z

Haehn:

File:Xtkblack.png

2012-06-15T20:06:26Z

Haehn:

File:Xtkabdom.png

2012-06-15T20:06:20Z

Haehn:

2012 Summer Project Week:XTK

2012-06-15T20:04:47Z

Haehn: Created page with '__NOTOC__ <gallery> Image:PW-MIT2012.png|Projects List Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus…'

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
Image:genuFAp.jpg|Scatter plot of the original FA data through the genu of the corpus callosum of a normal brain.
Image:genuFA.jpg|Regression of FA data; solid line represents the mean and dotted lines the standard deviation.
</gallery>

==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>

==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 .

2012 Summer Project Week

2012-06-15T20:04:21Z

Haehn: /* Infrastructure */

Back to [[Events]]

[[image:PW-MIT2012.png|200px]]

*'''Dates:''' June 18-22, 2012
*'''Location:''' MIT

==Agenda==

{|border="1"
|-style="background:#b0d5e6;color:#02186f"
!style="width:10%" |Time
!style="width:18%" |Monday, June 18
!style="width:18%" |Tuesday, June 19
!style="width:18%" |Wednesday, June 20
!style="width:18%" |Thursday, June 21
!style="width:18%" |Friday, June 22
|-
|
|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-10am:''' What's new in Slicer4 (Charts - Jim, DICOM - Steve) <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>----------------------------------------<br>
'''10-11am''' Slicer4 Python Q & A <br>
[[MIT_Project_Week_Rooms|Grier Room (Left)]]
<br>----------------------------------------<br>
|'''9am-11pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Project Week Breakout Session: SimpleITK|Slicer and SimpleITK]] (Hans)
[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
<br>----------------------------------------<br>
'''10am-12pm: <font color="#4020ff">Computation Core PIs: closed meeting with Ron:'''</font><br>
[[MIT_Project_Week_Rooms#Star|Star Room]]
|'''9am-12pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:OpenIGTLink|OpenIGTLink]] (Junichi)
[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|'''10am-12pm:''' [[#Projects|Project Progress Updates]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
|-
|bgcolor="#ffffdd"|'''12pm-1pm'''
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm
|-
|bgcolor="#ffffdd"|'''1pm-5:30pm'''
|'''1-1:05pm: <font color="#503020">Ron Kikinis: Welcome</font>'''
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''1:05-3:30pm:''' [[#Projects|Project Introductions]] (all Project Leads)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3:30-4:30pm''' Slicer4 Extensions (JC) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
|'''3-4pm:''' [[2012_Tutorial_Contest|Tutorial Contest Presentations]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''4-5pm:''' Breakout Session: DICOM, Networking, RT, Segmentations (Steve, Greg, Andras, Andre)
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Star Room]]
|'''12:45-1pm:''' [[Events:TutorialContestJune2012|Tutorial Contest Winner Announcement]]
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Rooms]]
<br>----------------------------------------<br>
'''3-30pm: <font color="#4020ff">Breakout Session:'''</font>Qt Testing (JC)
|'''1-3pm: <font color="#4020ff">Breakout Session:'''</font><br> [[2012 Summer Project Week Breakout Session:Ultrasound|Ultrasound]] (Tamas)
[[MIT_Project_Week_Rooms#Kiva_32-G449|Kiva Room]]
|
|-
|bgcolor="#ffffdd"|'''5:30pm'''
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|bgcolor="#f0e68b"|Adjourn for the day
|
|}

==Projects==

Please use [http://wiki.na-mic.org/Wiki/index.php/Project_Week/Template THIS TEMPLATE] to create project pages for this event.

==='''Neurosurgery, Brain and Spine, Traumatic Brain Injury'''===

# [[2012_Summer_Project_Week:Early_Dementia_Diagnostic |Early Dementia Diagnostic Tools]] (Marcel Koek, Sonia Pujol)
# [[2012_Summer_Project_Week:Intraoperative_Tract_Detection | Intraoperative White Matter Tract Detection Module]] (Lauren O'Donnell, Isaiah Norton)
# [[Semiautomatic longitudinal segmentation of MR volumes in traumatic brain injury]] (Andrei Irimia, Danielle Pace, Micah Chambers, Stephen Aylward)
# [[2012_Summer_Project_Week:Radnostics |Spine Segmentation & Osteoporosis Detection In CT Imaging Studies]] (Anthony Blumfield, Ron Kikinis)
# [[2012_Summer_Project_Week:4D_Segmentation_TBI|4D Segmentation of longitudinal MRI of TBI patients]] (Bo Wang, Marcel Prastawa, Andrei Irimia, Micah Chambers, Jack van Horn, Guido Gerig)
# An Intraoperative Transcranial Ultrasound Brain Shift Monitor (Jason White, Alex Golby, Isaiah Norton)
#[[2012_Summer_Project_Week:TimeSeriesMonitoringIntracranialBones| Monitoring time series images of intracranial bones in meningioma ]] (Karl Diedrich)

==='''Radiation Therapy'''===
#[[2012_Summer_Project_Week:Overlapping_structures| First class structure set support in Slicer]] (Greg Sharp, James Shackleford, Steve Pieper)
#[[2012_Summer_Project_Week:Atlas_based_segmentation_for_head_and_neck| Atlas-based segmentation for head and neck]] (Amelia Arbisser, Nadya Shusharina, James Shackleford, Greg Sharp, Polina Golland)
#[[2012_Summer_Project_Week:SlicerRT| Radiotherapy extensions for Slicer 4]] (Andras Lasso, Csaba Pinter, Kevin Wang)
#[[2012_Summer_Project_Week:Deformable_Registration_for_Head_and_Neck| Deformable Registration for Head and Neck ]] (Ivan Kolesov, Greg Sharp, Yi Gao, Allen Tannenbaum)
#[[2012_Summer_Project_Week:PlastimatchIntegration| Plastimatch integration]] (James Shackleford, Greg Sharp)

==='''Huntington's Disease'''===
# [[2012_Summer_Project_Week:DTIPrep|DTIPrep]] (David Welch, Hans Johnson)
# [[2012_Summer_Project_Week:Fast Fiducial Registration|Fast Fiducial Registration Module]] (David Welch, Hans Johnson, Nicole Aucoin, Ron Kikinis)
# [[2012_Summer_Project_Week:ANTS Registation|ANTS Registation Module]] (David Welch, Hans Johnson)
# [[2012_Summer_Project_Week:Nipype Integration|Slicer/Nipype Integration]] (Hans Johnson)
# [[2012_Summer_Project_Week:DicomToNrrd|DicomToNrrdConverter Integration]] (Kent Williams)
# [[2012_Summer_Project_Week:4D shape analysis|4D shape analysis]] (James Fishbaugh, Marcel Prastawa, Guido Gerig)
# [[2012_Summer_Project_Week:DTI-Reg|DTI atlas based fiber analysis]] (Francois Budin)

==='''Atrial Fibrillation'''===
# Model-based segmentation of left Atrium using Graph-cuts (Gopal Veni, Ross Whitaker)
# [[2012_Summer_Project_Week:UtahCardiacRegistration|Cardiac MRI Registration Module]] (Alan Morris, Danny Perry, Josh Cates, Greg Gardner, Rob MacLeod)
# [[2012_Summer_Project_Week:UtahAutoScar|Automatic Left Atrial Scar Detection]] (Danny Perry, Alan Morris, Josh Cates, Rob MacLeod)
# [[2012_Summer_Project_Week:UtahInhomogeneity|MRI Inhomogeneity Correction Filter]] (Alan Morris, Eugene Kholmovski, Josh Cates, Danny Perry, Rob MacLeod)
# OpenIGT for realtime MRI-guided RF ablation (Rob MacLeod, and Junichi Tokuda) ??
# [[2012_Summer_Project_Week:VecReg|Vector-Valued Cardiac MRI Registration]] (Yi Gao, Josh Cates, Liang-Jia Zhu, Alan Morris, Danny Perry, Greg Gardner, Rob MacLeod, Sylvain Bouix, Allen Tannenbaum)
# [[2012_Summer_Project_Week:RidgeExtractionAtrialWallSegmentation|Perceptual Ridge Extraction for Atrial Wall Segmentation in MRI]] (Arie Nakhmani, Allen Tannenbaum)

==='''Device Integration with Slicer and Image Guided Therapy'''===
# [[2012_Summer_Project_Week:iGyne|iGyne for Gyne Brachytherapy]] (Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper)
# [[2012_Summer_Project_Week:SteeredRegistration|Steered Registration for Image Guided Therapy]] (Guillaume Pernelle BWH, Jan Egger, Tina Kapur, Steve Pieper, Jim Miller, Kunlin Cao)
# [[2012_Summer_Project_Week:Open_source_electromagnetic_trackers_using OpenIGTLink|Open-source electromagnetic trackers using OpenIGTLink]] (Peter Traneus Anderson, Tina Kapur, Sonia Pujol)
# [[2012_Summer_Project_Week:LiveUltrasound|Live Ultrasound]] (Tamas Ungi, Andinet Enquobahrie, Junichi Tokuda)
# [[2012_Summer_Project_Week:TransformRecorder|Transform Recorder]] (Simrin Nagpal, Tamas Ungi)
# [[2012_Summer_Project_Week:VertebraCTUSReg|Single Vertebra CT-US Registration]] (Samira Sojoudi, Saman Nouranian, Simrin Nagpal, Tamas Ungi, David Welch)
# [[2012_Summer_Project_Week:ProstateBxReviewWorkflow_Slicer4|Prostate biopsy multiparametric MRI review using Slicer4]] (Andrey Fedorov, Kemal Tuncali, Steve Pieper, Pat Mongkolwat)
# [[2012_Summer_Project_Week:LeanSlicer|Lean Slicer to facilitate regulatory approval]] (Andras Lasso, Chris Wedlake)
# [[2012_Summer_Project_Week:4D_Ultrasound_Slicer4|4D Ultrasound on Slicer4]] (Nobuhiko Hata, Laurent Chauvin)
# [[2012_Summer_Project_Week:Kinect4Slicer|Kinect4Slicer]] (Nobuhiko Hata, Laurent Chauvin)
# [[2012_Summer_Project_Week:Needle Tip Tracking | Needle Tip Tracking for complex MR images]] (Atsushi Yamada, Nobuhiko Hata)
# [[2012_Summer_Project_Week:BK-PLUS_Integration|Integration of BK ProFocus US with Slicer via PLUS library]] (Andras Lasso, Andrey Fedorov, Isaiah Norton, Saman)
# [[2012_Summer_Project_Week:OpenIGTLinkIF|Improvement of OpenIGTLink IF for Slicer 4]] (Junichi Tokuda)

==='''General Segmentation'''===
#[[2012_Summer_Project_Week:SemiAutomatedAirwaySegmentationfrom0.64mmLungCTDatasets|Semi-automated airway segmentation from 0.64mm lung CT datasets]] (Padraig Cantillon-Murphy, Raul San Jose Estepar, Pietro Nardelli)
# [[2012_Summer_Project_Week:QuantitativePETImageAnalysisModule|Quantitative PET Image Analysis Module]] (Markus Van Tol)
#Segmentation with Label Fusion (Ramesh Sridharan, Christian Wachinger, Polina Golland)
#[[Loading and segmentation of histopathology imaging for radiological-pathological correlation]] (Andrey Fedorov, Tobias Penzkofer)
#[[2012_Summer_Project_Week:ABC_Slicer4|Porting ABC extension to Slicer 4]] (Marcel Prastawa, Bo Wang, Guido Gerig)

==='''General Registration'''===
# [[2012_Summer_Project_Week:NiftyReg|NiftyReg integration]] (Marc Modat, Sonia Pujol)
# [[2012_Summer_Project_Week:ElastixIntegration| Elastix integration]] (Stefan Klein, Sonia Pujol)
# [[2012_Summer_Project_Week:DTIRegistration| Highly Deformable DTI Registration for cases with large pathological variations]] (Aditya Gupta, Martin Styner, Matthew Toews)
# [[2012_Summer_Project_Week:DifficultRegistration| Registration of Difficult Images]] (Matthew Toews, Stefan Klein, Marc Modat, Aditya Gupta, Martin Styner, Dominik Meier, William Wells)

==='''Informatics'''===
# [[2012_Summer_Project_Week:AIM_for_QIN|Applicability of AIM to QIN use cases]] (Andrey Fedorov, Reinhard Beichel, Jayashree Kalpathy-Cramer, Pat Mongkolwat, Daniel Rubin)

==='''Infrastructure'''===

# [[2012_Summer_Project_Week:SelfTesting|Built-In Self-Testing (BIST) for Slicer]] (Steve, Julien, Jc, Sonia)
# [[2012_Summer_Project_Week:AnnotationModule|Annotation module redesign for Slicer]] (Nicole)
# [[2012_Summer_Project_Week:MultiVolumeSupport|Multivolume support]] (Andrey, Jim)
# Python CLI modules (Demian, JC, Julien). See [http://www.na-mic.org/Bug/view.php?id=2039 #2039]
# [[2012_Summer_Project_Week:Charting|Charting]] (Jim)
# [[2012_Summer_Project_Week:SimpleITK Integration|SimpleITK Integration]] (Hans Johnson, Bradley Lowekamp)
# GPU Editor Effects
# [[2012_Summer_Project_Week:XTK|XTK/WebGL Exporter]] (Daniel, Nicolas - Boston Children's Hospital)
# General Usability issues (e.g. LM,FG,BG blending)
# Callback/Events/Observation best practice + Performance bottleneck discussion (Julien, Steve,...)
# [[2012_Summer_Project_Week:XNATSlicerIntegration|XNAT/Slicer Integration]] (Sunil, Dan, Steve,...)
# Pilot QIN use cases for Slicer/XNAT integration (Sunil, Steve, Dan, Andriy, Jayashree,...)
# [[2012_Summer_Project_Week:ITKv4 Integration|ITKv4 Integration]] (Hans Johnson, Julien Finet, Jim). See [http://www.na-mic.org/Bug/view.php?id=2007 #2007]
# [[2012_Summer_Project_Week:Reporting|Reporting module]] (Andrey, Nicole, Steve, Ron, Pat)
# [[2012_Summer_Project_Week:LongitudinalPETCTModule|Slicer Module for longitudinal analysis of PET-CT]] (Paul, Andriy, Ron, Markus,...)
# [[2012_Summer_Project_Week:Threat Modeling|Threat Modeling]] (JC, J2, Anthony)

==Background==

We are pleased to announce the 15th PROJECT WEEK of hands-on research and development activity for applications in Neuroscience, Image-Guided Therapy and several additional areas of biomedical research that enable personalized medicine. Participants will engage in open source programming using the [[NA-MIC-Kit|NA-MIC Kit]], algorithm design, medical imaging sequence development, tracking experiments, and clinical application. The main goal of this event is to move forward the translational research deliverables of the sponsoring centers and their collaborators. Active and potential collaborators are encouraged and welcome to attend this event. This event will be set up to maximize informal interaction between participants. If you would like to learn more about this event, please [http://public.kitware.com/cgi-bin/mailman/listinfo/na-mic-project-week click here to join our mailing list].

Active preparation begins on Thursday, April 26th at 3pm ET, with a kick-off teleconference. Invitations to this call will be sent to members of the sponsoring communities, their collaborators, past attendees of the event, as well as any parties who have expressed an interest in working with these centers. The main goal of the kick-off call is to get an idea of which groups/projects will be active at the upcoming event, and to ensure that there is sufficient coverage for all. Subsequent teleconferences will allow for more focused discussions on individual projects and allow the hosts to finalize the project teams, consolidate any common components, and identify topics that should be discussed in breakout sessions. In the final days leading upto the meeting, all project teams will be asked to fill in a template page on this wiki that describes the objectives and plan of their projects.

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

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

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

== Logistics ==
*'''Dates:''' June 18-22, 2012.
*'''Location:''' MIT. [[Meeting_Locations:MIT_Grier_A_%26B|Grier Rooms A & B: 34-401A & 34-401B]].
*'''REGISTRATION:''' Please click [https://www.regonline.com/namic2012summerprojweek HERE] to do an on-line registration for the meeting that will allow you to pay by credit card. No checks will be accepted.
*'''Registration Fee:''' $300 (covers the cost of breakfast, lunch and coffee breaks for the week).
*'''Hotel:''' No room blocks have been reserved in any area hotel. Please select a [http://web.mit.edu/institute-events/visitor/stay.html |hotel of your choice] and make reservations as early as possible. Some area hotels are:
**marriott cambridge center
**marriott residence inn kendall square
**le meridien central square
**hotel marlowe cambridge
**royal sonesta hotel cambridge

== 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 26, 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 10, all participants to add a one line title of their project to #Projects
# By 3pm ET on Thursday June 7, 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 14: Create a directory for each project on the [[Engineering:SandBox|NAMIC Sandbox]] (Matt)
## Commit on each sandbox directory the code examples/snippets that represent our first guesses of appropriate methods. (Luis and Steve will help with this, as needed)
## Gather test images in any of the Data sharing resources we have (e.g. XNAT/MIDAS). These ones don't have to be many. At least three different cases, so we can get an idea of the modality-specific characteristics of these images. Put the IDs of these data sets on the wiki page. (the participants must do this.)
## Where possible, setup nightly tests on a separate Dashboard, where we will run the methods that we are experimenting with. The test should post result images and computation time. (Matt)
# Please note that by the time we get to the project event, we should be trying to close off a project milestone rather than starting to work on one...
# People doing Slicer related projects should come to project week with slicer built on your laptop.
## See the [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers Developer Section of slicer.org] for information.
## Projects to develop extension modules should be built against the latest Slicer4 trunk.

==Registrants==

Do not add your name to this list- it is maintained by the organizers based on your paid registration. ([http://www.regonline.com/Register/Checkin.aspx?EventID=1089602 Please click here to register.])

#Anderson, Peter, retired, traneus@verizon.net
#Arbisser, Amelia, MIT, arbisser@mit.edu
#Aucoin, Nicole, BWH, Nicole@bwh.harvard.edu
#Aylward, Stephen, Kitware, stephen.aylward@kitware.com
#Blevins, Scott, BWH, stblevins@gmail.com
#Blumfield, Anthony, Radnostics, Anthony.Blumfield@Radnostics.com
#Budin, Francis, NIRAL-UNC, fbudin@unc.edu
#Cao, Kunlin, GE Research, cao@ge.com
#Chambers, Micah, UCLA, micahcc@ucla.edu
#Chauvin, Laurent, SPL, lchauvin@bwh.harvard.edu
#Chen, Elvis, Robarts, chene@robarts.ca
#Chen, Xiaojun, SPL, xiaojun@bwh.harvard.edu
#Datar, Manasi, Utah SCI, datar@sci.utah.edu
#Diedrich, Karl, AZE R&D, karl.diedrich@azeresearch.com
#Egger, Jan, BWH, egger@bwh.harvard.edu
#Farhat, Nabgha, SPL, nfarhat@bwh.harvard.edu
#Fedorov, Andriy, BWH, fedorov@bwh.harvard.edu
#Fillion-Robin, Jean-Christophe, Kitware, jchris.fillionr@kitware.com
#Finet, Julien, Kitware, julien.finet@kitware.com
#Fishbaugh, James, SCI, jfishbau@sci.utah.edu
#Gao, Yi, BWH, gaoyi@bwh.harvard.edu
#Gardner, Greg, SCI, ggardner@sci.utah.edu
#Golland, Polina, MIT CSAIL, polina@csail.mit.edu
#Gouaillard, Alexandre, A*STAR, agouaillard@gmail.com
#Gupta, Aditya, NIRAL UNC, aditya_gupta@med.unc.edu
#Jagadeesan, Jayender, SPL, jayender@bwh.harvard.edu
#Johnson, Hans, Univ Iowa, hans-johnson@uiowa.edu
#Kalpathy-Cramer, Jayashree, MGH, kalpathy@nmr.mgh.harvard.edu
#Kapur, Tina, BWH HMS, tkapur@bwh.harvard.edu
#Kikinis, Ron, HMS, kikinis@bwh.harvard.edu
#Klein, Stefan, Erasmus MC, s.klein@erasmusmc.nl
#Koek, Marcel, Erasmus MC, m.koek@erasmusmc.nl
#Kolesov, Ivan, GA Tech, ivan.kolesov@gatech.edu
#Kumar, Sunil, Washington Univ St Louis, kumars@mir.wustl.edu
#Lasso, Andras, Queen's Univ, lasso@cs.queensu.ca
#Lowekamp, Bradley, NLM/NIH, bradley.lowekamp@nih.gov
#Macule, Raul, AZE R&D, raul.macule@azeresearch.com
#Mastrogiacomo, Katie, SPL, BWH, kmast@bwh.harvard.edu
#Meier, Dominik, BWH, meier@bwh.harvard.edu
#Mercea, Paul, SPL, pmercea@bwh.harvard.edu
#Miller, Jim, GE Research, millerjv@ge.com
#Mizutani, Tatsushi, Nagoya Univ, tatsushi0207@me.com
#Modat, Marc, Univ College London, m.modat@ucl.ac.uk
#Moloney, Brendan, AIRC, moloney.brendan@gmail.com
#Mongkolwat, Pattanasak, Northwestern U, p-mongkolwat@northwestern.edu
#Montillo, Albert, GE Research, montillo@ge.com
#Nagpal, Simrin, Queen’s Univ, 7sn6@cs.queensu.ca
#Nakhmani, Arie, BU, nakhmani@gmail.com
#Nardelli, Pietro, Univ College Cork, pie.nardelli@gmal.com
#Norton, Isaiah, BWH, inorton@partners.org
#Nouranian, Saman, Univ BC, samann@ece.ubc.ca
#O'Donnell, Lauren, BWH, odonnell@bwh.harvard.edu
#Oyama, Rie, BWH, royama@bwh.harvard.edu
#Paniagua, Beatriz, Univ NC Chapel Hill, bpaniagua@gmail.com
#Penzkofer, Tobias, SPL, pt@bwh.harvard.edu
#Pernelle, Guillaume, BWH, gpernelle@gmail.com
#Pieper, Steve, Isomics, pieper@bwh.harvard.edu
#Pinter, Csaba, Queen's Univ, pinter@cs.queensu.ca
#Pujol, Sonia, BWH, spujol@bwh.harvard.edu
#Rannou, Nicolas, Childrens Hospital, nicolas.rannou@childrens.harvard.edu
#Razzaque, Sharif, InnerOptic Technology, sharif@inneroptic.com
#San Jose, Raul, BWH, rjosest@bwh.harvard.edu
#Shackleford, James, MGH, jshackleford@partners.org
#Sharp, Greg, MGH, gcsharp@partners.org
#Shusharina, Nadya, MGH, nshusharina@partners.org
#Sojoudi, Samira, Univ BC, samiras@ece.ubc.ca
#Spindler, Wolf, Fraunhofer MEVIS, wolf.spindler@mevis.fraunhofer.de
#Sridharan, Ramesh, MIT CSAIL, rameshvs@MIT.EDU
#State, Andrei, InnerOptic Technology, andrei@inneroptic.com
#Tiwari, Pallavi, Rutgers, pallavi.tiwar@gmail.com
#Toews, Matthew, BWH HMS, mt@bwh.harvard.edu
#Tokuda, Junichi, BWH, tokuda@bwh.harvard.edu
#Ungi, Tamas, Queen's Univ, ungi@cs.queensu.ca
#Van Tol, Markus, Univ Iowa, mvantol@engineering.uiowa.edu
#Vosburgh, Kirby, BWH, kirby@bwh.harvard.edu
#Wang, Bo, SCI, bowang@sci.utah.edu
#Wang, Kevin, Princess Margaret Hospital, kevin.wang@rmp.uhn.on.ca
#Wedlake, Chris, Robarts, cwedlake@robarts.ca
#Welch, David, Univ Iowa, david-welch@uiowa.edu
#Whitaker, Ross, SCI, whitaker@cs.utah.edu
#White, Phillip, BWH HMS, white@bwh.harvard.edu
#Yamada, Atsushi, BWH, ayamada@bwh.harvard.edu
#Yarmakovich, Alex, Isomics, alexy@bwh.harvard.edu

Training:Slicer3.6 101 Test Table

2011-11-10T17:12:05Z

Haehn:

This table contains all the tests of the Slicer3.6 101 page tutorials.

*For Training Workshop specific module testing results, please refer to the [http://www.na-mic.org/Wiki/index.php/Journal_of_Slicer_Workshop_Tests Journal of Slicer Workshop Tests ]
*For previous module testing results for Slicer versions 3.6 and older, please refer to the [http://wiki.na-mic.org/Wiki/index.php/Journal_of_Slicer_Tests#Concept Journal of Slicer Tests]

<table>
{| class="wikitable sortable labelpage labelpagetable" border="1" align="left"}
|-
|'''Tutorial Name'''||'''Slicer Version'''||'''Platform'''||'''Test Date'''||'''Comments/Mantis Links'''
|-
|-
| |[http://wiki.na-mic.org/Wiki/images/a/aa/VMTK_Slicer_3.6.3_Updated_OCT_2011.pdf Centerline Extraction of Coronary Arteries]||| [http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz '''Release ''' Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz]
|Mac Darwin|| 11-10-11 || OK (Tested by Daniel)
|-
| |[http://wiki.na-mic.org/Wiki/images/a/aa/VMTK_Slicer_3.6.3_Updated_OCT_2011.pdf Centerline Extraction of Coronary Arteries]||| [http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.3-2011-03-04-win32.exe '''Release ''' Slicer3-3.6.3-2011-03-04-win32.exe]
|Windows|| 11-10-11 || OK (Tested by Daniel)
|-
| |[http://wiki.na-mic.org/Wiki/images/a/aa/VMTK_Slicer_3.6.3_Updated_OCT_2011.pdf Centerline Extraction of Coronary Arteries]||| [http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz '''Release ''' Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz]
|Linux 64|| 11-10-11 || OK (Tested by Daniel)
|-
| |[http://www.na-mic.org/Wiki/images/6/66/EMSegmenterEndUserTasks_TutorialContestSummer2011.pdf EM Segmenter (End User Tasks)]||| [http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz '''Release ''' Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz]
|Mac Darwin|| 06-10-11 || OK (Tested by Dominique)
|-
| |[http://www.na-mic.org/Wiki/images/6/66/EMSegmenterEndUserTasks_TutorialContestSummer2011.pdf EM Segmenter (End User Tasks)]||| [http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.3-2011-03-04-win32.exe '''Release ''' Slicer3-3.6.3-2011-03-04-win32.exe]
|Windows|| 06-10-11 || OK (Tested by Dominique)
|-
| |[http://www.na-mic.org/Wiki/images/6/66/EMSegmenterEndUserTasks_TutorialContestSummer2011.pdf EM Segmenter (End User Tasks)]||| [http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz '''Release ''' Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz]
|Linux 64|| 06-10-11 || OK (Tested by Dominique)
|-
|[http://www.na-mic.org/Wiki/images/6/66/EMSegmenterEndUserTasks_TutorialContestSummer2011.pdf EM Segmenter (End User Tasks)] ||| [http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz '''Release ''' Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz]
|Linux 32|| 06-10-11 || OK (Tested by Dominique)
|-
| |[http://www.slicer.org/slicerWiki/images/4/4e/EMSegmenterTutorialAdvancedMode-Slicer-3.6.3-2.pdf EM Segmenter (Advanced Mode)]||| [http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz '''Release ''' Slicer3-3.6.3-2011-03-04-darwin-x86.tar.gz]
|Mac Darwin|| 05-20-11 || OK (Tested by Dominique)
|-
| |[http://www.slicer.org/slicerWiki/images/4/4e/EMSegmenterTutorialAdvancedMode-Slicer-3.6.3-2.pdf EM Segmenter (Advanced Mode)]||| [http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.3-2011-03-04-win32.exe '''Release ''' Slicer3-3.6.3-2011-03-04-win32.exe]
|Windows|| 05-13-11 || OK
|-
| |[http://www.slicer.org/slicerWiki/images/4/4e/EMSegmenterTutorialAdvancedMode-Slicer-3.6.3-2.pdf EM Segmenter (Advanced Mode)]||| [http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz '''Release ''' Slicer3-3.6.3-2011-03-04-linux-x86_64.tar.gz]
|Linux 64|| 05-17-11 || OK (Tested by Dominique)
|-
|[http://www.slicer.org/slicerWiki/images/4/4e/EMSegmenterTutorialAdvancedMode-Slicer-3.6.3-2.pdf EM Segmenter (Advanced Mode)] ||| [http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz '''Release ''' (Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz)]
|Linux 32|| 03-23-2011 || OK (Tested by Dominique)
|-
|[http://www.slicer.org/slicerWiki/images/e/e3/EMSegmenterTutorialSimpleMode-Slicer-3.6.3-1.pdf EM Segmenter (Simple Mode)] ||| [http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz '''Release ''' (Slicer3-3.6.3-2011-03-04-linux-x86.tar.gz)]
|Linux 32|| 03-23-2011 || OK (Tested by Dominique)
|-
|[http://www.slicer.org/slicerWiki/images/3/3f/EMSegmenterTutorialSimpleMode-2010-Dec.pdf EM Segmenter (Simple Mode)] ||| [http://www.slicer.org/download_files/Release/darwin-x86/Slicer3-3.6.2-2010-11-03-darwin-x86.tar.gz '''Release ''' (Slicer3-3.6.2-2010-11-03-darwin-x86.tar.gz)]
|Mac Darwin|| 12-30-2010 || OK (Tested by Daniel)
|-
|[http://www.slicer.org/slicerWiki/images/3/3f/EMSegmenterTutorialSimpleMode-2010-Dec.pdf EM Segmenter (Simple Mode)] ||| [http://www.slicer.org/download_files/Release/linux-x86/Slicer3-3.6.2-2010-11-03-linux-x86_64.tar.gz '''Release ''' (Slicer3-3.6.2-2010-11-03-linux-x86_64.tar.gz)]
|Linux 64|| 12-29-2010 || OK (Tested by Dominique)
|-
|[http://www.slicer.org/slicerWiki/images/3/3f/EMSegmenterTutorialSimpleMode-2010-Dec.pdf EM Segmenter (Simple Mode)] ||| [http://www.slicer.org/download_files/Release/linux-x86/Slicer3-3.6.2-2010-11-03-linux-x86.tar.gz '''Release ''' (Slicer3-3.6.2-2010-11-03-linux-x86.tar.gz)]
|Linux 32|| 12-29-2010 || OK (Tested by Dominique)
|-
|[http://www.slicer.org/slicerWiki/images/3/3f/EMSegmenterTutorialSimpleMode-2010-Dec.pdf EM Segmenter (Simple Mode)] ||| [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6.3-beta-2010-12-03-win32.exe '''Windows ''' (Slicer3-3.6.2-2010-12-03-win32.exe)]
|Windows XP || 12-07-2010 || OK (Tested by SPujol)
|-
|[http://www.slicer.org/slicerWiki/images/b/bc/OpenIGTLinkTutorial_Slicer3.6.2_JunichiTokuda_Dec2010.ppt OpenIGTLink OpenIGTLink Slides] ||| [[media:Slicer3-3.6.3-beta-2010-12-03-linux-x86.tar.gz‎ | '''Linux 32''' (Slicer3-3.6.2-2010-12-03-linux-x86.tar.gz Linux-x32)]]
|Linux 32|| 12-07-2010 || OK (Tested by Junichi)
|-
|[http://www.slicer.org/slicerWiki/images/b/bc/OpenIGTLinkTutorial_Slicer3.6.2_JunichiTokuda_Dec2010.ppt OpenIGTLink OpenIGTLink Slides] ||| [http://www.na-mic.org/Slicer/Download/Nightly/Slicer3-3.6.3-beta-2010-12-03-win32.exe '''Windows ''' (Slicer3-3.6.2-2010-12-03-win32.exe)]
|Windows XP || 12-04-2010 || OK (Tested by Junichi)
|-
|[http://www.slicer.org/slicerWiki/images/b/bc/OpenIGTLinkTutorial_Slicer3.6.2_JunichiTokuda_Dec2010.ppt OpenIGTLink OpenIGTLink Slides] |||[[media:Slicer3-3.6.3-beta-2010-12-03-darwin-x86.tar.gz‎ | '''Mac Darwin''' (Slicer3-3.6.2-2010-12-03-darwin-x86.tar.gz)]]
|Mac Darwin || 12-04-2010 || OK (Tested by Junichi)
|-
|[http://www.slicer.org/slicerWiki/images/b/bc/OpenIGTLinkTutorial_Slicer3.6.2_JunichiTokuda_Dec2010.ppt OpenIGTLink OpenIGTLink Slides] ||| [[media:Slicer3-3.6.3-beta-2010-12-03-linux-x86_64.tar.gz‎ | '''Linux 64''' (Slicer3-3.6.2-2010-12-03-linux-x86_64.tar.gz Linux-x64)]]
|Linux 64|| 12-04-2010 || OK (Tested by Junichi)
|-
|[http://www.na-mic.org/Wiki/index.php/File:3DVisualization_SoniaPujol_RSNA2010.ppt] | 3D Interactive Visualization of DICOM Images for Radiology Applications||http://boggs.bwh.harvard.edu/slicer/3.6.2-RC1/Slicer3-3.6.2-2010-10-22-darwin-x86.tar.gz ||Mac ||11-2-2010 || All OK
|-
|[http://www.na-mic.org/Wiki/index.php/File:3DVisualization_SoniaPujol_RSNA2010.ppt] | 3D Interactive Visualization of DICOM Images for Radiology Applications||http://boggs.bwh.harvard.edu/slicer/3.6.2-RC1/Slicer3-3.6.2-2010-10-22-linux-x86.tar.gz||Linux 32||11-2-2010|| All OK
|-
|[http://www.na-mic.org/Wiki/index.php/File:3DVisualization_SoniaPujol_RSNA2010.ppt] | 3D Interactive Visualization of DICOM Images for Radiology Applications|| http://boggs.bwh.harvard.edu/slicer/3.6.2-RC1/Slicer3-3.6.2-2010-10-22-linux-x86_64.tar.gz||Linux 64|| 11-2-2010|| All OK
|-
|[http://www.na-mic.org/Wiki/index.php/File:3DVisualization_SoniaPujol_RSNA2010.ppt] | 3D Interactive Visualization of DICOM Images for Radiology Applications|| http://boggs.bwh.harvard.edu/slicer/3.6.2-RC1/Slicer3-3.6.2-2010-10-22-win32.exe|| Win XP&7|| 11-2-2010|| All OK
|-
|[http://www.slicer.org/slicerWiki/images/6/67/PerkStationModule_TutorialContestSummer2010.pdf PERK Station Tutorial]||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7 ||10-25-2010||All OK
|-
|VMTK Centrelines Tutorial||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||10-25-2010||All OK
|-
|Confocal Microscopy Tutorial||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||10-25-2010||All OK
|-
|EM Fibre Clustering||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||10-23-2010||All OK
|-
|EM Fibre Clustering||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7 ||10-23-2010||All OK
|-
|Confocal Microscopy Tutorial||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||10-23-2010||All OK
|-
|Confocal Microscopy Tutorial||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7 ||10-23-2010||All OK
|-
|Confocal Microscopy Tutorial||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||10-22-2010||All OK
|-
|VMTK Centrelines Tutorial||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||10-22-2010||All OK
|-
|EM Fibre Clustering||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||10-22-2010||All OK
|-
|Liver Segmentation Tutorial||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||10-21-2010||All OK
|-
|Liver Segmentation Tutorial||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||10-21-2010||All OK
|-
|Liver Segmentation Tutorial||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||10-21-2010||All OK
|-
|Liver Segmentation Tutorial||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7 ||10-21-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/9/90/Stochastic_Tractography_TutorialContestSummer2010.pdf Stochastic Tractography] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||10-21-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/9/90/Stochastic_Tractography_TutorialContestSummer2010.pdf Stochastic Tractography] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||10-20-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/9/90/Stochastic_Tractography_TutorialContestSummer2010.pdf Stochastic Tractography] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||10-12-2010||All OK
|-
|Dicom to NRRD||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||10-12-2010||All OK
|-
|Dicom to NRRD||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7 ||10-12-2010||All OK
|-
|Dicom to NRRD||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||10-12-2010||All OK
|-
|Dicom to NRRD||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||10-09-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/1/13/IAFEMesh-TutorialContestSummer2010.pdf Meshing Workflow Tutorial][http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||10-12-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/1/13/IAFEMesh-TutorialContestSummer2010.pdf Meshing Workflow Tutorial][http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||10-12-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/0/06/ProstateNav_TutorialContestSummer2010.pdf Robot-Assisted MRI-Guided Prostate Biopsy] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||10-11-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/0/06/ProstateNav_TutorialContestSummer2010.pdf Robot-Assisted MRI-Guided Prostate Biopsy] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7 ||10-11-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/0/06/ProstateNav_TutorialContestSummer2010.pdf Robot-Assisted MRI-Guided Prostate Biopsy] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||10-11-2010||All OK
|-
|[http://wiki.slicer.org/slicerWiki/images/8/8c/Longitudinal_Lesion_Comparison_TutorialContest_2010.pdf Longitudinal Lesion Comparison] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||10-10-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/0/06/ProstateNav_TutorialContestSummer2010.pdf Robot-Assisted MRI-Guided Prostate Biopsy] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||10-09-2010||All OK
|-
|[http://wiki.slicer.org/slicerWiki/images/8/8c/Longitudinal_Lesion_Comparison_TutorialContest_2010.pdf Longitudinal Lesion Comparison] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||10-09-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/1/13/IAFEMesh-TutorialContestSummer2010.pdf Meshing Workflow Tutorial][http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||10-09-2010||All OK
|-
|[http://wiki.slicer.org/slicerWiki/images/6/66/Fiducials_TutorialContestSummer2010.pdf Fiducials Tutorial] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||10-06-2010||All OK
|-
|[http://wiki.slicer.org/slicerWiki/images/6/66/Fiducials_TutorialContestSummer2010.pdf Fiducials Tutorial] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||10-06-2010||All OK
|-
|[http://wiki.slicer.org/slicerWiki/images/6/66/Fiducials_TutorialContestSummer2010.pdf Fiducials Tutorial] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||10-06-2010||All OK
|-
|[http://wiki.slicer.org/slicerWiki/images/6/66/Fiducials_TutorialContestSummer2010.pdf Fiducials Tutorial] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7 ||10-06-2010||All OK
|-
|Robust Statistics Segmentation [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||09-29-2010||All OK; tutorial slide edits in progress
|-
|Robust Statistics Segmentation [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||09-29-2010||All OK; tutorial slide edits in progress
|-
|Robust Statistics Segmentation [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||09-29-2010||All OK; tutorial slide edits in progress
|-
|Atlas Label Merging & Surface Based Registration Tutorial [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7 ||09-29-2010||All OK; tutorial slide edits in progress
|-
|Atlas Label Merging & Surface Based Registration Tutorial [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||09-27-2010||All OK; tutorial slide edits in progress
|-
|Atlas Label Merging & Surface Based Registration Tutorial [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||09-22-2010||All OK; tutorial slide edits in progress
|-
|Atlas Label Merging & Surface Based Registration Tutorial [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||09-22-2010||All OK; tutorial slide edits in progress
|-
|[http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf Programming in Slicer3] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 ||09-09-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf Programming in Slicer3] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||09-09-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf Programming in Slicer3] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7 ||09-09-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/2/22/ProgrammingIntoSlicer3.6_SoniaPujol.pdf Programming in Slicer3] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||09-09-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/e/eb/Slicer3Minute_SoniaPujol_3.6.1.pdf Slicer3Minute][http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32||09-03-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/f/f7/FreeSurferCourse_Slicer3.6_SoniaPujol.pdf Freesurfer Tutorial] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32||09-03-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']|| [http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32||09-03-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/3/3c/ProgrammingIntoSlicer3.6.1_HelloPython_MICCAI2010_SoniaPujol.pdf Programming in Slicer3 with Python] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32||09-03-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/0/00/InteractiveEditorTutorial_Slicer3.6_SoniaPujol.pdf Interactive Editor] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32||09-02-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/f/fc/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.pdf Diffusion Tensor Imaging] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32||09-02-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/0/0a/ManualRegistration_Slicer3.6.pdf Manual Registration] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32||09-02-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/f/f3/SlicerNeurosurgeryTutorial-3.6.1.pdf Neurosurgical Planning] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux x64 |||09-01-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/f/f3/SlicerNeurosurgeryTutorial-3.6.1.pdf Neurosurgical Planning] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32||09-01-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/f/f3/SlicerNeurosurgeryTutorial-3.6.1.pdf Neurosurgical Planning] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP & 7 |||09-01-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/f/f3/SlicerNeurosurgeryTutorial-3.6.1.pdf Neurosurgical Planning] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin |||09-01-2010||All OK
|-
|[http://www.slicer.org/slicerWiki/images/a/a1/Slicer3.6-ChangeTrackerTutorial.pdf ChangeTracker] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86/Slicer3-3.6.1-2010-08-20-linux-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Linux 32 ||08-27-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/a/a1/Slicer3.6-ChangeTrackerTutorial.pdf ChangeTracker] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux 64 ||08-27-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/a/a1/Slicer3.6-ChangeTrackerTutorial.pdf ChangeTracker] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||08-27-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/a/a1/Slicer3.6-ChangeTrackerTutorial.pdf ChangeTracker] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP&7 ||08-27-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux 64 ||08-27-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/f/f7/FreeSurferCourse_Slicer3.6_SoniaPujol.pdf Freesurfer Tutorial] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux 64 ||08-27-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/f/fc/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.pdf Diffusion Tensor Imaging] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux 64 ||08-27-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/3/3c/ProgrammingIntoSlicer3.6.1_HelloPython_MICCAI2010_SoniaPujol.pdf Programming in Slicer3 with Python] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux 64 ||08-27-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/0/0a/ManualRegistration_Slicer3.6.pdf Manual Registration] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux 64 ||08-27-2010 ||All OK
|-
||[http://www.slicer.org/slicerWiki/images/e/eb/Slicer3Minute_SoniaPujol_3.6.1.pdf Slicer3Minute] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux 64 ||08-27-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/0/00/InteractiveEditorTutorial_Slicer3.6_SoniaPujol.pdf Interactive Editor] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/linux-x86_64/Slicer3-3.6.1-2010-08-23-linux-x86_64.tar.gz Slicer3-3.6.1-2010-08-23] || Linux 64 ||08-27-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||08-25-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/f/f7/FreeSurferCourse_Slicer3.6_SoniaPujol.pdf Freesurfer Tutorial] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||08-25-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/f/fc/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.pdf Diffusion Tensor Imaging] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||08-25-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/3/3c/ProgrammingIntoSlicer3.6.1_HelloPython_MICCAI2010_SoniaPujol.pdf Programming in Slicer3 with Python] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||08-25-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/0/0a/ManualRegistration_Slicer3.6.pdf Manual Registration] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.12010-08-20] || Mac Darwin ||08-25-2010 ||All OK
|-
||[http://www.slicer.org/slicerWiki/images/e/eb/Slicer3Minute_SoniaPujol_3.6.1.pdf Slicer3Minute] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||08-25-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/0/00/InteractiveEditorTutorial_Slicer3.6_SoniaPujol.pdf Interactive Editor] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/darwin-x86/Slicer3-3.6.1-2010-08-20-darwin-x86.tar.gz Slicer3-3.6.1-2010-08-20] || Mac Darwin ||08-25-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/3/3b/Slicer3_DataLoadingAndVisualization_SoniaPujol3.6.pdf Data Loading and 3D Visualization] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP&7 ||08-25-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/f/f7/FreeSurferCourse_Slicer3.6_SoniaPujol.pdf Freesurfer Tutorial] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP&7 ||08-25-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/f/fc/DiffusionMRITutorial_Slicer3.6.1_SoniaPujol_Aug2010.pdf Diffusion Tensor Imaging] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP&7 ||08-25-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/3/3c/ProgrammingIntoSlicer3.6.1_HelloPython_MICCAI2010_SoniaPujol.pdf Programming in Slicer3 with Python] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP&7 ||08-25-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/0/0a/ManualRegistration_Slicer3.6.pdf Manual Registration] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP&7 ||08-25-2010 ||All OK
|-
||[http://www.slicer.org/slicerWiki/images/e/eb/Slicer3Minute_SoniaPujol_3.6.1.pdf Slicer3Minute] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP&7 ||08-25-2010 ||All OK
|-
|[http://www.slicer.org/slicerWiki/images/0/00/InteractiveEditorTutorial_Slicer3.6_SoniaPujol.pdf Interactive Editor] [http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training '''Slicer3.6 101 page''']||[http://www.na-mic.org/Slicer/Download/Release/win32/Slicer3-3.6.1-2010-08-23-win32.exe Slicer3-3.6.1-2010-08-23] || Windows XP&7 ||08-25-2010 ||All OK
|-

Questions, comments, and feedback can be sent to Kathryn Hayes (hayes@nmr.mgh.harvard.edu)

File:VMTK Slicer 3.6.3 Updated OCT 2011.pdf

2011-11-10T17:08:11Z

Haehn: New version of the SlicerVmtk tutorial on Coronary Arteries. Thx to Ana Ortiz.

New version of the SlicerVmtk tutorial on Coronary Arteries. Thx to Ana Ortiz.

Projects:ARRA:miAnnotation:Feedback

2011-09-13T20:45:23Z

Haehn: /* Displayable Manager */

= Feedback from Ron 08/24/11 =
* in general: Ron is very pleased with the top-level things

== The Text Dilemma ==
* problem: annotations are obstructing the images: this should NOT be the case
** fonts ugly
** text gets in the way of things you want to see
* different direction needed: show information in left bottom corner
** two kinds of information
*** software wants to show information (push)
*** user requests information (pull)
** in viewers: minimal information
** in bottom left corner of Slicer GUI: medium details
** somewhere else (in the annotation module): full details
** cdash example: way of not to do it -> important information is covered by annotations
** ohloh example: good example -> first minimal, then under cursor more details when probing
=== Possible Solution ===
* assign names (F1,F2,F3 for Fiducials, M1,M2,M3 for measurements, R1,R2 for ROI... ) and descriptions
** name appears in viewers
** description in bottom lower left on roll-over in viewers
** in annotation module: full details: Name, description, options

== General Changes (Target for RSNA release) ==
* take everything out which does not work properly (except for critical functionality)
=== Targeting the Text Dilemma ===
* name+description in bottom lower left (Steve)
** possible problem: mouse over event on vtk widgets might not be easily realizable. Plan C could be a query mechanism, where the user requests this information through a keystroke or such (if annotation detail is not available we will only show slice information and add annotation detail later).
* <strike> in viewers only name </strike>(Nicole)
** one letter naming checked in to svn 17837.
** using name instead of text checked into svn 17889.

=== Slim down the Annotation Module ===
* <strike>get rid of text annotation
* get rid of bidimensional annotation
* just three annotation types: fiducials, measurements (ruler), ROIs</strike>
** done in svn 17835

=== vtkWidget Changes ===
* <strike>ruler: ticks only in 2D, every centimeter, can be turned off </strike>(Alex)
** For now, turn off ticks in both 2D and 3D (Alex)
** Later, fix zooming in 2D, only have long (major) ticks at 1cm.
** Later, change to spheres for ticks (at 1cm) in 3D
* <strike>handles for all annotations zooming behavior: should be like Slicer3 </strike>(Alex)
* ROI needs a name in the future: requires infrastructure change (not for RSNA) (Alex)
* Later: don't turn off ruler visibility when endpoints are outside the viewport

=== Displayable Manager ===

* <strike>Coordinate issues</strike> (Daniel)
** <strike>Fiducials and Rulers show up in all slice views when they shouldn't</strike>
** <strike>Fiducials and Rulers 'jump' on mouse over</strike>
** fixed in rev. 18042

=== Qt GUI Changes ===
* property dialog re-design
** <strike>for RSNA: change default tab in property box: point tab for Fiducial, Ruler; ROI tab for ROI</strike> (Daniel)
** <strike>sliders in fiducial properties jumps weird: should have dynamic range or 0..20 for the beginning</strike> (Nicole) - fix checked in to svn 17904
*** size presets: medium is actual size, small and large presets (Nicole)
** property linking between elements of widgets so that the user has to change colors at one location
*** <strike>GUI: Qt Widgets</strike> (Daniel) (WIP uploaded to SVN 17896 and 17898)
*** MRML: DisplayNode changes (Nicole) to be done post-RSNA
*** add a button to change colour for all elements of an annotation (Nicole)

* <strike>hotspot icons for ruler placement: new icons on wendy's todo list</strike> (Wendy and Nicole) svn 17993.

* TreeView
** <strike> second eye should be removed</strike> (Nicole) - svn 18041.
** <strike> allow display/editing of node names</strike> (Nicole) - svn 18041.

* <strike>remove Create Panel</strike> (Daniel)
** <strike>replace by toolbar - do we really want to have the toolbar 2x? No!</strike> (Daniel)
** <strike>view transform in the toolbar: should be cancel</strike> (Daniel)
*** add a key (maybe ctrl) to have it pause mode (TODO later - now just option to cancel).

* <strike>screenshots and sceneviews go into toolbar</strike> (Nicole)

* <strike>take out advanced panel</strike> (svn rev. 17835)

=== MRML Changes ===
* changes related to linking properties (Jim)
* fiducial list, so that saving many fiducials do not creates so many files (Nicole)
** not creating a new node, will look at options to consolidate the fiducial files and support transforms of hierarchies of fiducials

=== Performance and Stability ===

* Testing (Nicole)
** <strike>add multiple fiducials, ROIs, rulers for timing</strike>
** test named py_AnnotationsTestingAddManyFiducials (adds 20 fids) added in svn 17892. Memory leaks causes test to fail on dashboard.
** tests named py_AnnotationsTestingAddManyRulers and py_AnnotationsTestingAddManyROIs added in svn 17900. ROIs leaking even more than Fids and Rulers.
* (Steve) Run tests on mac to profile where time is spent
* Volume Rendering multiple renders when fiducials are present (may be inherent in the widgets) (?) (Will + Julien)
* Fixing why the annotations lead to slowdowns
* Fix random crashes (all)
** Undo/Redo - disable all GUI appearances of undo/redo. (Alex)

Projects:ARRA:SlicerEM

2011-09-10T04:16:31Z

Haehn: /* Progress */

[[Projects:ARRASuplements|Back to Slicer ARRA home page]]
=Aim=
The EMSegmenter is a state-of-the-art segmentation tool within 3D Slicer. User feedback has reported that clinicians are currently unable to tune the approach to their acquisition protocol, as the user interface is too complex. This proposal addresses this issue by redesigning the user interface, focusing on hiding the complexity of the underlying segmentation algorithm. If successful, this will enable clinicians to automatically segment their own medical scans, even if the corresponding acquisition protocol deviates from the default setting for which the EMSegmenter is optimized.

=Research Plan=
The EMSegmenter is the result of 15 years of research in medical image segmentation. This has lead to a user interface that exposes a rich set of parameters. These parameters allow the tuning of the EMSegmenter to a wide variety of acquisition sequences. However, tuning these parameters is quite challanging. In addition, Slicer currently does not provide any tools for generating atlases, which are a set of parameters characterizing each structure of interest. We propose to address these issues by creating two user-friendly modules: one for generating the atlases and one for tuning the EMSegmenter to a specific acquisition sequence.

The first module, called Atlas Generator, builds the atlases characterizing each structure of interest. The user simply specifies the training data which can be done via querying XNAT, a database targeted towards medical image analysis. The user also selects the type of information to be extracted from the data. Possible types are the shape, intensity, or relative position of the structures of interest across the training set. Based on this input, the tool automatically generates the atlas.

The second module, called EMSegmenter-Simple, consists of a simple work flow that enables users to adjust the EMSegmenter to their specific acquisition sequence. As part of this proposal, we will create a library of templates, which parametrizes the tool to segmentation tasks frequently ancountered by our user community. User simply adopt the tool to their acquisition scenario by first selecting the proper template. In the second step, the user modifies the value of important parameters of the template. We simplify the tuning of these parameters by providing an instant feedback mechanism. The feedback mechanism updates the automatic segmentation according to the change in the parameter setting. This will allow users to to get an intuitive understanding about impact of certain parameters on the algorithm. In addition, each entry field will be accompanied with a help text. We will also create detailed documentation about the user interface and publish a tutorial for each template.

The project is viewed as successful if a properly trained clinician is able to modify the templates to their acquisition sequence within an hour.
= Events =
* Advanced EMSegmenter Training : How to parametrize the tool
** Where: 1249 Bolyston Street, Boston, MA
** When: 10 am - 1 pm , Feb 23, 2010

=Key Personnel=
20% Kilian Pohl <BR>
95% Dominique Belhachemi <BR>
5% Daniel Haehn<BR>
Kitware (Project Manager: Jean-Christophe Fillion-Robin)

= Documentation =
* [http://www.slicer.org/slicerWiki/index.php/Modules:EMSegmentTemplateBuilder3.6 EMSegmenter documentation] for Slicer 3.6
* [[Projects:ARRA:SlicerEM:Developer|Developer page]]

=Progress=
*09/10/11
**EMSegment4:
***'EMSegment Quick' in the works
***'Create new task' functionality done
*09/03/11
** EMSegment4:
*** fixed several issues (minor and major)
*** EMSegment4 extension in the works
* 08/26/11
** EMSegment4:
*** EMSegment wizard for Slicer4 done and ready for testing
*** Minor issues open: http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerEM:Slicer4#EMSegment_GUI_in_Qt
* 08/19/11
** EMSegment4:
*** patched CTK to support workflows in the desired way (disable error text)
*** patched CTK to support matrix widgets in the desired way (setValue was made Q_INVOKABLE)
*** work on advanced wizard steps 7 and 9
* 08/12/11
** EMSegment4:
*** implemented manual sampling infrastructure
*** fixed compilation issues and tests
*** optimized simple mode
*** work on advanced wizard step 7
*** created CTK patch to enhance the workflow functionality which is used by the EMSegmenter
* 08/05/11
** EMSegment3:
*** Restructuring internal task files to support multiple registration methods
*** acceleration bias field calculation by avoiding exp/log calculations
*** work on integrating Plastimatch registration, work on bugfixes
*** work on integrating DRAMMS registration, work on bugfixes
*** work on integrating ANTS registration, work on creating a extension based on ITK4
** EMSegment4:
*** Simple mode now running for all tasks
*** work on advanced mode
* 07/29/11
** EMSegment4:
*** all tests now run properly on different machines
*** preprocessing called from the GUI now runs properly
*** first successful segmentation using the new EMSegment GUI in 3D Slicer4
*** smaller fixes
** AtlasCreator:
*** fixed some bugs when using the dynamic mode
* 07/22/11
** EMSegment3:
*** work on integrating Plastimatch registration
*** work on integrating DRAMMS registration
*** work on integrating DEMONS registration
* 07/15/11
** EMSegment4:
*** work on finalizing wizard steps
*** work on the QtWidgets to reflect the behavior of Slicer3
**** support parcellation maps
*** added ability to change color map for labels in step 3
*** hooked up step 5 completely to mrml (registration types, interpolation, toolkit..)
** AtlasCreator:
*** integrated optional DRAMMS registration
* 07/01/11
** EMSegment4:
*** wizard GUI in Slicer4 almost like the Slicer3 versions
*** added ability to read dynamic frames from the tcl task files
*** first successful segmentation in Slicer4 running the commandline tool
*** worked on extension infrastructure for Slicer4
*** all EMSegment QT widgets are now available in Python scripted modules
*** a lot of cleanup
* 06/17/11
** EMSegment3:
*** Start working on white matter lesion segmentation pipeline
*** Added BiasCorrectionType to mrml structure to switch between different implementations
*** created new tutorial "EMSegmenter End User Tasks"
* 06/10/11
** EMSegment3:
*** Fixed WinXP 64bit bug (Avoid usage of 'mktemp' and 'touch' commands)
*** Implemented bias field correction
*** Tested mouse registration with CMTK
* 06/04/11
** EMSegment4:
*** Started development of the EMSegment4 wizard in Python (first in parallel to the C++ version, then later decide which to develop further)
**** Python would speed up development and provides cleaner code
*** Added compilation of the existing Qt widgets for the EMSegment as a static library which is accessible in Python
**** No re-write of the existing widgets (anatomical tree etc.) necessary when developing the wizard in Python
*** Created the AddDataIOToScene functionality for Slicer4 in team work with Slicer Core Developers
*** Fixed some bugs in the Slicer4 Tcl interface (Tpycl)
*** The EMSegmentCommandline Tool now runs better (still some issues)
**** Solved problem which prevented MRML NodeAdded and NodeRemoved events to be caught properly
* 05/27/11
** EMSegment3
*** Investigating how to add bias field correction code into the EMSegmenter
** EMSegment4
*** Finished Tcl Adapter for Slicer4
**** Added test: vtkSlicerCommonInterfaceTest1 to test the Tcl Adapter in both Slicer3 and Slicer4
*** Enabled compilation of all EMSegment Tests in Slicer4 including copying testdata to the appropriate places
*** Ran the NonHuman-Primate Segmentation Tcl Task file in Slicer4 without crashes
**** Problem: infrastructure for AddDataIOToScene is still missing in Slicer4 so MRML can not be loaded properly
* 05/20/11
** EMSegment3 Updates:
*** fixed a casting bug in the cineMR task
*** updated EMSegmenter tutorial
*** added option to command line module to load volumes centered
*** fixed failing tests (caused by the load volumes centered option)
*** merged branch with trunk
*** updated task page
*** start working on a bias field correction implementation (will be integrated into the EMSegmenter base algorithm)
** AtlasCreator
*** added the ignoreTemplateSegmentation option to the GUI
*** renamed the error if CMTK was not found to a warning
*** included detection of the background label when using automatic label detection (in most cases label 0)
**** use all segmentations to detect the labels automatically instead of only the first segmentation
*** added support for rigid registration with 6 DOF
*** added support for affine registration with 12 DOF
*** modified the GUI to be able to choose between "Rigid", "Affine (9 DOF)", "Affine (12 DOF)" and "Non-Rigid" registration
*** modified the commandline tool to be able to choose between the four deformation types
*** added a new example to the commandline tool
*** added a new test for "Affine (12 DOF)" registration
*** untied the AC completely from the EMSegmenter
** EMSegment4:
*** since the commandline tool does not compile in the Slicer4 extension, moved it temporarily to my local build and fixed some compilation issues
*** added the following functionality to the vtkSlicerCommonInterface to be usable from Slicer4:
**** EvaluateTcl(..)
**** SourceTclFile(..)
*** made progress on passing the vtkObjects through Python to Tcl in Slicer4
*** created http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerEM:Slicer4 to organize the transition to Slicer4
* 05/13/11
** EMSegment3 Updates:
*** integrated softDice computation in cineMR task
*** merged files carefully into the branch
*** integrate AtlasCreator (AC) in cineMR task
*** debugged a AC casting issue
*** added test for the AtlasCreator task
*** added intensity correction to cineMR task
*** added option --ignoretemplatesegmentation to EMSegmenter's AtlasCreator function in general
*** added cluster command text field to AC tasks
*** use centerImage="1" in all mrml files
*** fixed misalignment in MRIHumanBRainFullParcellation task
*** investigated whether or not the hammerwml module can be integrated in the EMSegmenter
*** helped user with their mouse brain task
** EMSegment4 Updates:
*** added Python support to the vtkSlicerCommonInterface
*** added infrastructure to use the AtlasCreator in EMSegment3 Tasks
*** fixed compilation of EMSegment4 and ported it to the Slicer3 trunk to have all EMSegment related code in one repository
*** worked on Tcl Connector
*** untied last strings between Commandline tool and KWWidgets
*** integrated the EMSegmentCommandline tool into EMSegment4 (only compiles in a Slicer4 tree not as part of an extension yet)
*** fixed compilation issue when Python was disabled
** AtlasCreator Updates:
*** merged into 3.6 branch
*** made generated scripts accesible by all
*** use lowercase strings to describe image types (fixed AC casting issue)
*** synced the Slicer base testing macros between trunk and branch to be able to compile the AtlasCreator tests properly
* 05/06/11
** EMSegment3 Updates:
*** New MRI-Human-Brain-Hemisphere task
*** Tested if the GUI produces same results as the command line (for the Human Eye task)
*** New cardiac segmentation task
*** let LogMean test fail if log file contains error string
*** fixed memory leaks
*** fixed differences in segmentation results between command line and GUI
*** Updated wiki
*** added compare test
*** integrated atlas creator in a EMSegmenter task
** EMSegment4 Updates:
*** initialize the AtlasCreatorCxx libraries in the Commandline Tool to be able to use the vtkMRMLAtlasCreatorNode from Tcl
*** worked on using the AtlasCreator python module in the EMSegment Commandline Tool
*** worked on the python-tcl interface for slicer4
*** purged KWLogic class and replaced it with the logic
*** outsourced all Tcl commands in a separate class which is valid for Slicer3 and Slicer4: vtkSlicerCommonInterface
*** switched the EMSegmentCommandline, TclInterpreter, Converter to the new vtkSlicerCommonInterface
** AtlasCreator Updates:
*** added the option to specify the number of Threads
*** in command line: --numberOfThreads X
*** in the GUI: Number of Threads under Misc.
*** if the number of threads are not specified, the AtlasCreator always sets the maximal number of threads for the individual machine
*** setting the cluster mode has no effect on this setting and it will behave the same way (maximal number of threads by default)
*** save the template as template.nrrd insteaf of template..nrrd
* 04/29/11
** EMSegment3 Updates:
*** Added function call to simplify GenericTask.tcl
**** proc CMTKGetPixelTypeFromVolumeNode { volumeNode }
*** Updated HumanEye task
*** Updated CT-Hand-Bone task
*** Updated MRI-Human-Brain task
** EMSegment4 Updates:
*** Adopted the newly available Slicer4 extension infrastructure for the EMSegment4 extension
**** worked together with Kitware on solving issues due to the complexity of our extension (still work in progress)
*** fixed some segfaults and changes in the API (f.e. vtkMRMLAnnotationROINode instead of vtkMRMLROINode, vtkGraph calls etc..)
*** introduced TclConnector which provides an interface to Tcl in Slicer3 and Slicer4 (still work in progress)
** AtlasCreator:
*** disabled tests on Windows in Trunk and Branch
*** modified Wiki page with a hint
*** added feature: show hostname of the head node in the logs
*** fixed bug: use the correct file extension for saving the template
*** fixed bug: don't always use testmode in commandline mode
* 04/22/11
** EMSegment4 Updates:
*** Removed the old versions of the EMSegmenter in Slicer4 since we want to include it now as an extension
*** Created first version of the Slicer4 EMSegment extension, available at a Git repository: https://github.com/haehn/EMSegment4 until the extension infrastructure in Slicer4 is ready
*** The new extension uses the algorithm and logic parts of the Slicer3 module to avoid code duplication and to include all recent changes
*** Modified the Qt GUI to support the new EMSegmenter MRML structure: MRML files from tasks in Slicer3 can now be loaded into Slicer4 to start configuring the GUI
** EMSegment3 Updates:
*** fixed failing test EMSegCL_Task_NonHumanPrimate_BRAINS_small by setting LogCovarianceCorrection="0.01 "
*** fixed failing test EMSegCL_Task_MRIHumanBrainExp_BRAINS_small by setting LogCovarianceCorrection="0.01 0 | 0.01 0 "
*** removed unused label(class) 3 and 7 from Human Eye task
*** applied the Human Eye task on 5 test cases
*** Updated the CT-Hand-Bone task. Replaced the anatomical tree. This task is now using a medical terminology to describes the anatomical tree.
* 04/15/11
**Congealing Updates:
***Created a Slicer extension for the Congealing project based on ( https://github.com/debonet/Congealing )
***The extension is compiling successfully in debug mode on Linux and Mac
**EMSegmenter Updates:
*** Added new task 'Human Eye'
*** Separated EMSegmenter GUI (using KWWidgets) from EMSegmenter base code.
*** Future versions of the EMSegmenter GUI in Slicer4 (using Qt) can be linked against the same base code.
*** Fixed tests
**AtlasCreator Updates:
*** included monitoring mode: ComputeMeanImage-, Registration-, Resampling- and CombineToAtlas-Jobs are now monitored for successful computations.
**** Whenever a failure happens, these jobs get restarted up to 4 times. After that, the Atlas Generation will continue if possible or abort if something required is missing.
*** Added 4 Tests which run on a Nightly base to check if the AtlasCreator is still working.
*** Added version 0.4 to Slicer Trunk and 3.6 Branch
*** Updated the 3.6 Branch Base with necessary recent patches to make the AtlasCreator work
*** Successful manual tests
*** Added Documentation for the Atlas Creator: http://www.slicer.org/slicerWiki/index.php/Modules:AtlasCreator
* 04/08/11
**EMSegmenter Updates:
*** Changed the default colormap to "GenericAnatomyColors.txt"
*** Added new commandline option to switch on/off particular preprocessing steps (--TaskPreProcessingSetting="|C0|C0")
*** Added commandline option (--atlasVolumeFileNames), so we can use the original mrml files, instead of duplicating them
*** Prepared new CMTK extensions for all 3 platforms (Linux,Mac,Windows), compiled in Release mode with platform specific optimization flags. The speed up is 5x-6x
*** Implemented a new task to call the AtlasCreator from within the EMSegmenter
**Atlas Creator Updates:
*** detect labels automatically when using external invocation or the command line tool which was so far only possible in the GUI
*** normalization of atlases does not force the float type anymore
*** finished first version of CongealingCLI wrapper in terms of our un-biased groupwise registration effort and commited it to the Slicer3 trunk
**** created documentation for the wrapper: http://www.slicer.org/slicerWiki/index.php/Modules:AtlasCreator:CongealingCLI
*** added infrastructure to Slicer base to support the Invoke function in connection with KWWidgets
*** handle events in MRML/GUI now properly and loop-safe
*** only create new output folder if the configured one is not empty (now consistent between CLI and GUI)
*** fixed a bug in connection with normalize when using the GUI
*** fixed a possible crash when using the GUI and loading the generated atlases into Slicer
*** added events to the comboboxes and write out MRML on change using the new Invoke method
*** fixed possible memory leaks when using the GUI and exiting Slicer
*** in pair fixed mode, also consider the defaultCase segmentation when combining to an atlas
*** in pair fixed mode, also consider the defaultCase original when generating the normalized IntensityMap of all aligned images
*** fixed possible error when selecting the defaultCase in the GUI: instead of the originals, a segmentation was selected
*** added Testing, for now only a simple vtkMRMLAtlasCreatorNode test
*** also, made sure to copy the TestData to the Slicer3 shared modules directory
* 04/01/11
**Atlas Creator Updates:
*** introduced vtkMRMLAtlasCreatorNode::InitializeByDefault() to set default values to the attributes of the MRML node
*** re-structured the complete Graphical User Interface
**** added events for all GUI elements to store the current state to MRML
*** tested MRML import/load concept with AtlasCreator configurations successfully
*** ran tests on SBIA cluster and identified need of mechanism to restart unsuccessful registration jobs
*** optimized clean-up on Slicer shutdown
*** added infrastructure to the 3D Slicer base to support listening to MRMLScene events without a corresponding calldata like the MRMLClose event
*** PCA Analysis now fully integrated
**** added new options to configure PCA modelling --pcaMaxEigenVectors X and --pcaCombine to the command line tool and the GUI
*** Groupwise Registration effort:
**** hands on Congealing sourcecode and successfully compiled it in different environments
**** analyzed code and defined next steps with collaborators
*** updated http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerEM:AtlasCreator#Priority_List
* 03/25/11
**EMSegmenter Updates:
*** The Atlas Creator can now be called from within a tcl script.
*** Added a test script for this kind of invocation
*** The results of the Atlas Creator are now written back to the MRML scene for further processing
*** Performed static code analysis on the EMSegmenter
*** Helped user (WUSTL) to find the optimal setting to segment their MRI data.
*** Restructured the EMSegmenter tests
**Atlas Creator Updates:
*** finished ITK implementation of combineToAtlas step (including normalization, re-casting..) called ACCombiner
*** a lot of bug-fixing, tweaking and performance enhancing
*** replaced the deprecated os.system calls to execute processes by the subprocess methods (new python API)
*** re-structured advanced panel in GUI
*** included PCA analysis capabilities using TCL (80%)
**** available in the command line tool using --pca flag
*** switched the CLI and the logic from the old configuration containers to use the vtkMRMLAtlasCreatorNode
**** it is now possible to configure a MRML Node and invoke a launch event to start an AtlasCreator computation
****also, the API of vtkMRMLAtlasCreatorNode slightly changed to support the NormalizeTo and the DebugMode and DryrunMode settings
*** moved ACCombiner to ACITKTools
**** added new pure ITK tool in ACITKTools, called ACMeanImage to compute a meanImage of a bunch of images
**** edited the AtlasCreator logic to use the ACMeanImage tool instead of computing it in the logic class
**** integrated the ACMeanImage tool in the AtlasCreator cluster API
**** as a result, finally all computation is moved from the headnode in cluster mode, even no images get loaded on the headnode
*** added the feature to return as output as well the normalized intensity maps of aligned cases in dynamic and static mode
*** coordinated effort on integrating Groupwise Registration (see http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerEM:AtlasCreator:Groupwise)
* 03/18/11
**EMSegmenter Updates:
***ENH: Use Colormap="vtkMRMLColorTableNodeFileSlicer3_2010_Brain_Labels.txt"
***ENH: Update description of preprocessing checkboxes
***BUG: CMTK's registration/warp command cannot change the scalar type of the output volume, resample the atlas in an additional step
***ENH: Adding task for skull stripped brain images
***BUG: (BSplineToDeformationField) Send normal output to stdout instead of stderr , Use 'eval exec ' to execute a command
***BUG: Improve error handling for function calcDFVolumeNode
**Atlas Creator Updates:
*** added fix to perform re-casting only when necessary to enhance performance
*** included distributed computation of the last step: combineToAtlas including re-casting and normalization
**** pure ITK code without XDISPLAY dependency
**** as a result, all computation steps (registration, resampling, combining) now support a cluster environment
*** solved problem of compiling CMTK on SPL cluster
*** added the ability to normalize the atlases to 0..X instead of only 0..1
**** supported in GUI and command line tool
*** added fix to only register/resample images where segmentations exist and vice-versa
*** created proof of concept to run the Atlas Creator from the EMSegmenter using MRML
*** coordinated effort on integrating PCA Analysis (see http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerEM:AtlasCreator:PCA)
*** coordinated effort on integrating Groupwise Registration (see http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerEM:AtlasCreator:Groupwise)
* 03/11/11
**EMSegmenter Updates:
*** Moved IO related functionality into base code
*** ENH: Moved duplicated initialization code into a methed, bumped version number to 3.6.4-beta
*** ENH: pass --fast --verbose options to each CMTK call
*** ENH: Refactoring, move replicated code to new EMSegmentHelper file
*** Adjusted Sandbox so it can use the current EMSegmenterHelper file
*** Investigated a segfault during registration, CMTK's (nrrd reader) couldn't handle uint's , this is now fixed in the newest CMTK
** Atlas Creator Updates:
*** Ran several tests and uploaded the data to http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerEM:AtlasCreator:Tests
*** Identified and fixed problem with CMTK where certain labels were included in other atlases (see URL above, f.e. label 3 and label 9)
*** Commited new version to the Slicer trunk including:
**** Don't use Slicer temp dir anymore, use a temp dir in the output dir instead
**** Refactored cluster mode to be based on a script
**** Cluster script template (template.sh) is configurable for individual needs
**** Added support for CMTK non-rigid registration
**** De-activated multi-threading in cluster-mode for CMTK and BRAINSFit
**** Different wait time for cluster mode for observing finished jobs
**** Added date to print timestamps
**** Distributed computation of Resampling
*** Updated Priority List for new releases on http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerEM:AtlasCreator
*** Started working on integrating PCA Analysis (see http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerEM:AtlasCreator:PCA)
*** Started effort to include Groupwise Registration (see http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerEM:AtlasCreator:Groupwise)
* 03/04/11
** Update MRI Human Brain Atlas (removed area around the brain)
** Tutorial-Simple updated for Slicer 3.6.3 release
** Tutorial-Advanced updated for Slicer 3.6.3 release
** Tutorial tested for 101 training page
** further work on the skull striper
** work on integrating I/O function into base
** Maintenance work for the Slicer 3.6.3 release
** Atlas Creator Updates:
*** fixed a huge bug which modified the orientation of images during save/load cycle
*** added feature to create a unique output directory automatically
*** added guess background level functionality using EMSegment logic for CMTK and BRAINSFit
*** released AtlasCreator version 0.21 as a fully usable module
*** created test and example section for created atlases ( http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerEM:AtlasCreator:Tests )
**** including fixed and dynamic registrations using CMTK and BRAINSFit on 50 cases
*** planned coming releases v0.3 and v0.4 http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerEM:AtlasCreator#Priority_List
*** installed Slicer Trunk on SPL cluster
**** commited required fixes to Slicer base
**** documented on SPL Intweb ( https://intweb.spl.harvard.edu/Dell_Linux_Cluster#How_to_compile_3D_Slicer_3_on_the_cluster.3F )
* 02/25/11
** EMSegmenter Updates:
*** CMTK: Added support for multiple scalartypes
*** CMTK: set the backgroundLevel to get rid of the segmentation errors outside the target volume
*** updated the MRI Human Brain atlas
*** work on the skull striper
*** use qsub for running Slicer tools in the cluster (batch mode)
*** use xvfb for Slicer tools which use the X protocol
** Atlas Creator Updates:
*** introduced vtkMRMLAtlasCreatorNode
**** It is possible to create a new AtlasCreator MRML Node and configure it
**** the node can then be used to trigger an Atlas Creator computation by firing a Launch event
*** introduced CMTK integration
**** command line interface of the AtlasCreator supports adding the "--cmtk" flag to the command
**** CMTK gets automatically detected, if installed as a Slicer extension
*** optimized the handling of Double and Float images with BRAINSFit
*** fixed and dynamic registration ran successfully on the SBIA cluster
*** implemented the ability to listen to MRMLScene events in the Slicer3 Python Framework (Slicer Base)
**** this enables listening to custom MRML Node events
**** created small example on Slicer wiki: http://www.slicer.org/slicerWiki/index.php/Slicer3:Python:ProcessMRMLEvents
*** provided mrml scene example for a fixed registration with 6 cases ( http://wiki.na-mic.org/Wiki/index.php/File:SceneFixed6Cases.zip )
*** fixed bug in the Slicer3 Python Framework (Slicer Base) to exit Slicer correctly after using --evalpython
*** created infrastructure to include C++ code in the AtlasCreator module using a GUI-less module approach
**** included vtkImagePCAFilter and vtkImageKilianDistanceTransform as C++ filters successfully
*** fixed overflow problem in connection with dynamic registration
*** added the feature to remove all used temporary resources (cleanup)
*** enabled the AtlasCreator C++ Code in the EMSegmentTclInterpreter (to test PCA filters)
*** additional smaller fixes
* 02/18/11
** EMSegmenter Updates:
*** Our Mac OS X Server is submitting 2 fresh nightly builds of the Slicer3/branch-3-6 and the Slicer3/trunk to the dashboard. The names are MORRICONE and MINKOWSKI.
*** Slicer3 (with python support) has been successfully installed on UPenn's SBIA cluster. OS: CentOS release 5.5 (Final)
*** Adjusted parameter for CMTK so that it can be used in a fast mode (below one hour) and in a accurate mode (multiple hours).
*** EMSegmenter maintenance
** Atlas Creator Updates:
*** created a new command line interface (python atlascreator.py)
**** including help and examples
**** details available at the website http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerEM:AtlasCreator#The_Atlas_Creator_Command_Line_Interface
*** fixed a blocker, where the resampled images where not used for Atlas generation
*** found a BRAINSFit error in connection with dynamic registration which only appears on SPL machines
**** investigated how to use CMTK as an alternative to BRAINSFit
*** identified a problem with Slicer3 --evalpython
*** commited a fix for a memory leak error when running the Atlas Creator
*** Enabled code for PCA computation on local Slicer, still in the works, commited some fixes to specific SVN
*** created and included UML diagrams on Wiki site
*** created and included screenshots on Wiki site
*** template now gets loaded into Slicer as well.
*** temporary files are now saved in a subdirectory with a unique name so the Atlas Creator can be run multiple files without moving anything.
*** in cluster mode, multi threading is now disabled.
* 02/11/11
** Installed MacOS and WindowsXP test machines
** It is now possible to use a temporary directory with white spaces (this was a bug on Windows XP)
** Added manual sampling to EMSegmenter module
** Atlas Creator Updates:
*** Generalized API to be able to run the Atlas Creator from external modules or using the Slicer launcher via command-line
**** Used the opportunity to extensively comment the code
*** Implemented Support for Parallelized Computation on a Cluster
*** Finished Dynamic Registration against Mean of images
*** Added mode to use existing transforms (f.e. to re-generate an Atlas)
*** Added in-module help
*** Smaller Fixes and Changes
*** Merged latest version to Slicer 3.6.3 branch - ready for release
*** Updated [[Projects:ARRA:SlicerEM:AtlasCreator]]
* 02/04/11
** option intermediate results directory is created for the user
** clarified the usage, helped collaborators with the EMSegmenter
** Windows specific runtime bug fixed, happened whenever we used an iterator two times.
** Included detailed verbose printout in EMSegmentCommandLine
** Added test results to MIDAS server
** Use CMake to compare segmentation results with precomputed segmentation results
** Further cleanup code (Number of registration flags simplified)
** Simplified MRML structure(removed nodes)
** Check if atlas files are properly downloaded to avoid FetchMI checksum checks
** Fixed bug in test EMSegCL_IntermediateResults: "UpdateScene: error getting 0th storage node"
** Updated template creator to new MRML structure ([[Projects:ARRA:SlicerEM#MRML_Structure|new MRML structure]])
** Fixed the updated functionality for EMSegmenter
*** also transferred fix to Extension wizard (was very quick)
*** added new repository for 3.6.3 for EMSegment tasks
*** fix for the new webserver index files and therefore do not need the index.html
*** committed all code to 3.6.3 Branch and Trunk
*** tested on Mac and Linux
** Atlas Creator Updates:
*** Created diagram of Atlas Creator workflow
*** Support for Normalization of output Atlases done
*** Support for Selecting the Output Cast done
*** Re-Designed API
**** Focus on Cluster proposal
**** Focus on external invocation (command line or 3rd party module in 3D Slicer)
*** Introduced Configuration Concept
*** Documentation, Diagram and Priority List updated at [[Projects:ARRA:SlicerEM:AtlasCreator]]
* 01/28/11
** Fixed a bug in the test 'intermediateResultsDirectory'. The test doesn't use the results file which is specified in the mrml scene. Instead it is using a test specific results file(specified in the CMake template).
** Fixed a Slicer4 bug : "ENH: Call the GeneralGauss(...) functions instead of the FastGauss(...) functions - this avoids type punning" Modules/EMSegment/Graph/vtkImageCurveRegion.cxx [15896]
** Fixed a Slicer4 bug : "BUG: Use a normal gauss function to avoid type-punning" QTModules/EMSegment/Widgets/vtkPlotGaussian.cxx
** Worked on the CT-Hand-Bone task
** Worked on a EMSegmenter specific skull stripper
** Atlas Creator Updates:
*** Research and Proposal of running the Atlas Creator in a cluster environment
*** Several GUI Fixes
*** Support Dynamic Registration (in the works)
*** Support for using existing Registrations by loading deformation fields (in the works)
*** Support for Normalization of output Atlases (in the works)
*** Support for Selecting the Output Cast (in the works)
*** Merged Export of Deformation Fields and Export of Transforms
* 01/21/11
** Worked on new CT-Hand-Bone task
** Maintaining work on existing tasks
** Added new features to the Atlas Creator
*** New wiki page [[Projects:ARRA:SlicerEM:AtlasCreator]]
* 01/14/11
** Created a test for the MRI-Human-Brain-Full-Parcellation task
** Worked on failing tests if compiling Slicer3 with Superbuild
** Worked on new CT-Hand-Bone task
** Worked with Wendy on new ideas how to make FetchMI more rubust
* 01/07/11
** Created new Atlas Creator module for Slicer3
** Created new Wiki page for [http://www.slicer.org/slicerWiki/index.php/EMSegmenter-UseCaseAdvertisement Call for Datasets for the EM Segmenter Use Case Library]
* 12/31/10
** Help debugging FetchMI bugs [http://www.na-mic.org/Bug/view.php?id=1027 1027] [http://www.na-mic.org/Bug/view.php?id=983 983]
** Updated [http://www.slicer.org/slicerWiki/index.php/EMSegmenter-Tasks:MRI-Human-Brain-Parcellation MRI-Human-Brain-Parcellation]
* 12/24/10
** Add postprocessing to segmentation, which includes island removal and subparcellation of tissue classes
* 12/17/10
** Added down-sampled image data for testing purposes
** Added two tests for each task
** Added UPenn logo to the EMSegmenter acknowledgment section
** Work on FetchMI bugs
** Updated Wiki page for the task MRI-Human-Brain-Parcellation
* 12/10/10
** Added wrapper for SkullStripperCLI to GenericTask.tcl
** Updated CMTK extension, using now Torsten Rohlfing's repository: https://nitrc.org/svn/cmtk/tags/Slicer3
** Updated Advanced Tutorial based on Ron's comments
** Added functionality to threshold target image(s), negative values will be set to 0 so that the EMSegmenter can be used on those images
* 12/03/10
** Create a new Wiki page for the EMSegmenter Task Library [http://www.slicer.org/slicerWiki/index.php/EMSegmenter-Tasks]
** Updated task files and documentation
** [http://www.slicer.org/slicerWiki/index.php/EMSegmenter-Tasks:MRI-Human-Brain MRI-Human-Brain]
** [http://www.slicer.org/slicerWiki/index.php/EMSegmenter-Tasks:MRI-Human-Brain-Parcellation MRI-Human-Brain-Parcellation]
** [http://www.slicer.org/slicerWiki/index.php/EMSegmenter-Tasks:Non-Human-Primate Non-Human-Primate]
** Fixed a apache server issue to update tasks in Slicer 3.6.2
* 11/26/10
** Fixed bug: when creating new task that registration was performed regardless if it was selected or not
** Worked on test cases for 'Non Human Primate' pipeline
* 11/19/10
** Created a new EMSegmenter Tutorial (simple mode) - (for quick results, no need to change parameters, this will be useful to clinicians)
** Created a new EMSegmenter Tutorial (advanced mode) - for experienced user of the EMSegmenter
** Created the new 'MRI Human Brain Parcellation' pipeline and added to 3D Slicer 3.6.2 (collaborators: Padmapriya Srinivasan and Sylvain Bouix, PNL BWH)
* 11/12/10
** Restructuring EMSegmenter's Tasks folder to support multiple pipelines
** Start working on a 'MRI Human Brain Parcellation' pipeline (collaborators: Padmapriya Srinivasan and Sylvain Bouix, PNL BWH)
** Start working on a 'Non Human Primate' pipeline (collaborators: Andriy Fedorov, BWH)
** Slicer 3.6.2-RC2 maintenance
* 11/05/10
** software testing for Slicer 3.6.2 release
** Added new test for option --intermediateResultsDirectory
** Fixed bug 1023: MRML import doesn't read copied mrml scenes reliable
** Fixed bug 1025: Slicer crashes when BRAINSFit returns error
* 10/29/10
** Pop up error message when performing segmentation
** Add CMTK in Generic.tcl
** BUG: use .mat extension for transformation files" GenericTask.tcl
** Bug fixing with Slicer Base Code developers
* 10/23/10
** Bug fixes for Slicer 3.6.2 release
** Memory leak fixed
** comment-out unused code in MRI-Human-Brain.tcl
* 10/15/10
** Added function for automatically generating Template File
** Added function for downloading task files from web
** Added CMTK to extension module
** One can assign now tcl file when creating a new task
** Added class name to all tabs
** Tested command line
** Created virtual machines to submit tests reports to the dashboard
** Created Popup window when an error message appears in pre-processing and segmentation
** EMSegmenter works now with different image data types (short, float,...)
** Removed several bugs in mrml structure

* 10/8/10
** Added the --tmp_dir option to the start up allowing one to specify slicers temporary directory
** Fixed the leaks in the nightly tests
* 10/1/10
** Removed command line nodes from mrml scene after the command line is executed
** Added functionality to call N4ITKBiasFieldCorrectionCLI from EMSegmentCommandLine
** Added label - in addition to the tree - to show the selected anatomical tree node
** Patched KWWidgets to specify configuration directory (like /tmp/.3D\ Slicer\ Version\ 3.6.2-betarc)
** Working on parallel execution of multiple instances of the EMSegmentCommandLine
* 9/24/10
** Added check to make sure that the user cannot delete the root node
** Added a warning to avoid ambiguous input channel names
** Added check for emtpy 'Task Name'
** Added a label to show the selected node during specifying the priors
** Alpha value was not correctly transfered from node to vtkImageEMLocalSegmenter
* 9/17/10
** 969 fixed: missing quick timeout if connection to web resource is blocked (closed, see commit 14981+14982)
** 954 fixed:EMSegmentCommandLine throws errors if started from a current working directory different than ./Slicer3-build
** 948+958 fixed:EMSegmentCommandLine segfaults in cleaning up mrmlScene step
** 959 fixed: EMSegmenter ignores option --disableMultithreading
** Added progress dialogs for pre-processing and segmentation
** Test GUI on Linux, Windows, and Apple for Slicer 3.6.2 release
* 9/10/10
** Investigating a critical segfault bug 948+958
** Reviewing use of the extension manager for our needs
** Resolved bugs 970, 959, 944, 943
* 9/3/10
** Updated [[Projects:ARRA:SlicerEM#Image_gallery|Image gallery]]
** Refine Anatomical tree widget (Probability map integrated, Icon associated with structure name, ...)
** Now possible to design step directly from QtDesigner
** Discussed integration of PNL kMeans pipeline into Slicer 3.6
** Discussed integration of CNL workflow as a EMSegmenter pipeline into Slicer 3.6
** Discussed differences between the SBIA cluster and the BWH cluster,
*** Conclusion: SGE seems to be easier to handle than Lava
** Working on bug 959: EMSegmenter ignores option --disableMultithreading

* 8/27/10
** Integrated Workflow manager with QtModule
** Review Workflow manager API
** Fix bug related to PythonQt wrapping
** Now possible to update atlas class weight, atlas weight and alpha value directly from the Anatomical tree
** Updated EMSegmenter related Wiki pages
** Testing EMSegmenter command line executable in a Sun Grid Engine (SGE) environment (branch 3.6 + trunk)
*** working on related bugs 954, 955, 948
*** changing some stderr output to stdout
** Updating EMSegmenter tutorial for Slicer 3.6
* 8/20/10
** Ported anatomical tree widget and list of input channel - The anatomical tree is generic enough and re-used.
** Added [[Projects:ARRA:SlicerEM#Image_gallery|Image gallery]]
* 8/13/10
** Meet with Kilian - review panels and widgets and talked about which features should be improved, changed or omitted
* 8/6/10
** Now possible to enable wrapping of QtModule (Gui, UItools) in Slicer through CTK/PythonQt
** Discuss how TCL script interacted with the KWWidgets workflow manager
* 7/30/10
** The port of the Workflow manager is initiated
** Created Qt static panel skeleton corresponding to the step of MRI human brain workflow
** Ability to script task in python is something important. Re-prioritize the task.
** Discussed how dynamic panel could be ported.
* 7/23/10
** Reviewed [[Projects:ARRA:SlicerEM:Developer#Milestones|milestone]] and list of [[Projects:ARRA:SlicerEM:Developer:QtWidgets|widgets to port]]
** Created initial directory structure
** Initiated the conversion of Graph/Algorithm/MRML code to separate shared module
** The port of existing TCL function related to processing is low priority
* 7/16/10
** First weekly meeting between Kitware and UPenn. Meeting will always be held after the Annotation/QT tcon.
* 7/9/10
** Remove bugs
** Set up contract with Kitware to port GUI to QT
* 7/2/10
** Hired Dominique Belhachemi
** Transfered grant from IBM to UPenn
** Wrote Progress Report
* 6/25/10
** Addressed all EMSegmenter bug in Mentis
* 6/18/10
** Revising task for MRI brain segmentation
** Started search for new hire
** Make EMSegmenter work with Slicer Superbuild
* 6/11/10
** Updated [http://www.slicer.org/slicerWiki/index.php/Modules:EMSegmentTemplateBuilder3.6 EMSegmenter documentation] to reflect changes in Slicer 3.6 interface
** Fixed major bugs so that Slicer 3 does not crash when creating a new task
* 6/04/10
** Imbedded BRAINSFit registration in the pipeline
* 5/28/10
** Changed Simple version of EMSegmenter to work with new preprocessing structure
* 5/21/10
** Fixed class overview window
* 5/14/10
** Fixed Intensity graph distribution display
* 5/07/10
** Fixed EMSegmenter command line module
* 4/30/10
** Debugged EMSegmenter for Slicer 3.6 release
* 4/23/10
** Added segmentation button at each Step of the Wizard
** Integration of 3D/2D Bounding Box selection
*4/16/10
** Updated Slicer 3.6 Documentation
** Modified workflow of Slicer 3.6
*4/9/10
** Created simple interface for preprocessing
*4/2/10
** Incorporated Bug fixes from Slicer 3.4 into trunk
** Removed bugs so that selecting tasks from a list properly works
** Rolled EMSegmenter back to Slicer version 3.4
** EMSegmenter Research environment now compiles under windows
*3/26/10 Help users of EMSegment to adopt the tools to their needs
*3/19/10 Manuscript was accepted by CVPR 2010 for poster presentation
*3/12/10 Start organizing tutorials for EMSegmenter
*3/05/10 Extended first step in EMSegmenter to include default task list
*2/26/10 Removed bug so that api interface returns the same results as GUI version in Slicer2.6 . Trained members of CNL, BWH in segmenting lesions from MR brain images. Introduced CNL team to post processing tools for lesion segmentation.
*2/19/10 Working with Andrey Fedorov begin_of_the_skype_highlighting end_of_the_skype_highlighting begin_of_the_skype_highlighting end_of_the_skype_highlighting begin_of_the_skype_highlighting end_of_the_skype_highlighting begin_of_the_skype_highlighting end_of_the_skype_highlighting begin_of_the_skype_highlighting end_of_the_skype_highlighting, BWH, to customize the EMSegmenter to non-human primate brain images
*2/12/10 Presented Slicer to IBM Health Care Division
*2/05/10 Transferring Responsibilities for the EMSegmenter in Slicer 3.5 from MIT to IBM
*1/29/10 Migrated EMSegmenter Research Environment from Slicer2 to Slicer3
*1/22/10 Created slides for NAC Site visit
*1/15/10 Started to resolve bugs that requires collaboration between Kitware, BWH, and IBM team
*1/8/10 Trained members from BWH and Virginia Tech on using EMSegmenter on Non-Human primate data
*1/1/10 Addressed all major bugs listed in Mantis for Slicer Version 3.4
*12/25/09 Setup Slicer environment for new hire
*12/18/09 Hired Yong Zhang to help with maintenance of EMSegmenter
*12/11/09 Learned about programming user interfaces in Qt
*12/04/09 Interviewed applicant for Post Doc position to work on this project
*11/29/09 Removed bugs related to updated CMake version
*11/20/09 Organize bugs related to EMSegmenter
*11/13/09 Tcon featuring the EMSegmenter - participants Andriy Fedorov, Sylvain Jaume, Stuart Wallace, Kilian Pohl - Result of discussion
** Sylvain will fix EMSEgmenter bugs Slicer 3.5
** Kilian will fix any EMSegmenter bugs in Slicer 3.4 and earlier
** Andriy is developing a segmentation pipeline for the Wake Forest Data
** Stuart will do testing of the EMSegmenter module
*11/06/09 Meet with Jean-Christophe Fillion-Robin from Kitware to discuss integration of Qt in 3D Slicer
*10/30/09 Organized Monthly TCon between EMSegmenter developers
*10/23/09 Organized onsite interview , got in contact with Steve Pieper to discuss next steps, installed Slicer3
*10/17/09 Started interviewing postdoc as well as solving several HR issues for hiring personal<BR>

= Image gallery =

<gallery heights=300px widths=350px perrow=3 caption="EM Segmenter - Port to Qt">
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep1.png|Step1 - Define Task
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep2.png|Step2 - Define input channels (Advanced mode)
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep3.png|Step3 - Define anatomical tree (Advanced mode)
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep4.png|Step4 - Define atlas (Advanced mode)
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep5.png|Step5 - Edit Registration Parameters (Advanced mode)
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep6.png|Step6 - Define preprocessing (Advanced mode)
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep6-q1.png|Step6 - Define preprocessing (Advanced mode)
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep6-q2.png|Step6 - Do you want to redo preprocessing of input images ? (Advanced mode)
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep7.png|Step7 - Specify Intensity Distribution (Advanced mode)
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep7-plot.png|Step7 - Plot Distribution (Advanced mode)
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep8.png|Step8 - Edit node-based parameters (Advanced mode))
Image:Projects-ARRA-SlicerEM-Developer-EMSegment_Qtstep9.png|Step9 - Run Segmentation)
</gallery>

=MRML Structure=

<gallery heights=300px widths=600px perrow=2 caption="EM Segmenter - MRML Structure">
Image:EMS MRML Structure 2010.png | EMS MRML Structure 2010
Image:EMS MRML Structure 2011.png | EMS MRML Structure 2011
</gallery>

Projects:ARRA:miAnnotation

2011-09-10T04:14:33Z

Haehn: /* Progress */

[[Projects:ARRASuplements|Back to Slicer ARRA home page]]

= Aim =
[[Image:SlicerAM_QtAnnotation.png|241px|right|Annotation Module]]

Medical images often contain a wealth of information, such as anatomy and pathology, not explicitly accessible. One way to address this issue is via image annotation and markup. We propose to create a comprehensive framework for annotation and markup within 3D Slicer, enabling users to capture structured information easily. Furthermore, we will develop schemas for saving and recovering this information into and from XNAT, allowing queries of larger data sets of medical scans. This tool will provide clinicians with a relatively simple way to capture information latent in medical scans, and also to select micro-cohorts of medical scans for studying diseases.

= Research Plan =
3D Slicer currently provides very basic technology for annotating images. This limits users in their ability to properly capture semantic information contained in images and data sets. We propose to address this issue by expanding Slicer's mark up and annotation capabilities. New features will include:
* a rich set of geometric objects for improved visual differentiation between annotations
* markers for measuring anatomical characteristics, such as the volume of an annotated region, to provide patient specific information difficult to extract from visual inspection
* entry fields beyond free-text, such as graphics and external data, to capture comprehensive information and support for emerging domain specific ontologiesand
* a full integration of these capabilities with the mrml tree to support Scenesnapshots, load, save both to disk and XNAT.

We will implement these features by developing two different modules. The first module, called Marker Module, creates different types of markers based on current ITK technology. The user defines the appearance of the marker by specifying its color, size, and shape, such as points and 3D boxes. The user also labels each marker with tags and specifies its function, such as measuring the volume of a region.

The Annotation Module, the second module, provides the interface for annotating images with these markers. Users place the markers on the image and further specify the semantic information through free text, plots, and references to ontology and internet. The annotations are shown both in 3D and 2D viewers. The module also allows annotating entire scenes by linking annotations across images, as well as within an image. All annotations are stored in a database targeted towards medical imaging, called XNAT. The structure of the database is automatically defined by the tags of the markers. Thus, users can query across large image data sets by looking for specific tag values.

Both modules are accompanied by training materials and documentation to ensure usability.
=Design of Module=
* Current [[Media:AMI-GUI-Design.ppt | GUI ]] outline - [[Media:SlicerAM QtAnnotation.png | Screenhot]] in Slicer
* Suggested [[Media:AMI_MRMLMarkUpNode.ppt | MRML ]] outline
* Wendy's Mouse Mode sketches http://www.slicer.org/slicerWiki/index.php/Slicer4:UIDesign:MouseModeSketches

= Documentation=
* [[ miAnnotation_Documentation | Documentation ]] of the module
* Using the [[Media:Slicer4_miAnnotation.ppt | module]] with corresponding data ([[Media:Slicer4_miAnnotation_data.zip | sample data]] )

=Key Personnel=
10% Kilian Pohl (UPenn) <BR>
95% Daniel Haehn (UPenn) <BR>
5% Dominique Belhachemi (UPenn) <BR>

=Past Contributors=
Yong Zhang (IBM) <br>

=Events=
* 05/18/10 [[Media:miAnnotation_May2010_Yong.pdf | Presentation]] at the Department of Healthcare Informatics, IBM, Almaden
* 12/16/09 - 12/17/09 [[Dec-2009-SlicerAIMBrainstorming | Annotation Brain Storming]]
* 01/06/10 [[AHM2010:AnnotationBreakout | Break out session]] at AHM 2010
* 01/19/10 Biweekly Annotation Tcon from 4:00 - 5:00 pm EST (next meeting 2/9): Tel: (218) 862-1115 Conference ID: 348265#, [https://www.lotuslive.com/join?schedid=4572317 Desktop Sharing ]
* 08/30/10 Budget Year 1 [[ Projects:ARRA:SlicerAM:Meeting20100831 | Review meeting ]]

=Progress=
*09/10/11
** work on [[Projects:ARRA:miAnnotation:Feedback]]
*09/03/11
** work on [[Projects:ARRA:miAnnotation:Feedback]]
* 08/26/11
** 'Feedback by Ron' Session: [[Projects:ARRA:miAnnotation:Feedback]]
** work on the requested changes (see status updates on page above)
* 08/19/11
** work on lightbox support (not supported by vtkWidgets yet, wrote test for Kitware)
** work on undo/redo mrml support which stopped working
* 08/12/11
** work on new Qt widgets to enable (row-based) editing of point, line and text properties
** fixed locking issue
** fixed jump slices behavior
* 08/05/11
** new property dialog in the works..
* 07/29/11
** preparation to be able to easily set properties for a complete widget (see http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=17587 for details)
** facelift draft for the property dialog by Ron: http://www.na-mic.org/Bug/view.php?id=1302
** new default colors for annotations
* 07/22/11
** switched color dialogs to the slicer custom ones
** 2D ROI Annotations
** fixes on mouse-modes and hierarchies
** simplified module GUI
** tweaks to placement icons
* 07/15/11
** new place-mode: integrated in the toolbar
** Fixed bug: Stop widgets from disappearing when panning, zooming the sliceViews.
** Cancel placement now uses events on the interaction Node and works properly again.
* 07/08/11
** deactivated bidimensional widget in 3D until it is properly realized as a 3D widget/representation
** other fixes
* 07/01/11
*** several performance and stability updates
*** presentation and user-feedback during the NA-MIC project week
* 06/24/11
*** the annotation module is now called 'Annotations'
*** re-structured module panels
* 06/17/11
*** added selected vs. highlighted mode when choosing annotations
*** optimized mouse-modes
*** upgraded screenshot functionality to support scale factor
* 06/10/11
*** made all annotations transformable
*** annotation widgets now available in python scripted modules
*** several hierarchy discussions and fixes
* 06/03/11
** fixed flickering when changing fiducial properties
** added scalefactor to screenshot dialog
** optimized event handling and performance
** rulers: added infrastructure to change properties
** roi: added infrastructure to change properties
* 05/27/11
** fixed a huge blocker where the fiducial coordinates between 2D and 3D were not stable. Now they get properly synchronized in a robuste way.
** added backup methods to be able to cancel annotation property settings which then restores the node
* 05/20/11
** change mouse cursor when in place modes to the specific icons
** place-once as the default mode in the annotation module
*** added advanced panel to activate persistence place when using the annotaton module
** work on the keypress event to place fiducials
* 05/13/11
** MRML: add required modified events for certain display properties
** add opacity slider to text properties in the property dialog
** add a spacer to the property dialog to have a consistent design for text, point and line properties
** add label position to the display node
** add utility methods to get the text, point, line display nodes for a given mrml node id
** handle the main annotation types when setting them active in the selection node
** hook up the text opacity, the point material properties. Grey out the line tab if no line display node. Add the point values to the table in the points tab
** removed the Save panel from the module GUI and moved the buttons for report and screenshot in the edit toolbar (this might change at one point)
** added a storage node for the annotation screen snapshot node to properly save the screenshots
** cleanup of annotation snapshot nodes
** use the text opacity, the point material properties
** add value constraints for several sliders in the property dialog
** MRML: add new method SetControlPoint(id, coords) without the visible and selected flags
** property dialog now complete for text, point, line! (not for hierarchies yet)
* 05/06/11
** fiducials are now shown the same way in 2D and 3D
** the property dialog is connected to configure point colors and glyph types for fiducials
** it is possible to add text to a fiducial in 3D
** meeting with Ron to discuss further development and usability issues
* 04/29/11
** fixed the flickering when placing or interacting with fiducials and rulers
** removed some obsolete render calls to enhance performance
* 04/22/11
** worked together with Nicole
*** finally fixed the crash on Slicer exit
*** investigated why MRMLScene import works fine with the annotations but MRMLScene load does not
**** first success: import and load mrml scenes now both load the annotations in 2D and 3D
* 04/15/11
** Maintenance
* 04/08/11
** Maintenance
* 04/01/11
** Maintenance
* 03/25/11
** Maintenance
* 03/18/11
** Work on MRML Load/Save issues (Nicole)
** Maintenance
* 03/11/11
** Work on hierarchies (Nicole)
** Maintenance
* 03/04/11
** Maintenance
* 02/25/11
** Maintenance
* 02/18/11
** Maintenance
** Communication with Daniel Rubin from Stanford to plan AIM integration
*** provided Annotation MRML examples
* 02/11/11
** Maintenance
* 02/04/11
** Clarified how to add Node Selectors for Annotations to the GUI of 3rd Party 3D Slicer Modules
*** Kitware provided necessary infrastructure
*** Proof of Concept in the new CropVolume module with ROI Annotations (Andriy)
** Clearing up the Annotation Storage Node Tests (Nicole)
* 01/28/11
** Presented Annotation module and SceneView module at NAC EAB Meeting
** Smaller bugs and maintenance
** Meeting with Nicole and Alex concerning the final API of hierarchies in Slicer4
* 01/21/11
** Re-activated ROI annotation with backwards compatibility to the old vtkMRMLROINode
*** Tested successfully with a scene from Slicer3
*** Provided documentation to relevant people
** Rulers now support the measurement tape behavior
** Changed the UPenn logo
** Several smaller fixes
** provided Wendy with Screenshots for NAC Poster
*** [[File:Annotation.png|none|thumb|The current state of the Annotation module.]]
*** [[File:Report.png|none|thumb|The report dialog.]]
** Found displayableManager inconsistency between 2D and 3D and the MRML Node Added Event
** MRML backwards compatibility fix for all Annotations
*** new tag "visible", old tag "visibility"
* 01/14/11
** Attended NA-MIC project week
**Enabled picking when placing annotations in 3D.
**Fixed display of ruler intersections.
**Added new icons.
**Use only three seeds to place bidimensional widgets which results in more stability.
**It is also now possible to add annotations to the toplevel hierarchy after another hierarchy was created by clicking in an empty space of the treeView.
**Re-added the ROI functionality, so now we have 5 widgets
**Ruler: enabled display of ticks (measuring tape mode) in 2D and 3D
* 01/07/11
** re-factored the annotation module in terms of changes in the Slicer4 environment
*** ready for the new developer release
** worked on the outsourced SceneView functionality to make SceneViews survive round-trips (mrml load and save)
* 12/31/10
** Maintenance
** Documentation
* 12/24/10
** Maintenance
** Received the first bug reports of potential users
*** Updated bugtracker
* 12/17/10
** Extended Report functionality
*** now includes screenshots
*** shows the hierarchies
** Sorting of Annotations now possible
** Widgets:
*** added the 3D representation of rulers
*** removed the vtkInteractorRecorder hack by placing the widgets programmatically
** Outsourced the former integrated scene snapshot functionality
*** Wrote a new module called SceneViews
*** vtkMRMLSceneViewNode replaces the old snapshot node and includes thumbnail, description..
**** is not part of the displayable framework anymore
** Added confirmation questions prior to removing annotations
** Worked on MRML save/load
** Updated the priority list: http://www.na-mic.org/Wiki/index.php/Projects:ARRA:miAnnotation:PriorityList
** Added a section for known issues: http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:miAnnotation#Known_issues
** Annotation module Lines of Code (without .ui files and no blank lines): 24820
* 12/10/10
** Changed some things in the MRML architecture to enhance encapsulation
*** Adding new Annotations should be easier now
** Lock selected, toggle visibility of selected and delete selected implemented
** Report functionality works again
*** Added support to print and export as a HTML report
* 12/03/10
** Added icons to the hierarchy tree
** Configured a proxy model to display only vtkMRMLAnnotationHierarchyNodes and vtkMRMLAnnotationNodes in the hierarchy tree
** Smaller layout fixes
** Added 'full layout' thumbnail functionality to Annotation snapshots
** Removed the old table and replaced fully by the treeView
** Over 1000 of lines of code were removed
*** Hierarchies are now usable
*** [[File:Annotationscreenshot.png|none|thumb|Screenshot of an example Annotation using the new features]]
* 11/26/10
** Added functionality to the module logic to be able to place fiducials programmatically
*** This will be used if one presses the 'p' key on a slice view
** Re-activated the text annotation
*** Used vtkCaptionWidget instead vtkTextWidget to be able to have an anchorpoint in 3D space
** The scene, camera and view nodes are now hidden from the hierarchy tree
*** The toplevel annotation hierarchy is the new root and also hidden
** Added functionality to show Annotation snapshot nodes in the hierarchy tree
*** This required adding the original snapshot node to the displayable framework (as a workaround)
*** Later, we will add thumbnail and description directly to vtkMRMLNode, so that a screenshot can be attached to every MRML node
** Overall code polishing in terms of code conventions
*** including the destruction of the frozen seedWidget on Slicer exit
* 11/19/10
** Small fixes to the Annotation snapshot functionality
** New functionality: reset view to when the annotation was placed
** Derived qMRMLAnnotationTreeWidget and qMRMLSceneAnnotationModel to support hierarchies in the module
*** the widgets let us customize the look and feel of the treeWidget
*** in this context, fixed the creation of hierarchies to a specific order in the scene (which is need for the widget)
*** the Annotation hierarchy nodes and the Annotations get already displayed in the treeWidget
** Fixed stack smashing in connection with a recently introduced compiler flag
* 11/12/10
** All widgets are now restricted to the current renderer which makes the interaction more robust.
** Fixed funky behavior after fiducials were placed.
** New functionality: Annotation snapshots (screenshot + description + scene snapshot) implemented.
*** [[File:snapshot1.png|none|thumb|The new annotation snapshot functionality (part 1)]] [[File:snapshot2.png|none|thumb|The new annotation snapshot functionality (part 2)]]
* 11/05/10
** Widget Design Fiesta http://www.na-mic.org/Wiki/index.php/WidgetDesign2010
** Widget intersections works nearly perfectly
*** Unfortunately, only for centered datasets
** Restrict ruler placement to the current renderer works now. This means, the ruler does not disappear when one point moves outside the sliceview.
* 10/29/10
** Lightbox view works for Fiducials
*** Other widgets have to be refined to be used in a lightbox view due to inconsistent VTK API. The VTK Widget Fiesta should target this.
** Widget intersections in the works, not perfectly working yet.
* 10/22/10
** Priority list for the December release of Slicer4: http://www.na-mic.org/Wiki/index.php/Projects:ARRA:miAnnotation:PriorityList
* 10/15/10
** Adopting the old TCL logic to enable 2D widgets on reformats and lightbox views
*** Still working on the lightbox view (very close)
* 10/08/10
** Code-cleanup of the logic class - any old and clumsy code was removed.
** Introducing the StringHolder design pattern [(c) Steve] to always show measurement correctly in the GUI.
** Widget creation now works on Unix aswell.
** Added the RegisterNodes method to register node classes when the scene gets attached to the logic class.
** Hierarchy nodes get added when an annotation is created (code workflow to be optimized).
** Configured a nightly build system to build and test the annotation code every night on a SPL workstation.
* 10/01/10
** The hierarchy changes will replace the table in the GUI with a tree widget
*** Added a tree widget to the GUI additionally to the table to display both during the transition stage
** Fixed the follower bug, which sometimes dragged the second controlpoint of a widget behind when the other controlpoint was moved.
* 9/24/10
** Wrote performance test for vtkWidgets in a standalone VTK mode
*** compared performance in Slicer against standalone VTK
*** rendering of text labels was found to be the performance hog, disabling these labels increases performance inside and outside Slicer dramatically
** Meeting between Wendy, Nicole, Steve and Daniel to review the Annotation module status
*** Notes: [[Projects:ARRA:SlicerAM:Meeting20100921]]
** Annotation hierarchy in the works
* 9/17/10
** 2D placement of Rulers, Bidimensional and Fiducials works now
*** The widgets get synchronized along the slice viewers and the 3D view
** Added extra layer on top of vtkWidgets and vtkWidgetRepresentations to add some extra functionality like calculating distances of measurement correctly in 2D
*** bidimensional measurement and rulers now show the correct distance also in 2D
** Fixed possible null pointer exception in vtkMRMLSliceLogic
** Refactored GetSliceOffSet from vtkMRMLSliceLogic to vtkMRMLSliceNode
* 9/10/10
** 2D placement of Annotations in the works
*** change of the underlying architecture to use one displayableManager for 2D and 3D resulting in less code duplication
*** to perform the changes, all annotations but fiducials were disabled for now
* 9/3/10
** Annotation module status review and planning meeting took place in 1249 Boylston
*** Agenda and Notes: http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerAM:Meeting20100831
**** includes new generated class diagram
** Property dialog updated (see screenshot)
*** [[File:Annotationpropertydialog.png|none|thumb|The new annotation property dialog.]]
*** first MRML-Widget synchronization works, the text tab in the property dialog works well with the text widget
** new icons for bidimensional measurement and ROI by Wendy
** updated ctkColorPickerButton to include the ability to disable the setting of the color hexcode as the buttontext to avoid the workaround we had in the annotation module
* 08/27/10
** added a work-around to initialize renderer properly resulting in improved display of annotations in 3D viewer
** cleaned up the code (more then 1000 lines of code where obsolete)
** updating property dialog, which includes revisiting the displayableManagers to support MRML and widget updates
* 08/20/10
** fiducials and sticky node work now
** ruler and spline work now
*** spline widget causes problems b/c after one spline was placed, no interaction with 3D scene possible
** ROI works now
** all annotations now can be placed to examine widget behavior
** started working on a new interface for the property dialog
** consolidated experts for 2D slice displayableManagers
** started working on synchronizing the widgets with MRML display nodes
** fixed GUI problem: the table did not expand even if there was free space in the module frame. now it works.
* 08/13/10
** Wendy, Nicole and Daniel discussed how to integrate mouse modes of Slicer into Annotation module and vice versa. Solution is a widget which appears in the Annotation module panel but can also be shown outside of it as a toplevel window in Slicer (maybe with keybinding), see here: http://wiki.na-mic.org/Wiki/index.php/File:Widget.png
** current status (workflow, user places seeds and widget appears):
*** angle annotations work (note: the widget did not support programmatical placement. a trick is used to place the widget where the user has clicked)
*** text annotations work
** modified vtkMRMLInteractionNode to have a customTag for place modes not only from annotation module but all modules
* 08/06/10
** Enhanced the workflow for creating text annotations. This approach should serve as a general framework for all annotations (sequence diagram available http://wiki.na-mic.org/Wiki/index.php/File:TextAnnotationWorkflow.png)
** modified vtkMRMLInteractionNode to support the place modes for the annotations
*** meet with Wendy next week to discuss integration
** added a click counter class to support the creation of widgets with multiple clicks (very generalized to support all annotations)
*** plan is to place seeds before the actual widget gets created
* 07/29/10
** Created an extra layer called vtkMRMLAnnotationDisplayableManager which serves as a superclass for all specific Annotation displayableManagers. F.e. the vtkMRMLAnnotationTextDisplayableManager is now really lightweight.
** Coordinated with Wendy to add additions interaction modes to vtkMRMLInteractionNode to support different interaction types for different annotations. This will happen under the hood, so the user sees only the "place" mode.
** Got together with members of the 3D & Advanced Imaging Lab at UPENN to investigate how commercial products realize annotations (see http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerAM:vtkWidgets#How_do_they_do_it.3F).
** Interactive placement of text annotations is now possible. This should be the standard way of placing annotations for all available types.
** Added a test for the creation of a text annotation and its widget without a displayableManager (vtkMRMLAnnotationTextNodeAndWidgetTest1)
** Removed initial values from AnnotationNodes due to different seg-fault errors when properties where not initialized. To cut down confusion, no initializations are now necessary.
* 07/22/10
** Meeting of Nicole, Steve and Daniel to talk about architecture
*** biggest change is the introduction of a hierarchy for annotation
**** more information and discussion during the tcon:[[Projects:ARRA:miAnnotation_Meeting_07202010|Meeting / Weekly meeting]]
** fixed AnnotationTextDisplayableManager to support multiple text annotations
** added a test for the AnnotationTextDisplayableManager
** property dialog for annotations gets displayed again, nevertheless the connection to the MRML display nodes needs further work
* 07/15/10
** add text nodes using the new displayable manager architecture is now possible
*** nevertheless, full functionality is not restored yet
** added fiducial displayable manager
** new Slicer bug tracker category: Annotations
*** filed open bugs and feature requests - please add all new requests there
* 07/08/10
** moved tests to Testing/Cxx
** created a superclass for all displayable managers (vtkMRMLAnnotationDisplayableManager)
** created vtkMRMLAnnotationTextDisplayableManager based on the old qMRMLAnnotationTextManager
** working on the add text node functionality with the new displayable manager
** fixed linking errors appearing on the Slicer Dashboard
* 07/01/10
** re-factored module from miAnnotation to Annotation
** re-integrating functionality without KWWidgets
*** MRMLDisplayableManager was created by Kitware guys and includes base functionality for the re-integration
*** starting with adding text nodes
**** UML diagram for involved classes: [[MiAnnotation_Documentation#Development]] (needs to be checked for logic/manager/mrml pattern consistency)
** added option to set helptext for the module in consistency with qSlicerWidget
* 06/24/10
** Compiling without KWWidgets on Mac OS is now possible.
** Starting to include the functionality of KWWidgets in pure QT code.
** Daniel Haehn took over project from Yong Zhang.
* 06/18/10
** Tutorial is created.
** GetAnnotationMeasurement is modified to return multiple measurements.
** ROI annotation is modified to display extension measurements.
** Bidimensional annotation is modified to display bi-line measurements.
* 06/11/10
** Documentation page is created.
** Bugs for property dialog are fixed.
** Constructions of Bidimensional and Spline annotations are modified using proper control point initialization.
** Bugs for showing values for some annotation types are fixed.
* 06/04/10
** vtkSlicerAnnotationROIManager is implemented.
** vtkSlicerAnnotationTextManager is implemented.
** vtkSlicerAnnotationSplineManager is implemented.
** vtkSlicerAnnotationBidimensionalManager is implemented.
* 05/28/10
** vtkMRMLAnnotationROINode is added;
** vtkMRMLAnnotationBiDimensionalNode is added;
** vtkMRMLAnnotationSplineNode is added.
** Logic and ModuleWidget are modified to include new Nodes
* 05/21/10
** ROI, Text, BiDimensional, and Spline Annotations are initialized.
** fixed BUG: HTML report cannot be saved properly.
* 05/14/10
** fixed BUG: When opening display properties from Sticky note -> reduce frame and enlarge it again by pressing triangle next to title : value and coordinates appear
** fixed BUG: fiducial manager is added.
** fixed BUG: AnnotationMouseModePick/Place are updated.
* 05/07/10
** fixed BUG: Lock does not lock the position of a widget in the 3D Viewer
** fixed BUG: changing coordinates to AngleNode does not have any effects on the Angle Widget.
** fixed BUG: fix coloring for annotation selection
*04/30/10
** fixed BUG: changing control points cannot be done when property dialog is open.
** fixed BUG: annotation is not highlighted when selected.
** fixed BUG: starting from the 2nd annotation, changing the location of the left point for ruler or center point for angle does not update the table properly.
** fixed Bug : changing the center point of angle node does not update table properly
* 04/23/10
** Created a ruler widget manager
* 04/16/10
** Created the new annotation type sticky note, which allows you to enter text independent from the viewer
* 04/09/10
** Modified source code to be compliant with VTK 5.6
** Grid out your buttons (Create Frame)
** Fixed BUG: When changing line color in Display Properties it changes the Text Color
** Added script for testing color setting
** Fixed BUG: Label of line color changes in property window when defining a unselected color

* 04/02/10
** Fixed BUG: Nothing happens when Property Window is open and you press the edit button for another annotation
** Restructured Annotation MRML
** Fixed Bug: Resetting of Lines and Points does not work correctly GetNumberOfLines > 0

* 03/26/10
** The property restoration is now implemented properly.
** Property Modification is re-designed to simplify the operation.
** Removed bug: ruler/angle disappear after adding fiducials
** Removed BUG: in property dialog, when editing the text, the character is entered from right to left.
** include lock annotation into option button (use same logic as for new (De)select All button)
** For each annotation type provide list outlining which display property can be changed, which cannot , and which one you do not know
** Resolved BUG: When saving a report with a file name that already exists then the following message appears in the command shell "Error: cannot make directory" and directory with files is not updated
** Resolved BUG: Annotation Properties: (Un)selected color is initially white even though widget in 3D viewer is different
** Resolved BUG: Select Color window does not show the correct color
** Resolved BUG: Selected and Unselected Color are switched
** Define Tooltips for fiducial, angle, ruler,report, save mrml button
** In table: Add proper tool tip for visualization and edit button
** Resolved BUG: when saving report with out ending html to the file name - icons will not be saved under Linux
** Created Test Module for testing miAnnotation logic
** In collaboration with Nicole Aucoin figured out line display bug in 3D Viewer
** Use the Kitware slider and colorPicker under Display Property
** Fixed BUG: Slicer crashes when creating an annotation while Display properties is open, and when closing the property window and then pressing edit for the new annotation

* 03/19/10
** In the property window display properties are shown via collapsed frame by default
** List all attributes for text/point/line and implement those that can be modified
** Fixed BUG: When pressing the property button warning messages pop up in my command shell
** Annotation Properties: For Angle and Ruler Widget also shows now values of AnnotationDisplayNode and AnnotationControlPointsNode
** Change design of html report
** Implemented text edition and update for ruler and angle widgets.
** Changed the default mouse mode icon to MousePick.
** Modified Report Dialog to avoid horizontal slider when screen shot is included in the report.
** Removed multiple warning messages.
** Fixed Bug in Report: empty text fields are displayed without boundaries
** Ruler Distance is now displayed just in mm
** After talking to BWH changed name of tool from Reporting to miAnnotation
* 03/12/10
** Created icons for:
*** edit conditioning for all annotation types (done),
*** mouse mode icons, pause, play, cancel, ok/done, (Un)lock (done)
*** new the annotation types poly line, spline with control points, volume information extractor, and sticky note (done)
*** Modify fiducial icon just to show one star and change save annotation icon (done)
*** Modify save annotation and save scene icons (done)
*** Modify move up/down delete icons (done)
** Write 5 page, double column, AMIA paper about Reporting
* 03/05/10
** Removed Warning Messages when compiling
** Fixed Bug: When entering text in property box (under linux) it is entered from right to left instead left to right
** Fixed Bug: Annotation Property: funny behavior with selecting set of digits in a numerical value and typing in a numeric value - only the first digit gets change.
** Fixed Bug: Value of Angle node is not update in table
** Fixed Bug: Updating the value in the table slows down the operations
** Changed the default ruler from 1mm to 500mm.
** Angle Widget is added by manually clicking three points on the viewer. The angle value is now shown in the table. The behavior of the angle button is in the "toggle down" state until all three control points are set
** When selecting annotation in table, color of annotation in 3D Viewer changes to selected color
** Revised "add ruler" button to click-style instead of toggle-style
** When creating a new annotation, set this entry to selected and all other table entries to unselected
** (De) Select All button: change as discussed with Wendy Plesniak, BWH, to option button with proper logic
** Setting color/selected color for individual Ruler and Angle widgets in property dialog
** Fixed Bug: hiding/unhiding ruler and angle annotations
** Change display property for each annotation individually
** Lots of warning messages when compiling code
* 02/26/10
** Created pop up window showing screen shot
** Manual editing of coordinates via "Property Window"
** Resolved column width problem in table ([http://wiki.na-mic.org/Wiki/index.php/File:Screenshot-Form.JPG original problem], [http://wiki.na-mic.org/Wiki/index.php/File:ARRA_SlicerAM_Screenshot_TableV2.png second screen shot problem])
** Fixed bug where hide icon changed size in table
** Include icons when saving html report in a directory with the same name as the html file
** [http://wiki.na-mic.org/Wiki/index.php/File:ARRA_SlicerAM_Screenshot_GUI.png Reorganized GUI] based on feedback from Wendy Plesniak, BWH
** Include screen shots (if any) in the report (see [http://wiki.na-mic.org/Wiki/index.php/File:ARRA_SlicerAM_Screenshot_ReportV1.png an example])
** Fixed the following bug: After resizing the 3D Window taking a screen shot only displays the window with the original size (see [http://wiki.na-mic.org/Wiki/index.php/File:ARRA_SlicerAM_Screenshot_Window.png screen shot])
** Fixed Bug: Value update of ruler widget is slow
** Text defined in property box now shows up in table
** Integrated vtkMRMLAnnotationAngleNode with AngleWidget
** Added new buttons to create frame based on feedback from BWH
* 02/19/10
** Implement a general structure for vtkMRMLAnnotation*Node
** Work together with Kitware to resolve QT Table layout problem
** Allow defining long text annotations for each widget
** Improve user interaction through pop up windows when trying to modify an existing annotation
** Creating and removing ruler now works correctly
** Use correct label format to display measurement values in Annotation Property window
** Created a "Save annotation" Window
** Fixed changing icon size in table (see original [http://wiki.na-mic.org/Wiki/index.php/File:ARRA_SlicerAM_Screenshot_Table-IconProblem.png screen shot] )
** Fixed slicer crashing closing the property window
** Renamed and resized columns in Table
*02/12/10 removed bugs related to table buttons, linked button to angle widget and ruler widget
*02/05/10 implemented "Save Annotation Report" button and "Move up/down" buttons; added extra column in the report table for visibility; modified annotation property dialog; implemented button-click in the table.
*01/29/10 implemented functionality for "Annotation Property Modification" button, "Create Report" button, and integrated new icons for buttons.
*01/22/10 Set up the source control for the reporting module; implemented functionality for "Select All" button, "Visible" button, and "Delete" button in the GUI; created new icons for buttons
*01/15/10 Organized biweekly Tcon
*01/08/10 Participated in all week All Hands Meeting in Utah; Expanded QT interface with functionality to set seeds in images; Defined a final MRML Structure for storing annotation.
*01/01/10 Generated a [[Media:SlicerAM QtAnnotation.png | GUI interface]] via QT for the annotation module. [[Projects:ARRA:SlicerAM#Widget_related_action_items | Reviewed ]] all VTK Widgets related to annotation.
*12/25/09 Created [[ 2010_Winter_Project_Week_mComment | project ]] and organized [[ AHM2010:AnnotationBreakout | break out session ]] at AHM meeting. Coordinated efforts with BWH team in preparation of the meeting.
*12/18/09 Held workshop to integrate AMI into 3D Slicer. Hired new person to implement AMI in Slicer.
*12/11/09 [[ Projects:ARRA:SlicerAM_RSNA09Report | Summary ]] of tools demoed at RSNA
*12/04/09 Visited RSNA to review annotation tools by GE, Siemens & Phillips. Connected to caBIG AIM project to see how we can make use of their data scheme
*11/29/09 Created GUI for MarkUp module
*11/20/09 Design MRML Structure of Annotation and MarkUp Module
*11/13/09 Organize [[Dec-2009-SlicerAIMBrainstorming | Annotation Brain Storming]] Session
*11/06/09 Designed User Interface , Meet with Julien Finet and Jean-Christophe Fillion-Robin from Kitware to discuss integration of Qt in 3D Slicer
*10/30/09 Participated in Qt-Tcon, Interviewed candidate at Almaden, coordinated efforts with Nicole Aucoin
*10/23/09 Organized onsite interview , got in contact with Steve Pieper to discuss next steps, installed Slicer3
*10/17/09 Started interviewing postdoc as well as solving several HR issues for hiring personal

= Feature Request =
== VTK Widgets ==
* For further detail go [[ Projects:ARRA:SlicerAM:KWWidgets | here ]]

== QT Related ==
* Submit bugs and feature request via [http://na-mic.org/Mantis/search.php?project_id=1&category=QtGUI&sticky_issues=on&sortby=last_updated&dir=DESC&hide_status_id=90 Mantis]
* Feature requests that may open discussions can be added [http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Developers:Projects:QtSlicer/OpenDiscussions here]

== Daniel ==
All features/issues are listed here: http://www.na-mic.org/Wiki/index.php/Projects:ARRA:miAnnotation:PriorityList
=== Known issues ===
* MRML
** <strike>After loading of scene, the annotations are not displayed in the hierarchy tree anymore</strike>
** Load scene does not display 3D widgets, Import scene does
** After importing or load, the user has to click on the widget to enable the connection between tree entry and widget
* Annotations
** Property dialog does not work yet and might crash
** Pick mode does not work correctly, if placement was paused and resumed (the first picked coordinate gets lost)
** <strike>Screenshot imagedata does not get saved on Scene save</strike>
* GUI
** if moving an annotation up or down inside a hierarchy, the tree gets confused
** Drag and drop does not work
** <strike>after creating hierarchies, the selected item does not reflect the hierarchy which new annotations get added to</strike>
** save buttons not implemented
** <strike>widget intersections do not work</strike>
** <strike>Slicer4 crashes on exit after annotations were placed and the scene was not closed manually prior exiting Slicer</strike>

==== Feedback by Users ====
* Ron
<pre>
1. I sometime like the fiducials to be spheres, not crosses. In Slicer 3 we had a whole list of options. Can I have them for Slicer4? Can I also change their size?
2. The ruler has different colors in the 3D view and in the slice views. That is wrong.
3. The properties popup require a lot of clicking, including double click. Usability will need to be optimized.
4. No drag and drop in the module.
5. text annotation: arrow in the slice view, but not in the 3d view (see attached)
6. text is not in the box in the slice view
7. the font is butt-ugly. In addition, part of the letter n is cut off by the t. The space between the capital V and the e is too big
8. Slicer 3 let you jump to a fiducial location by right clicking in the list in the module.
9. Also, The ruler does have issues with visibility, when the slice is rendered as well. See attached screensnapshot: little dots to the left, no dots to the right.
</pre>
* Isaiah
<pre>
1) need "selected" parameter for each fiducial, separate from visibility. It's used as boolean inclusion criteria in several modules - in my case DTI FiducialSeeding but also some other ones like segmentation and for CLI modules.
2) need to set properties for groups of fiducials at once. This is tricky because the hierarchy is generic, but ability to set all parameters for a group of fiducials in one place is important.
3) meta visibility control is helpful but maybe not imperative, ie show/hide a whole group but still maintain the individual visibility settings.
4) flicker of fiducials in 2d-view slice whenever other fiducial is moved across that slice. I have two coplanar fiducials in coronal slice, and move a third back/forth across the axial slice. Each time the third crosses the coronal there is a noticeable flicker of the two fiducials in-plane.
5) positioning with decimal precision rather than integer?
6) the persistent-drag mouse interaction in both 2d and 3d is not ideal (at least to me).
7) deleting a hierarchy with ~30 fiducials incurs a noticeable delay around 7s. I compiled with the standard (debug mode?) instructions on x86, ubuntu 10.04.
8) there are some strange mouse interactions when placing in the 3d view after clicking the "cancel" or "accept" buttons. for example, the first time I create a list it works fine: one click to place each. However, if I stop, delete, and start adding again then it doesn't work the same way: the first click makes a fiducial, but subsequent clicks only occasionally place new fidus. I think the problem is that the interactor is selecting the new first fiducial even if the mouse is very far away - can click on the other side of the screen and drag that fiducial, even after pressing "stop" again.
8a) minor style: is it possible to use stop-sign or something else rather than the current x-in-circle for "cancel"?... my brain sees that as the fiducial button 1/2 the time :)
9) I'm confused by the edit properties display (window) for fiducials. What is the purpose for each tab: text, points, lines? points seems to be a place for a list, but x/y/z is empty and position is instead displayed under "Measurement value" on the text tab.
</pre>

==== Meeting with Ron 05/06/11 ====
Nicole and Daniel met with Ron to discuss usability issues and future development.

* <strike>Ron would like the 3d sphere to be the default setting for the glyphs.</strike> (H)
* <strike>Change the mouse cursor when in place mode, use the images from the mouse modes toolbar icons.</strike> (H)
* Text annotations
** line breaks for long text, automatic (H) - breaks are done, not automatic yet
** show some of the text (first 20chars?) in the fiducial text box with ... to denote more visible in the Qt interface (M)
** sometimes don't want an arrow head (M)
** consolidate the text and fiducials into one conceptual package allowing turning on/off the text box, detaching it, leader, etc. (L)
** <strike>get the text working in 2d slice windows (H)</strike>
* <strike>Set one time place as the default in the annotation module (add a persistent radio button?) </strike>(H)
* Rulers
** <strike>expose the tick mark options in the GUI (need to support mice, humans, galaxies) (L)</strike>
** use the NeuroDTI example data set from Ron's drop box (H)
** <strike>3d tumor model when measuring it's diameter, the measurement text is hidden inside of it, add an option to position the text at and end or in the middle (H)</strike> label position parameter exposed
** toggle label visibility (M)
* Bidim
** does RECIST need to be orthogonal? Yes
** add the word orthogonal to the tooltip (done)
** make a new icon with a quarter circle between two arms of the axes and use it (L)
* Reformat widget
** estimated time to implementation? (email sent to Will S.)
* Save
** <strike>Ron vetoed the Save panel in the Annotation module, all saving is to be done via the centralised widget (H)</strike>
** <strike>take out the save/load buttons, move the report buttons to another part of the GUI (H)</strike>
** <strike>add the screen snapshot functionality (especially the over sampling) to the scene views pop up window and bring it up from the shortcut box in the lower left of the GUI (this may need some infrastructure changes) (H)</strike>
* Workflows
** use the DTI Tumor scene as a sample (M)
** when Ron created the views, each scene view is a workflow end point
** once the annotation functionality is all there, Nicole will meet with Ron and add the annotations to the scene view and save a new scene, and also document the process for usability improvements and testing (M)
* ROIs
** see the Slicer3 crop volume module for a good initialization method: make the ROI node and then update it by clicking in the 2d slice (M)
** 2d annotation ROI -> label map (H)
** match handle colours of the widget to 2d elements in the GUI (H)
** implement the fit ROI to volume functionality (L)
*** once it is included in volume rendering in Slicer 4 please take a look at this functionality - if it is easy to import than it has high priority
* Scene views (M)
** test the Neuro DTI file on Slicer4
** create a new Slicer4 Annotation Testing mrml file and upload it to the drop box

= Display Properties of Widgets =
* Unavailable / Unknown:
** Set text colors for Ruler and Angle Widget
** Get/Set glyph scale / point size for point display node
** Get/Set text opacity/ambient/diffuse/specular from text display node
** Color of "angle line" cannot be defined
* Available:
** Get/Set text colors from display node
** Get/Set text scale from display node
** Get/Set point colors from point display node
** Get/Set point opacity/ambient/diffuse/specular from point display node
** Get/Set line colors from line display node
** Get/Set line width/opacity/ambient/diffuse/specular from line display node
** Get text format for angle and ruler

Projects:ARRA:SlicerEM:Slicer4

2011-09-07T21:52:59Z

Haehn: /* EMSegment GUI in Qt */

= EMSegmenter in Slicer4 =

== TODO ==
* <strike>untie KWWidgets from EMSegment base</strike>
* <strike>untie KWWidgets from EMSegment commandline tool</strike>
* <strike>create EMSegment4 as an extension for Slicer4</strike>
** <strike>include the commandline tool in the extension (Problem: infrastructure is not ready yet)</strike>
* <strike>Merge old EMSegment4 and the new extension all in Slicer3 repository</strike>
* <strike>introduce Slicer Common Interface (SCI) which holds functionality which is different between Slicer3 and Slicer4 but provides the same API for both</strike>
** <strike>provide EMSegment3 functionality in the SCI</strike>
** <strike>provide EMSegment4 functionality in the SCI (work in progress)</strike>
* update EMSegment4 Qt Gui
* provide nightly extension builds

=== Slicer Common Interface (SCI) ===
The Slicer Common Interface is a class with a unified API for Slicer3 and Slicer4 which includes functionality which has to be realized differently among the two Slicer versions.

==== Progress ====
{|border="1"
| '''Task'''
| '''Slicer3'''
| '''Slicer4'''
|-
| GetTclInterpeter
| <font color='green'>DONE</font>
| <font color='green'>obsolete</font>
|-
| SourceTclFile
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| EvaluateTcl
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| GetTclNameFromPointer
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| RegisterObjectWithTcl
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| GetApplicationTclName
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| InitializePythonViaTcl
| <font color='green'>DONE</font>
| <font color='green'>obsolete</font>
|-
| EvaluatePython
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| GetTemporaryDirectory
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| GetBinDirectory
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| GetRepositoryRevision
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| SetApplicationBinDir
| <font color='green'>DONE</font>
| <font color='green'>obsolete</font>
|-
| GetHTTPHandler
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| PromptBeforeExitOff
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| DestroySlicerApplication
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| AddDataIOToScene
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| RemoveDataIOFromScene
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|}

=== EMSegment GUI in Qt ===

Wizard steps
* Step1: Define Task
** <strike>create new task functionality</strike>
** <strike>all done</strike>
* Step2: Define input channels
** <strike>in Simple mode show dynamic frame</strike>
** <strike>all done</strike>
* Step3: Define anatomical tree
** <strike>qt widget does not support creating subclasses yet</strike>
** <strike>all done</strike>
* Step4: Define Atlas
** <strike>qt widget supports parcellation maps</strike>
** <strike>all done</strike>
* Step5: Edit Registration parameters
** <strike>problem: show input channels-volume map does not work yet</strike>
** <strike>all done</strike>
* <font color='orange'>Step6: Dynamic frame</font>
** '''support for dynamic textedits'''
* Step7: Specify Intensity Distributions
** <strike>manual sampling</strike>
** <strike>all done</strike>
* Step8: Edit node-based parameters
** <strike>advanced GUI not done yet</strike>
** <strike>all done</strike>
* Step9: Define Misc. Parameters
** <strike>all done</strike>

In general:
*<strike>segmentation call not hooked up yet</strike>
*<font color='red'>Extension infrastructure</font>
*<font color='red'>Testing and bug fixing</font>

=== Open issues reported by Kilian ===

* "Attempt to go to the finish step succeeded" message when clicking segment
** this is a ctk error
* step 3: <strike>reduce size of probability map fields</strike> (not possible)
* step 7: <strike>"Plot distribution" functionality</strike>
* step 7: <strike>incorrect mean in manual sampling mode (found the cause I think)</strike>
* step 7: <strike>incorrect reset of distribution</strike>
* step 7: <strike>size of anatomical tree not optimal</strike>
* <strike>step 7: remove auto-sampling</strike>
* <strike>step 9: grey out forward button</strike>
* <strike>put emsegmenter in category segmentation</strike>
* all steps: tooltips
* <strike>order task list alphabetically</strike>

Projects:ARRA:SlicerEM:Slicer4

2011-08-31T18:31:23Z

Haehn: /* Open issues reported by Kilian */

= EMSegmenter in Slicer4 =

== TODO ==
* <strike>untie KWWidgets from EMSegment base</strike>
* <strike>untie KWWidgets from EMSegment commandline tool</strike>
* <strike>create EMSegment4 as an extension for Slicer4</strike>
** <strike>include the commandline tool in the extension (Problem: infrastructure is not ready yet)</strike>
* <strike>Merge old EMSegment4 and the new extension all in Slicer3 repository</strike>
* <strike>introduce Slicer Common Interface (SCI) which holds functionality which is different between Slicer3 and Slicer4 but provides the same API for both</strike>
** <strike>provide EMSegment3 functionality in the SCI</strike>
** <strike>provide EMSegment4 functionality in the SCI (work in progress)</strike>
* update EMSegment4 Qt Gui
* provide nightly extension builds

=== Slicer Common Interface (SCI) ===
The Slicer Common Interface is a class with a unified API for Slicer3 and Slicer4 which includes functionality which has to be realized differently among the two Slicer versions.

==== Progress ====
{|border="1"
| '''Task'''
| '''Slicer3'''
| '''Slicer4'''
|-
| GetTclInterpeter
| <font color='green'>DONE</font>
| <font color='green'>obsolete</font>
|-
| SourceTclFile
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| EvaluateTcl
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| GetTclNameFromPointer
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| RegisterObjectWithTcl
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| GetApplicationTclName
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| InitializePythonViaTcl
| <font color='green'>DONE</font>
| <font color='green'>obsolete</font>
|-
| EvaluatePython
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| GetTemporaryDirectory
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| GetBinDirectory
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| GetRepositoryRevision
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| SetApplicationBinDir
| <font color='green'>DONE</font>
| <font color='green'>obsolete</font>
|-
| GetHTTPHandler
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| PromptBeforeExitOff
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| DestroySlicerApplication
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| AddDataIOToScene
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| RemoveDataIOFromScene
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|}

=== EMSegment GUI in Qt ===

Wizard steps
* <font color='red'>Step1: Define Task</font>
** '''create new task functionality'''
* Step2: Define input channels
** <strike>in Simple mode show dynamic frame</strike>
** <strike>all done</strike>
* Step3: Define anatomical tree
** <strike>qt widget does not support creating subclasses yet</strike>
** <strike>all done</strike>
* Step4: Define Atlas
** <strike>qt widget supports parcellation maps</strike>
** <strike>all done</strike>
* Step5: Edit Registration parameters
** <strike>problem: show input channels-volume map does not work yet</strike>
** <strike>all done</strike>
* <font color='orange'>Step6: Dynamic frame</font>
** '''support for dynamic textedits'''
* Step7: Specify Intensity Distributions
** <strike>manual sampling</strike>
** <strike>all done</strike>
* Step8: Edit node-based parameters
** <strike>advanced GUI not done yet</strike>
** <strike>all done</strike>
* Step9: Define Misc. Parameters
** <strike>all done</strike>

In general:
*<strike>segmentation call not hooked up yet</strike>
*<font color='red'>Extension infrastructure</font>
*<font color='red'>Testing and bug fixing</font>

=== Open issues reported by Kilian ===

* "Attempt to go to the finish step succeeded" message when clicking segment
** this is a ctk error
* step 3: <strike>reduce size of probability map fields</strike> (not possible)
* step 7: <strike>"Plot distribution" functionality</strike>
* step 7: <strike>incorrect mean in manual sampling mode (found the cause I think)</strike>
* step 7: <strike>incorrect reset of distribution</strike>
* step 7: <strike>size of anatomical tree not optimal</strike>
* <strike>step 7: remove auto-sampling</strike>
* <strike>step 9: grey out forward button</strike>
* <strike>put emsegmenter in category segmentation</strike>
* all steps: tooltips
* <strike>order task list alphabetically</strike>

Projects:ARRA:SlicerEM:Slicer4

2011-08-31T18:15:24Z

Haehn: /* Open issues reported by Kilian */

= EMSegmenter in Slicer4 =

== TODO ==
* <strike>untie KWWidgets from EMSegment base</strike>
* <strike>untie KWWidgets from EMSegment commandline tool</strike>
* <strike>create EMSegment4 as an extension for Slicer4</strike>
** <strike>include the commandline tool in the extension (Problem: infrastructure is not ready yet)</strike>
* <strike>Merge old EMSegment4 and the new extension all in Slicer3 repository</strike>
* <strike>introduce Slicer Common Interface (SCI) which holds functionality which is different between Slicer3 and Slicer4 but provides the same API for both</strike>
** <strike>provide EMSegment3 functionality in the SCI</strike>
** <strike>provide EMSegment4 functionality in the SCI (work in progress)</strike>
* update EMSegment4 Qt Gui
* provide nightly extension builds

=== Slicer Common Interface (SCI) ===
The Slicer Common Interface is a class with a unified API for Slicer3 and Slicer4 which includes functionality which has to be realized differently among the two Slicer versions.

==== Progress ====
{|border="1"
| '''Task'''
| '''Slicer3'''
| '''Slicer4'''
|-
| GetTclInterpeter
| <font color='green'>DONE</font>
| <font color='green'>obsolete</font>
|-
| SourceTclFile
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| EvaluateTcl
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| GetTclNameFromPointer
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| RegisterObjectWithTcl
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| GetApplicationTclName
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| InitializePythonViaTcl
| <font color='green'>DONE</font>
| <font color='green'>obsolete</font>
|-
| EvaluatePython
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| GetTemporaryDirectory
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| GetBinDirectory
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| GetRepositoryRevision
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| SetApplicationBinDir
| <font color='green'>DONE</font>
| <font color='green'>obsolete</font>
|-
| GetHTTPHandler
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| PromptBeforeExitOff
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| DestroySlicerApplication
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| AddDataIOToScene
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|-
| RemoveDataIOFromScene
| <font color='green'>DONE</font>
| <font color='green'>DONE</font>
|}

=== EMSegment GUI in Qt ===

Wizard steps
* <font color='red'>Step1: Define Task</font>
** '''create new task functionality'''
* Step2: Define input channels
** <strike>in Simple mode show dynamic frame</strike>
** <strike>all done</strike>
* Step3: Define anatomical tree
** <strike>qt widget does not support creating subclasses yet</strike>
** <strike>all done</strike>
* Step4: Define Atlas
** <strike>qt widget supports parcellation maps</strike>
** <strike>all done</strike>
* Step5: Edit Registration parameters
** <strike>problem: show input channels-volume map does not work yet</strike>
** <strike>all done</strike>
* <font color='orange'>Step6: Dynamic frame</font>
** '''support for dynamic textedits'''
* Step7: Specify Intensity Distributions
** <strike>manual sampling</strike>
** <strike>all done</strike>
* Step8: Edit node-based parameters
** <strike>advanced GUI not done yet</strike>
** <strike>all done</strike>
* Step9: Define Misc. Parameters
** <strike>all done</strike>

In general:
*<strike>segmentation call not hooked up yet</strike>
*<font color='red'>Extension infrastructure</font>
*<font color='red'>Testing and bug fixing</font>

=== Open issues reported by Kilian ===

* "Attempt to go to the finish step succeeded" message when clicking segment
** this is a ctk error
* step 3: reduce size of probability map fields
* step 7: <strike>"Plot distribution" functionality</strike>
* step 7: <strike>incorrect mean in manual sampling mode (found the cause I think)</strike>
* step 7: <strike>incorrect reset of distribution</strike>
* step 7: size of anatomical tree not optimal
* <strike>step 7: remove auto-sampling</strike>
* <strike>step 9: grey out forward button</strike>
* <strike>put emsegmenter in category segmentation</strike>
* all steps: tooltips
* <strike>order task list alphabetically</strike>

Projects:ARRA:miAnnotation:Feedback

2011-08-30T20:30:35Z

Haehn: /* Qt GUI Changes */

= Feedback from Ron 08/24/11 =
* in general: Ron is very pleased with the top-level things

== The Text Dilemma ==
* problem: annotations are obstructing the images: this should NOT be the case
** fonts ugly
** text gets in the way of things you want to see
* different direction needed: show information in left bottom corner
** two kinds of information
*** software wants to show information (push)
*** user requests information (pull)
** in viewers: minimal information
** in bottom left corner of Slicer GUI: medium details
** somewhere else (in the annotation module): full details
** cdash example: way of not to do it -> important information is covered by annotations
** ohloh example: good example -> first minimal, then under cursor more details when probing
=== Possible Solution ===
* assign names (F1,F2,F3 for Fiducials, M1,M2,M3 for measurements, R1,R2 for ROI... ) and descriptions
** name appears in viewers
** description in bottom lower left on roll-over in viewers
** in annotation module: full details: Name, description, options

== General Changes (Target for RSNA release) ==
* take everything out which does not work properly (except for critical functionality)
=== Targeting the Text Dilemma ===
* name+description in bottom lower left (Steve)
** possible problem: mouse over event on vtk widgets might not be easily realizable. Plan C could be a query mechanism, where the user requests this information through a keystroke or such (if annotation detail is not available we will only show slice information and add annotation detail later).
* <strike> in viewers only name </strike>(Nicole)
** one letter naming checked in to svn 17837.
** using name instead of text checked into svn 17889.

=== Slim down the Annotation Module ===
* <strike>get rid of text annotation
* get rid of bidimensional annotation
* just three annotation types: fiducials, measurements (ruler), ROIs</strike>
** done in svn 17835

=== vtkWidget Changes ===
* ruler: ticks only in 2D, every centimeter, can be turned off (Alex)
** For now, turn off ticks in both 2D and 3D (Alex)
** Later, fix zooming in 2D, only have long (major) ticks at 1cm.
** Later, change to spheres for ticks (at 1cm) in 3D
* <strike>handles for all annotations zooming behavior: should be like Slicer3 </strike>(Alex)
* ROI needs a name in the future: requires infrastructure change (not for RSNA) (Alex)
* Later: don't turn off ruler visibility when endpoints are outside the viewport

=== Displayable Manager ===

* Coordinate issues (Daniel)
** Fiducials and Rulers show up in all slice views when they shouldn't
** Fiducials and Rulers 'jump' on mouse over

=== Qt GUI Changes ===
* property dialog re-design
** <strike>for RSNA: change default tab in property box: point tab for Fiducial, Ruler; ROI tab for ROI</strike> (Daniel)
** sliders in fiducial properties jumps weird: should have dynamic range or 0..20 for the beginning
*** size presets: medium is actual size, small and large presets
** property linking between elements of widgets so that the user has to change colors at one location
*** <strike>GUI: Qt Widgets</strike> (Daniel) (WIP uploaded to SVN 17896 and 17898)
*** MRML: DisplayNode changes (Nicole)

* hotspot icons for ruler placement: new icons on wendy's todo list (Wendy)

* second eye should be removed in tree view (Julien)

* <strike>remove Create Panel</strike> (Daniel)
** <strike>replace by toolbar - do we really want to have the toolbar 2x? No!</strike> (Daniel)
** <strike>view transform in the toolbar: should be cancel</strike> (Daniel)
*** add a key (maybe ctrl) to have it pause mode (TODO later - now just option to cancel).

* screenshots and sceneviews go into toolbar (Nicole)

* <strike>take out advanced panel</strike> (svn rev. 17835)

=== MRML Changes ===
* changes related to linking properties (Jim)
* fiducial list, so that saving many fiducials do not creates so many files (Nicole)

=== Performance and Stability ===

* Testing (Nicole)
** add multiple fiducials, ROIs, rulers for timing
** test named py_AnnotationsTestingAddManyFiducials (adds 20 fids) added in svn 17892.
* Volume Rendering multiple renders when fiducials are present (may be inherent in the widgets) (?)
* Fixing why the annotations lead to slowdowns
* Fix random crashes (all)
** Undo/Redo - disable if it does not work (Alex)

Projects:ARRA:miAnnotation:Feedback

2011-08-30T20:04:30Z

Haehn: /* Qt GUI Changes */

= Feedback from Ron 08/24/11 =
* in general: Ron is very pleased with the top-level things

== The Text Dilemma ==
* problem: annotations are obstructing the images: this should NOT be the case
** fonts ugly
** text gets in the way of things you want to see
* different direction needed: show information in left bottom corner
** two kinds of information
*** software wants to show information (push)
*** user requests information (pull)
** in viewers: minimal information
** in bottom left corner of Slicer GUI: medium details
** somewhere else (in the annotation module): full details
** cdash example: way of not to do it -> important information is covered by annotations
** ohloh example: good example -> first minimal, then under cursor more details when probing
=== Possible Solution ===
* assign names (F1,F2,F3 for Fiducials, M1,M2,M3 for measurements, R1,R2 for ROI... ) and descriptions
** name appears in viewers
** description in bottom lower left on roll-over in viewers
** in annotation module: full details: Name, description, options

== General Changes (Target for RSNA release) ==
* take everything out which does not work properly (except for critical functionality)
=== Targeting the Text Dilemma ===
* name+description in bottom lower left (Steve)
** possible problem: mouse over event on vtk widgets might not be easily realizable. Plan C could be a query mechanism, where the user requests this information through a keystroke or such (if annotation detail is not available we will only show slice information and add annotation detail later).
* <strike> in viewers only name </strike>(Nicole)
** one letter naming checked in to svn 17837.
** using name instead of text checked into svn 17889.

=== Slim down the Annotation Module ===
* <strike>get rid of text annotation
* get rid of bidimensional annotation
* just three annotation types: fiducials, measurements (ruler), ROIs</strike>
** done in svn 17835

=== vtkWidget Changes ===
* ruler: ticks only in 2D, every centimeter, can be turned off (Alex)
** For now, turn off ticks in both 2D and 3D (Alex)
** Later, fix zooming in 2D, only have long (major) ticks at 1cm.
** Later, change to spheres for ticks (at 1cm) in 3D
* <strike>handles for all annotations zooming behavior: should be like Slicer3 </strike>(Alex)
* ROI needs a name in the future: requires infrastructure change (not for RSNA) (Alex)
* Later: don't turn off ruler visibility when endpoints are outside the viewport

=== Displayable Manager ===

* Coordinate issues (Daniel)
** Fiducials and Rulers show up in all slice views when they shouldn't
** Fiducials and Rulers 'jump' on mouse over

=== Qt GUI Changes ===
* property dialog re-design
** for RSNA: change default tab in property box: point tab for Fiducial, Ruler; ROI tab for ROI (Daniel)
** sliders in fiducial properties jumps weird: should have dynamic range or 0..20 for the beginning
*** size presets: medium is actual size, small and large presets
** property linking between elements of widgets so that the user has to change colors at one location
*** <strike>GUI: Qt Widgets</strike> (Daniel) (WIP uploaded to SVN 17896 and 17898)
*** MRML: DisplayNode changes (Nicole)

* hotspot icons for ruler placement: new icons on wendy's todo list (Wendy)

* second eye should be removed in tree view (Julien)

* <strike>remove Create Panel</strike> (Daniel)
** <strike>replace by toolbar - do we really want to have the toolbar 2x? No!</strike> (Daniel)
** <strike>view transform in the toolbar: should be cancel</strike> (Daniel)
*** add a key (maybe ctrl) to have it pause mode (TODO later - now just option to cancel).

* screenshots and sceneviews go into toolbar (Nicole)

* <strike>take out advanced panel</strike> (svn rev. 17835)

=== MRML Changes ===
* changes related to linking properties (Jim)
* fiducial list, so that saving many fiducials do not creates so many files (Nicole)

=== Performance and Stability ===

* Testing (Nicole)
** add multiple fiducials, ROIs, rulers for timing
** test named py_AnnotationsTestingAddManyFiducials (adds 20 fids) added in svn 17892.
* Volume Rendering multiple renders when fiducials are present (may be inherent in the widgets) (?)
* Fixing why the annotations lead to slowdowns
* Fix random crashes (all)
** Undo/Redo - disable if it does not work (Alex)

Projects:ARRA:miAnnotation:Feedback

2011-08-30T20:03:30Z

Haehn: /* Qt GUI Changes */

= Feedback from Ron 08/24/11 =
* in general: Ron is very pleased with the top-level things

== The Text Dilemma ==
* problem: annotations are obstructing the images: this should NOT be the case
** fonts ugly
** text gets in the way of things you want to see
* different direction needed: show information in left bottom corner
** two kinds of information
*** software wants to show information (push)
*** user requests information (pull)
** in viewers: minimal information
** in bottom left corner of Slicer GUI: medium details
** somewhere else (in the annotation module): full details
** cdash example: way of not to do it -> important information is covered by annotations
** ohloh example: good example -> first minimal, then under cursor more details when probing
=== Possible Solution ===
* assign names (F1,F2,F3 for Fiducials, M1,M2,M3 for measurements, R1,R2 for ROI... ) and descriptions
** name appears in viewers
** description in bottom lower left on roll-over in viewers
** in annotation module: full details: Name, description, options

== General Changes (Target for RSNA release) ==
* take everything out which does not work properly (except for critical functionality)
=== Targeting the Text Dilemma ===
* name+description in bottom lower left (Steve)
** possible problem: mouse over event on vtk widgets might not be easily realizable. Plan C could be a query mechanism, where the user requests this information through a keystroke or such (if annotation detail is not available we will only show slice information and add annotation detail later).
* <strike> in viewers only name </strike>(Nicole)
** one letter naming checked in to svn 17837.
** using name instead of text checked into svn 17889.

=== Slim down the Annotation Module ===
* <strike>get rid of text annotation
* get rid of bidimensional annotation
* just three annotation types: fiducials, measurements (ruler), ROIs</strike>
** done in svn 17835

=== vtkWidget Changes ===
* ruler: ticks only in 2D, every centimeter, can be turned off (Alex)
** For now, turn off ticks in both 2D and 3D (Alex)
** Later, fix zooming in 2D, only have long (major) ticks at 1cm.
** Later, change to spheres for ticks (at 1cm) in 3D
* <strike>handles for all annotations zooming behavior: should be like Slicer3 </strike>(Alex)
* ROI needs a name in the future: requires infrastructure change (not for RSNA) (Alex)
* Later: don't turn off ruler visibility when endpoints are outside the viewport

=== Displayable Manager ===

* Coordinate issues (Daniel)
** Fiducials and Rulers show up in all slice views when they shouldn't
** Fiducials and Rulers 'jump' on mouse over

=== Qt GUI Changes ===
* property dialog re-design
** for RSNA: change default tab in property box: point tab for Fiducial, Ruler; ROI tab for ROI (Daniel)
** sliders in fiducial properties jumps weird: should have dynamic range or 0..20 for the beginning
*** size presets: medium is actual size, small and large presets
** property linking between elements of widgets so that the user has to change colors at one location
*** GUI: Qt Widgets (Daniel)
*** MRML: DisplayNode changes (Nicole)

* hotspot icons for ruler placement: new icons on wendy's todo list (Wendy)

* second eye should be removed in tree view (Julien)

* <strike>remove Create Panel</strike> (Daniel)
** <strike>replace by toolbar - do we really want to have the toolbar 2x? No!</strike> (Daniel)
** <strike>view transform in the toolbar: should be cancel</strike> (Daniel)
*** add a key (maybe ctrl) to have it pause mode (TODO later - now just option to cancel).

* screenshots and sceneviews go into toolbar (Nicole)

* <strike>take out advanced panel</strike> (svn rev. 17835)

=== MRML Changes ===
* changes related to linking properties (Jim)
* fiducial list, so that saving many fiducials do not creates so many files (Nicole)

=== Performance and Stability ===

* Testing (Nicole)
** add multiple fiducials, ROIs, rulers for timing
** test named py_AnnotationsTestingAddManyFiducials (adds 20 fids) added in svn 17892.
* Volume Rendering multiple renders when fiducials are present (may be inherent in the widgets) (?)
* Fixing why the annotations lead to slowdowns
* Fix random crashes (all)
** Undo/Redo - disable if it does not work (Alex)

Projects:ARRA:miAnnotation:Feedback

2011-08-30T17:31:48Z

Haehn: /* Qt GUI Changes */

Projects:ARRA:miAnnotation:Feedback

2011-08-30T17:26:33Z

Haehn: /* Qt GUI Changes */

Projects:ARRA:miAnnotation:Feedback

2011-08-30T15:35:07Z

Haehn: /* Qt GUI Changes */

Projects:ARRA:miAnnotation:Feedback

2011-08-30T15:29:39Z

Haehn: /* Qt GUI Changes */

Projects:ARRA:miAnnotation:Feedback

2011-08-30T15:25:01Z

Haehn: /* Qt GUI Changes */

Projects:ARRA:miAnnotation:Feedback

2011-08-30T15:22:34Z

Haehn: /* vtkWidget Changes (Alex) */

Projects:ARRA:miAnnotation:Feedback

2011-08-30T15:22:18Z

Haehn: /* vtkWidget Changes */

Projects:ARRA:miAnnotation:Feedback

2011-08-30T15:22:08Z

Haehn: /* Targeting the Text Dilemma */

Projects:ARRA:miAnnotation:Feedback

2011-08-30T15:17:24Z

Haehn: /* Slim down the Annotation Module */