NAMIC Wiki - User contributions [en]

2013 Winter Project Week

2013-01-11T16:32:58Z

Finetjul: /* 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 | Coregistration of structural and diffusion MRI towards 4D modeling of TBI]] (Bo Wang, Andrei Irimia, Micah Chambers, Jack Van Horn, Marcel Prastawa, Guido Gerig)
* [[Clinically oriented structural, connectomic and functional analysis of traumatic brain injury in 3D Slicer]] (Andrei Irimia, Bo Wang, Micah Chambers, Jack Van Horn, Marcel Prastawa, Guido Gerig)
* [[UKF Tractography in Slicer 4]] (Ryan Eckbo, Yogesh Rathi, Demian Wassermann, C.F Westin, Ron Kikinis)
* [[4D DTI analysis via longitudinal modeling of tract diffusivities]] (Anuja Sharma, Bo Wang, Andrei Irimia, Micah Chambers, Jack Van Horn, Marcel Prastawa, Guido Gerig)

==Atrial Fibrillation==
* [[2013_Project_Week:CARMA_Scar_Segmentation|Scar Identification (LiangJia Zhu, Yi Gao, Josh Cates, Rob MacLeod, Allen Tannenbaum)]]
* [[2013_Project_Week:CARMA_PV_Antrum_Cut|SLICER MODULE: PV Antrum Cut Filter (Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod)]]
* [[2013_Project_Week:CARMA_LA_Seg_Gopal|SLICER MODULE: Automated LA Segmentation by Gopal (Gopal Veni, Salma Bengali, Greg Gardner, Alan Morris, Josh Cates, Rob MacLeod)]]
* [[2013_Project_Week:CARMA_2D_Dilate|SLICER MODULE: 2D Dilate Filter (Salma Bengali, Greg Gardner, Alan Morris, Josh Cates, Rob MacLeod)]]
* [[2013_Project_Week:CARMA_PractialLASeg|SLICER WORKFLOW: Practical Manual LA Segmentation in Slicer (Salma Bengali, Greg Gardner, Alan Morris, Josh Cates, Rob MacLeod)]]
* [[2013_Project_Week:CARMA_Isolated_Connected_Filter|SLICER MODULE: Isolated Connected Image Filter (Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod)]]
* [[2013_Project_Week:CARMA_Connected_Threshold_Filter|SLICER MODULE: Connected Threshold Image Filter (Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod)]]

==Slicer4 Extensions==
* [[2013_Project_Week:DTIExtension|Diffusion Tensor Images processing tools as Slicer4 extensions (Adrien Kaiser, Francois Budin, Martin Styner)]]
* [[2013_Project_Week:SPHARMExtension|SPHARM-PDM as Slicer4 extension (Beatriz Paniagua, Francois Budin, Martin Styner)]]

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

* [[2013_Project_Week:4DShapeAnalysis | 4D shape analysis: application to HD]] (James Fishbaugh, Marcel Prastawa, Hans Johnson, Guido Gerig)

==Head and Neck Cancer==
* [[2013_Winter_Project_Week:MABS|Multi atlas-based segmentation]] (Sharp, Shusharina, Golland)
* [[2013_Winter_Project_Week:Hybrid_registration|Hybrid interactive-automatic registration]] (Shusharina, Sharp, Pieper)
* [[2013_Winter_Project_Week:PointSetRegistration|Constrained Point Set Registration]] (Kolesov, Karasev, Sharp, Tannenbaum)
* [[2013_Winter_Project_Week:InteractiveSegmentation|Interactive Segmentation and Supporting Utilities]] (Karasev, Kolesov, Tannenbaum)

==Stroke==
* [[2013_Project_Week:WMH_Segmentation_for_Stroke|White Matter Hyperintensity Segmentation in Stroke (Adrian Dalca, Ramesh Sridharan, Polina Golland)]]
* [[2013_Project_Week:Imaging_Genetic_for_Stroke|Imaging Genetics for Stroke (Adrian Dalca, Kayhan Batmanghelich, Polina Golland)]]

==Image-Guided Interventions==
* [[2013_Project_Week:UnitedSlicerIGTExtension|United SlicerIGT extension, repository, website]] (Tamas Ungi, Junichi Tokuda, Adam Rankin)
* [[2013_Project_Week:MRIAblation|Thermal monitoring tools for MRI-guided laser ablation therapy of brain tumor]] (Laurent Chauvin, Noby Hata, Hatsuho Mamata, Alex Golby)
* [[2013_Project_Week:BRAINSFit_new_features|BRAINSFit in ITK4: extra functionality and testing for prostate MR registration (Andrey, Hans)]]
* [[2013_Project_Week:PkModeling_for_prostate_DCE_MRI|PkModeling for prostate DCE MRI (Jim, Andrey)]]
* [[2013_Winter_Project_Week_Gyne_Brachy|iGyne Needle Digitalization]] (Alireza Mehrtash, Csaba Pinter, Tina Kapur, Guillaume Pernelle, Jan Egger, Neha Agrawal, Antonio Damato)
* [[2013_Project_Week:AbdominalNavigationModule|Abdominal navigation module]] (Junichi Tokuda, Atsushi Yamada)
* [[2013_Project_Week:MobileImageOverlay|Mobile image overlay augmented reality needle guidance]] (Tamas Ungi, Adam Rankin)
* [[2013_Project_Week:US_IGT|Ultrasound Guidance for Neurosurgery]] (Matthew Toews, William Wells, Stephen Aylward, 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)

==Medical Robotics==
* [[Configurable fiducial-based device to image registration]] (Junichi Tokuda, Nobuhiko Hata)
* [[2013_Project_Week:RobotizedUltrasoundProbeFor3DVolumeReconstruction| Robotized Ultrasound Probe For 3D Volume Reconstruction]] (Laurent Chauvin, Junichi Tokuda, Noby Hata)
* [[2013_Project_Week:AgileMedicalRobot | Agile medical robotics development with Slicer: Case study with MRI compatible robot(Taka Kato, Atsushi Yamada, Noby Hata, Kazuhumi Onuma)]]
* [[2013_Project_Week:InvestigatingRoleOfOpenSourceInTranslationalResearch | Investigating role of open source in translational research (Miki Kumekawa)]]

==NA-MIC Kit Internals==
*[[2013_Project_Week:WebbasedAnatomicalTeachingFramework|Web-based anatomical teaching framework for mi2b2]] (Daniel Haehn, Steve Pieper, Sonia Pujol, Randy Gollub, Rudolph Pienaar, Ellen Grant)
*[[2013_Project_Week:ITKv4Default|ITKv4 Default in Superbuild]] - [http://www.na-mic.org/Bug/search.php?project_id=3&sticky_issues=on&sortby=last_updated&dir=DESC&hide_status_id=80&tag_string=ITKv4 Issues] (Matt McCormick, Luis Ibanez, Hans Johnson, Jc, Bill Lorensen, Bradley Lowekamp)
*[[2013_Project_Week:MarkupsModule|Slicer4 Markups Module]] (Nicole Aucoin)
*[[2013_Project_Week:ColorHierarchies|Slicer4 Color Hierarchies]] (Nicole Aucoin)
*[[2013_Project_Week:PatientHierarchy|Slicer4 Patient Hierarchy]] (Csaba Pinter, Andrey Fedorov, Nicole Aucoin, Steve Pieper)
*[[2013_Project_Week:ScalarBar|Slicer4 Scalar bar improvements]] (Kevin Wang, Nicole Aucoin Csaba Pinter)
*[[2013_Project_Week:CliMatlabInterface|Slicer4 CLI Matlab interface]] (Kevin Wang, Steve Pieper, Csaba Pinter)
*[[2013_Project_Week:SelfTests|Slicer4 Self Test and Sample Data Refactor]] (Steve Pieper, Jim Miller, Jc)
*[[2013_Project_Week:SpeedUp|Slicer4 Performance]] (Julien Finet)
*[[2013_Project_Week:SimplifyMRMLReference|Simplify MRML References]] - Issue [http://www.na-mic.org/Bug/view.php?id=2727 #2727] (Alex Yarmarkovich, Steve Pieper, Julien Finet ?, 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, Steve, Ron, Jc, Greg, Andriy)
*[[2013_Project_Week:SteeredRegistration|Interactive Registration for Image Guided Therapy]] (Dirk Padfield, Jim Miller, Steve Pieper, Kunlin Cao)
*[[2013_Project_Week:Threaded SimpleITK Modules|Threaded SimpleITK Modules]] (Brad Lowekamp, Steve Pieper)
*[[2013_Project_Week:Slicer Personal Cloud]] (Rui Li, Jim Miller)
*[[2013_Project_Week:XNATSlicer|XNATSlicer]] (Sunil Kumar, Dan Marcus, Steve Pieper, etc.)
*[[2013_Project_Week:PGP_Keysigning|PGP Keysigning]] (Matt McCormick, Luis Ibanez, Bradley Lowekamp)

2013 Project Week:SpeedUp

2013-01-11T16:31:11Z

Finetjul: Created page with '__NOTOC__ <gallery> Image:PW-SLC2013.png|Projects List Image:2013_01_11-ScenePerformance.png | Scene Performance self test Image:2013_01_11-…'

__NOTOC__
<gallery>
Image:PW-SLC2013.png|[[2013_Winter_Project_Week#Projects|Projects List]]
Image:2013_01_11-ScenePerformance.png | Scene Performance self test
Image:2013_01_11-Speedup.png| Performance speedup result
</gallery>

==Key Investigators==

* Julien Finet, Kitware

==Project Description==

<div style="margin: 20px;">
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Objective</h3>
* Assess scene performances for testing optimizations
* Improve performances for loading, closing, modifying a scene
</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Approach, Plan</h3>
Approach

* Create a self test for timing scene actions
* Improve performances See issue [http://na-mic.org/Mantis/view.php?id=2642 #2642]

</div>
<div style="width: 27%; float: left; padding-right: 3%;">
<h3>Progress</h3>
* Scene Performance self test created
*Improve performances:
** 50% faster for loading BrainAtlas2012 scene
** 60% faster to close BrainAtlas2012 scene
** 70% faster to restore a BrainAtlas2012 scene
** 30% faster to modify a node in BrainAtlas2012 scene
** 55% faster to add a node in BrainAtlas2012 scene
</div>
</div>

File:2013 01 11-ScenePerformance.png

2013-01-11T16:22:56Z

Finetjul:

File:2013 01 11-Speedup.png

2013-01-11T16:17:50Z

Finetjul:

2013 Winter Project Week

2013-01-11T16:15:57Z

Finetjul: /* 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 | Coregistration of structural and diffusion MRI towards 4D modeling of TBI]] (Bo Wang, Andrei Irimia, Micah Chambers, Jack Van Horn, Marcel Prastawa, Guido Gerig)
* [[Clinically oriented structural, connectomic and functional analysis of traumatic brain injury in 3D Slicer]] (Andrei Irimia, Bo Wang, Micah Chambers, Jack Van Horn, Marcel Prastawa, Guido Gerig)
* [[UKF Tractography in Slicer 4]] (Ryan Eckbo, Yogesh Rathi, Demian Wassermann, C.F Westin, Ron Kikinis)
* [[4D DTI analysis via longitudinal modeling of tract diffusivities]] (Anuja Sharma, Bo Wang, Andrei Irimia, Micah Chambers, Jack Van Horn, Marcel Prastawa, Guido Gerig)

==Atrial Fibrillation==
* [[2013_Project_Week:CARMA_Scar_Segmentation|Scar Identification (LiangJia Zhu, Yi Gao, Josh Cates, Rob MacLeod, Allen Tannenbaum)]]
* [[2013_Project_Week:CARMA_PV_Antrum_Cut|SLICER MODULE: PV Antrum Cut Filter (Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod)]]
* [[2013_Project_Week:CARMA_LA_Seg_Gopal|SLICER MODULE: Automated LA Segmentation by Gopal (Gopal Veni, Salma Bengali, Greg Gardner, Alan Morris, Josh Cates, Rob MacLeod)]]
* [[2013_Project_Week:CARMA_2D_Dilate|SLICER MODULE: 2D Dilate Filter (Salma Bengali, Greg Gardner, Alan Morris, Josh Cates, Rob MacLeod)]]
* [[2013_Project_Week:CARMA_PractialLASeg|SLICER WORKFLOW: Practical Manual LA Segmentation in Slicer (Salma Bengali, Greg Gardner, Alan Morris, Josh Cates, Rob MacLeod)]]
* [[2013_Project_Week:CARMA_Isolated_Connected_Filter|SLICER MODULE: Isolated Connected Image Filter (Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod)]]
* [[2013_Project_Week:CARMA_Connected_Threshold_Filter|SLICER MODULE: Connected Threshold Image Filter (Salma Bengali, Alan Morris, Josh Cates, Rob MacLeod)]]

==Slicer4 Extensions==
* [[2013_Project_Week:DTIExtension|Diffusion Tensor Images processing tools as Slicer4 extensions (Adrien Kaiser, Francois Budin, Martin Styner)]]
* [[2013_Project_Week:SPHARMExtension|SPHARM-PDM as Slicer4 extension (Beatriz Paniagua, Francois Budin, Martin Styner)]]

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

* [[2013_Project_Week:4DShapeAnalysis | 4D shape analysis: application to HD]] (James Fishbaugh, Marcel Prastawa, Hans Johnson, Guido Gerig)

==Head and Neck Cancer==
* [[2013_Winter_Project_Week:MABS|Multi atlas-based segmentation]] (Sharp, Shusharina, Golland)
* [[2013_Winter_Project_Week:Hybrid_registration|Hybrid interactive-automatic registration]] (Shusharina, Sharp, Pieper)
* [[2013_Winter_Project_Week:PointSetRegistration|Constrained Point Set Registration]] (Kolesov, Karasev, Sharp, Tannenbaum)
* [[2013_Winter_Project_Week:InteractiveSegmentation|Interactive Segmentation and Supporting Utilities]] (Karasev, Kolesov, Tannenbaum)

==Stroke==
* [[2013_Project_Week:WMH_Segmentation_for_Stroke|White Matter Hyperintensity Segmentation in Stroke (Adrian Dalca, Ramesh Sridharan, Polina Golland)]]
* [[2013_Project_Week:Imaging_Genetic_for_Stroke|Imaging Genetics for Stroke (Adrian Dalca, Kayhan Batmanghelich, Polina Golland)]]

==Image-Guided Interventions==
* [[2013_Project_Week:UnitedSlicerIGTExtension|United SlicerIGT extension, repository, website]] (Tamas Ungi, Junichi Tokuda, Adam Rankin)
* [[2013_Project_Week:MRIAblation|Thermal monitoring tools for MRI-guided laser ablation therapy of brain tumor]] (Laurent Chauvin, Noby Hata, Hatsuho Mamata, Alex Golby)
* [[2013_Project_Week:BRAINSFit_new_features|BRAINSFit in ITK4: extra functionality and testing for prostate MR registration (Andrey, Hans)]]
* [[2013_Project_Week:PkModeling_for_prostate_DCE_MRI|PkModeling for prostate DCE MRI (Jim, Andrey)]]
* [[2013_Winter_Project_Week_Gyne_Brachy|iGyne Needle Digitalization]] (Alireza Mehrtash, Csaba Pinter, Tina Kapur, Guillaume Pernelle, Jan Egger, Neha Agrawal, Antonio Damato)
* [[2013_Project_Week:AbdominalNavigationModule|Abdominal navigation module]] (Junichi Tokuda, Atsushi Yamada)
* [[2013_Project_Week:MobileImageOverlay|Mobile image overlay augmented reality needle guidance]] (Tamas Ungi, Adam Rankin)
* [[2013_Project_Week:US_IGT|Ultrasound Guidance for Neurosurgery]] (Matthew Toews, William Wells, Stephen Aylward, 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)

==Medical Robotics==
* [[Configurable fiducial-based device to image registration]] (Junichi Tokuda, Nobuhiko Hata)
* [[2013_Project_Week:RobotizedUltrasoundProbeFor3DVolumeReconstruction| Robotized Ultrasound Probe For 3D Volume Reconstruction]] (Laurent Chauvin, Junichi Tokuda, Noby Hata)
* [[2013_Project_Week:AgileMedicalRobot | Agile medical robotics development with Slicer: Case study with MRI compatible robot(Taka Kato, Atsushi Yamada, Noby Hata, Kazuhumi Onuma)]]
* [[2013_Project_Week:InvestigatingRoleOfOpenSourceInTranslationalResearch | Investigating role of open source in translational research (Miki Kumekawa)]]

==NA-MIC Kit Internals==
*[[2013_Project_Week:WebbasedAnatomicalTeachingFramework|Web-based anatomical teaching framework for mi2b2]] (Daniel Haehn, Steve Pieper, Sonia Pujol, Randy Gollub, Rudolph Pienaar, Ellen Grant)
*[[2013_Project_Week:ITKv4Default|ITKv4 Default in Superbuild]] - [http://www.na-mic.org/Bug/search.php?project_id=3&sticky_issues=on&sortby=last_updated&dir=DESC&hide_status_id=80&tag_string=ITKv4 Issues] (Matt McCormick, Luis Ibanez, Hans Johnson, Jc, Bill Lorensen, Bradley Lowekamp)
*[[2013_Project_Week:MarkupsModule|Slicer4 Markups Module]] (Nicole Aucoin)
*[[2013_Project_Week:ColorHierarchies|Slicer4 Color Hierarchies]] (Nicole Aucoin)
*[[2013_Project_Week:PatientHierarchy|Slicer4 Patient Hierarchy]] (Csaba Pinter, Andrey Fedorov, Nicole Aucoin, Steve Pieper)
*[[2013_Project_Week:ScalarBar|Slicer4 Scalar bar improvements]] (Kevin Wang, Nicole Aucoin Csaba Pinter)
*[[2013_Project_Week:CliMatlabInterface|Slicer4 CLI Matlab interface]] (Kevin Wang, Steve Pieper, Csaba Pinter)
*[[2013_Project_Week:SelfTests|Slicer4 Self Test and Sample Data Refactor]] (Steve Pieper, Jim Miller, Jc)
*[[2013_Project_Week:SimplifyMRMLReference|Simplify MRML References]] - Issue [http://www.na-mic.org/Bug/view.php?id=2727 #2727] (Alex Yarmarkovich, Steve Pieper, Julien Finet ?, 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, Steve, Ron, Jc, Greg, Andriy)
*[[2013_Project_Week:SteeredRegistration|Interactive Registration for Image Guided Therapy]] (Dirk Padfield, Jim Miller, Steve Pieper, Kunlin Cao)
*[[2013_Project_Week:Threaded SimpleITK Modules|Threaded SimpleITK Modules]] (Brad Lowekamp, Steve Pieper)
*[[2013_Project_Week:Slicer Personal Cloud]] (Rui Li, Jim Miller)
*[[2013_Project_Week:XNATSlicer|XNATSlicer]] (Sunil Kumar, Dan Marcus, Steve Pieper, etc.)
*[[2013_Project_Week:PGP_Keysigning|PGP Keysigning]] (Matt McCormick, Luis Ibanez, Bradley Lowekamp)
*[[2013_Project_Week:SpeedUp|Slicer4 Performance]] (Julien Finet)

2013 Project Week:ScalarBar

2013-01-08T01:19:50Z

Finetjul: /* References */

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


</gallery>

==Key Investigators==
* PMH, UHN Toronto: Kevin Wang
* Isomics: Steve Pieper
* Queen's: Csaba Pinter

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

<h3>Objective</h3>
The goal is to extend the usage of the scalar bar widget

</div>

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

<h3>Approach, Plan</h3>
* TODO:

</div>

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

<h3>Progress</h3>
Not yet available

</div>
</div>

==Delivery Mechanism==

This work will be delivered to the NA-MIC Kit as a change in the Slicer4 core

==References==
* [https://www.assembla.com/spaces/slicerrt/wiki SlicerRT]
* Corresponding issues
** [https://www.assembla.com/spaces/slicerrt/tickets/121#/activity/ticket: SlicerRT #121]
** [http://www.na-mic.org/Bug/view.php?id=2425 Mantis #2425]
** [https://www.assembla.com/spaces/slicerrt/tickets/139#/activity/ticket: SlicerRT #139]
* Previous work
** http://www.kitware.com/blog/home/post/278

2012 Summer Project Week:CUDA Volume Rendering Extension

2012-06-22T14:47:15Z

Finetjul: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Kitware: Julien Finet
* Robarts: Elvis Chen

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

<h3>Objective</h3>
* Support addition of Volume Rendering techniques as extensions
* Create a CUDA volume rendering extension
</div>

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

<h3>Approach, Plan</h3>

Redesign the VR display nodes and displayable managers
Wrap existing CUDA VR into a Slicer 4.1.1 extension.
</div>

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

<h3>Progress</h3>

* Refactoring/Redesign: done
* Extension: written
* 1 more build error but extension is almost ready !

</div>
</div>

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

==Delivery Mechanism==

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

#ITK Module
#Slicer Module - YES
##Built-in - NO
##Extension -- commandline
##Extension -- loadable - YES
#Other (Please specify)

==References==

</div>

2012 Summer Project Week:CUDA Volume Rendering Extension

2012-06-22T14:35:53Z

Finetjul:

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Kitware: Julien Finet
* Robarts: Elvis Chen

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

<h3>Objective</h3>
* Support addition of Volume Rendering techniques as extensions
* Create a CUDA volume rendering extension
</div>

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

<h3>Approach, Plan</h3>

Redesign the VR display nodes and displayable managers
Wrap existing CUDA VR into a Slicer 4.1.1 extension.
</div>

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

<h3>Progress</h3>

- Refactoring/Redesign: done
- Extension: written
- 1 more build error but extension is almost ready !

</div>
</div>

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

==Delivery Mechanism==

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

#ITK Module
#Slicer Module - YES
##Built-in - NO
##Extension -- commandline
##Extension -- loadable - YES
#Other (Please specify)

==References==

</div>

AHM2012-Slicer-Extension

2012-06-21T20:20:19Z

Finetjul: /* How to get started */ Link to module wizard

== Writing an s4ext file ==
* Extensions are described using a simple text file.
<pre>
#
# First token of each non-comment line is the keyword and the rest of the line
# (including spaces) is the value.
# - the value can be blank
#

# This is source code manager (i.e. svn)
scm local
scmurl Testing/LoadableExtensionTemplate

# list dependencies
# - These should be names of other modules that have .s4ext files
# - The dependencies will be built first
depends NA

# homepage
homepage http://www.slicer.org/slicerWiki/index.php/Slicer4:Developers:Projects:QtSlicer/Tutorials/ExtensionWriting

# Match category in the xml description of the module (where it shows up in Modules menu)
category Examples

# Give people an idea what to expect from this code
# - Is it just a test or something you stand beind?
status Beta

# One line stating what the module does
description This is an example of Qt loadable module built as an extension
</pre>

* This file will be automatically generated using information specified within your CMakeLists.txt

== Example of CMakeLists.txt ==
<pre>
cmake_minimum_required(VERSION 2.8.4)

set(EXTENSION_NAME LoadableExtensionTemplate)

#-----------------------------------------------------------------------------
# Prerequisites
#-----------------------------------------------------------------------------
if(NOT Slicer_SOURCE_DIR)
set(EXTENSION_HOMEPAGE "http://www.slicer.org/slicerWiki/index.php/Slicer4:Developers:Projects:QtSlicer/Tutorials/ExtensionWriting")
set(EXTENSION_CATEGORY "Examples")
set(EXTENSION_STATUS "Beta")
set(EXTENSION_DESCRIPTION "This is an example of Qt loadable module built as an extension")
set(EXTENSION_DEPENDS CLIExtensionTemplate) # Specified as a space separated list or 'NA' if any

find_package(Slicer REQUIRED)

# Additional C/CXX flags - Should be defined before including Slicer_USE_FILE
set(ADDITIONAL_C_FLAGS "" CACHE STRING "Additional ${EXTENSION_NAME} C Flags")
set(ADDITIONAL_CXX_FLAGS "" CACHE STRING "Additional ${EXTENSION_NAME} CXX Flags")

include(${Slicer_USE_FILE})

set(EXTENSION_LICENSE_FILE ${Slicer_LICENSE_FILE})
set(EXTENSION_README_FILE ${Slicer_README_FILE})

include(SlicerEnableExtensionTesting)

endif()

# Add subdirectories
add_subdirectory(Logic)

#-----------------------------------------------------------------------------
# Sources
#-----------------------------------------------------------------------------
set(qt_module_export_directive "Q_SLICER_QTMODULES_LOADABLEEXTENSIONTEMPLATE_EXPORT")

# Additional includes - Current_{source,binary} and Slicer_{Libs,Base} already included
set(qt_module_include_directories
${CMAKE_CURRENT_SOURCE_DIR}/Logic
${CMAKE_CURRENT_BINARY_DIR}/Logic
)

# Source files
set(qt_module_SRCS
qSlicerLoadableExtensionTemplateModule.cxx
qSlicerLoadableExtensionTemplateModule.h
qSlicerLoadableExtensionTemplateModuleWidget.cxx
qSlicerLoadableExtensionTemplateModuleWidget.h
)

# Headers that should run through moc
set(qt_module_MOC_SRCS
qSlicerLoadableExtensionTemplateModule.h
qSlicerLoadableExtensionTemplateModuleWidget.h
)

# UI files
set(qt_module_UI_SRCS
Resources/UI/qSlicerLoadableExtensionTemplateModule.ui
)

# Additional Target libraries
set(qt_module_target_libraries
vtkSlicerLoadableExtensionTemplateModuleLogic
)

# Resources
set(qt_module_resources
Resources/qSlicerLoadableExtensionTemplateModule.qrc
)

#-----------------------------------------------------------------------------
# Build
#-----------------------------------------------------------------------------
slicerMacroBuildQtModule(
NAME ${EXTENSION_NAME}
EXPORT_DIRECTIVE ${qt_module_export_directive}
INCLUDE_DIRECTORIES ${qt_module_include_directories}
SRCS ${qt_module_SRCS}
MOC_SRCS ${qt_module_MOC_SRCS}
UI_SRCS ${qt_module_UI_SRCS}
TARGET_LIBRARIES ${qt_module_target_libraries}
RESOURCES ${qt_module_resources}
)

#-----------------------------------------------------------------------------
# Testing
#-----------------------------------------------------------------------------
if(BUILD_TESTING)
add_subdirectory(Testing)
endif()

#-----------------------------------------------------------------------------
# Generate extension description file '<EXTENSION_NAME>.s4ext'
#-----------------------------------------------------------------------------
if(NOT Slicer_SOURCE_DIR)
include(SlicerFunctionGenerateExtensionDescription)
slicerFunctionGenerateExtensionDescription(
EXTENSION_NAME ${EXTENSION_NAME}
EXTENSION_CATEGORY ${EXTENSION_CATEGORY}
EXTENSION_STATUS ${EXTENSION_STATUS}
EXTENSION_HOMEPAGE ${EXTENSION_HOMEPAGE}
EXTENSION_DESCRIPTION ${EXTENSION_DESCRIPTION}
EXTENSION_DEPENDS ${EXTENSION_DEPENDS}
DESTINATION_DIR ${CMAKE_CURRENT_BINARY_DIR}
SLICER_WC_REVISION ${Slicer_WC_REVISION}
SLICER_WC_ROOT ${Slicer_WC_ROOT}
)
endif()

#-----------------------------------------------------------------------------
# Packaging
#-----------------------------------------------------------------------------
if(NOT Slicer_SOURCE_DIR)
include(${Slicer_EXTENSION_CPACK})
endif()
</pre>

== Testing your extension ==
* An extension is a ''container'' for one or more modules, writing test shouldn't be different.

== How users will access your extension ==
* Two options:
** Extension manager within Slicer
** Download from http://slicer.kitware.com/midas3/slicerpackages

== How to get started ==
* Look at the existing template living in [https://github.com/Slicer/Slicer/tree/master/Extensions/Testing Slicer/Extensions/Testing]
** [https://github.com/Slicer/Slicer/tree/master/Extensions/Testing/CLIExtensionTemplate CLIExtensionTemplate]
** [https://github.com/Slicer/Slicer/tree/master/Extensions/Testing/EditorExtensionTemplate EditorExtensionTemplate]
** [https://github.com/Slicer/Slicer/tree/master/Extensions/Testing/LoadableExtensionTemplate LoadableExtensionTemplate]
** [https://github.com/Slicer/Slicer/tree/master/Extensions/Testing/ScriptedLoadableExtensionTemplate ScriptedLoadableExtensionTemplate]
** [https://github.com/Slicer/Slicer/tree/master/Extensions/Testing/SuperBuildLoadableExtensionTemplate SuperBuildLoadableExtensionTemplate]

* Use [http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Developers/ModuleWizard module wizard] to create an extension

* Configure and build an extension
<pre>
$ pwd
/path/to/MyExtension
$ cd ..
$ mkdir MyExtension-build
$ cd MyExtension-build
$ cmake -DSlicer_DIR:PATH=/path/to/Slicer-build
$ make -j4
</pre>

* Test your extension and submit to CDash
<pre>
$ make Experimental
</pre>

* Test, submit to CDash and upload your extension on Midas
<pre>
$ make ExperimentalUpload
</pre>

Madrid-May-21-2012-Slicer-Workshop

2012-06-20T20:07:49Z

Finetjul: /* Preparation for the workshop */ Link to packages on MIDAS instead of CDash (been automatically deleted)

{| class="wikitable"
| colspan="3"|[[Image:logoURJC.jpg|right]][[Image:Mvis_logo.png|left]]
|-
| style="width:30%" |[[Image:NAMIC.jpg‎]]
| style="width:30%" |[[Image:Logo_nac.gif‎]]
|style="width:30%" |[[Image:NCIGTlogo.gif]]
|}

== Introduction ==

For the past seven years, the [http://www.na-mic.org/ '''National Alliance for Medical Image Computing (NA-MIC)]''', one of the seven National Centers for Biomedical Computing, part of the NIH Roadmap for medical research, has converted some of the major scientific advances made by the biomedical imaging community into open-source software tools, to fasten the deployment of cutting-edge image analysis and visualization techniques on a national and international scale.

As part of the NA-MIC toolkit, the [http://www.slicer.org/ '''3D Slicer open-source software'''] has been developed as a technology delivery platform that is both easy to use for clinical researchers, and easy to extend for software developers. 3D Slicer has become a multi-institution effort to share the latest advances in image analysis with the scientific and clinical community. To foster the translation of NA-MIC technology to clinical research applications, the NA-MIC Training Core has developed a series of courses and tutorials on medical image analysis topics using the software. This workshop combines a series of lectures and 3DSlicer hands-on sessions, and includes a poster presentation by local scientific teams to provide a forum for exchange and discussion on medical imaging research.

This workshop is organized in collaboration with the [http://mvisionconsortium.mit.edu/ Madrid-MIT+Vision Consortium].
[[image:Madrid2012.jpg|right|400px]]
== Local Organizer==
*[http://laimbio08.escet.urjc.es/index.php?id=76 Norberto Malpica, Ph.D.], Universidad Rey Juan Carlos, Mostoles, Madrid, Espana

==Faculty==
*[http://www.spl.harvard.edu/~kikinis Ron Kikinis, M.D.], Surgical Planning Laboratory, Harvard Medical School, Boston, USA
*[http://people.csail.mit.edu/polina/ Polina Golland, Ph.D.], Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, USA
*[http://www.spl.harvard.edu/~spujol Sonia Pujol, Ph.D.], Surgical Planning Laboratory, Harvard Medical School, Boston, USA

== Tentative Agenda ==

{| border="1" cellpadding="5" width="1000"
|- style="background:#ebeced; color:#663300; font-size:120%" align="center"
| style="width:10%" | '''Time'''
| style="width:90%" colspan="2"| '''Monday, May 21, 2012'''
|-
| style="background:#efefef; color:#663300"| '''8:30-9:00'''
| style="background:#FBF7BB; color:#522200" colspan="2"| Computer set-up and assistance by course instructors
|-
| style="background:#efefef; color:#663300"| '''9:00-9:10'''
| style="background:#FBF7BB; color:#522200" colspan="2"| Welcome and Presentation of day activities (Ron Kikinis/Sonia Pujol)
|-
| style="background:#efefef; color:#663300"| '''9:10-09:35'''
| style="background:#FBF7BB; color:#522200" colspan="2"| Presentation of the Madrid-MIT M+Vision Consortium (Norberto Malpica)
|-
| style="background:#efefef; color:#663300"| '''09:35-10:00'''
| style="background:#FBF7BB; color:#522200" colspan="2"| [[media:2012-05-21-AsPresented.pptx|3DSlicer: an open-source platform for collaborative research]] (Ron Kikinis)
|-
| style="background:#efefef; color:#663300"| '''10:00-11:15'''
| style="background:#FBF7BB; color:#522200" colspan="2"| [[media:DataLoadingAndVisualizationSlicer4_Madrid2012_SoniaPujol.pdf| Hands-on Session 1: Data Loading and 3D Visualization (Sonia Pujol)]]
|-
| style="background:#efefef; color:#663300"| '''11:15-11:30'''
| style="background:#F5EBD6; color:#522200" colspan="2"| Coffee-break
|-
| style="background:#efefef; color:#663300"| '''11:30-12:00'''
| style="background:#FBF7BB; color:#522200" colspan="2"| Algorithm Development within NA-MIC (Polina Golland)
|-
| style="background:#efefef; color:#663300"| '''12:00-13:30'''
| style="background:#F5EBD6; color:#522200" colspan="2"| Lunch Break
|-
| style="background:#efefef; color:#663300"| '''13:30-15:15'''
| style="background:#FBF7BB; color:#522200" colspan="2"| [[media:Slicer4_ProgrammingTutorial_SPujol-SPieper-Madrid2012.pdf| Hands-on Session 2: Programming into Slicer4 (Sonia Pujol) ]]
|-
| style="background:#efefef; color:#663300"| '''15:15-15:30'''
| style="background:#FBF7BB; color:#522200" colspan="2"| Coffee-Break
|-
| style="background:#efefef; color:#663300"| '''15:30-17:00'''
| style="background:#FBF7BB; color:#522200" colspan="2"| Poster/demo session by local research teams
|-
| style="background:#efefef; color:#663300"| '''17:00-17:30'''
| style="background:#FBF7BB; color:#522200" colspan="2"| Questions from the audience and discussion
|-
| style="background:#FFFFFF; height:35px" colspan="3" |
|-style="background:#ebeced; color:#663300; font-size:120%" align="center"
| style="width:10%" | '''Time'''
| style="width:90%" colspan="2"| '''Tuesday, May 22, 2012'''
|-
| style="background:#efefef; color:#663300"| '''09:00-10:15'''
| style="background:#FBF7BB; color:#522200" colspan="2"| [[media:DTI_Analysis_Tutorial_Slicer4.1_Madrid2012_SoniaPujol.pdf | Hands-on Session 3: Diffusion Tensor Imaging (Sonia Pujol)]]
|-
| style="background:#efefef; color:#663300"| '''10:15-11:30'''
| style="background:#FBF7BB; color:#522200" colspan="2"| [[media:WhiteMatterExplorationNeurosurgicalPlanning_Madrid2012_SoniaPujol.pdf| Hands-on Session 4: Neurosurgical Planning (Sonia Pujol)]]
|-
| style="background:#efefef; color:#663300"| '''11:30-11:45'''
| style="background:#F5EBD6; color:#522200" colspan="2"| Coffee Break
|-
| style="background:#efefef; color:#663300"| '''12:00-12:30'''
| style="background:#FBF7BB; color:#522200" colspan="2"| Towards validation of DTI tractography (Sonia Pujol)
|-
| style="background:#efefef; color:#663300"| '''12:30-13:00'''
| style="background:#FBF7BB; color:#522200" colspan="2"| Concluding Remarks and Discussion
|}

== Logistics ==
* Dates: The workshop will be held on Monday May 21 and Tuesday May 22, 2012.
* Location: Room 170, Departamental II Building, Móstoles Campus, Universidad Rey Juan Carlos, c/ Tulipán s/n, 28933 Móstoles

* Registration: Please fill in the [[Media:RegistrationForm_SlicerWorkshop_May21-22_2012.doc| Workshop Registration Form]] and send it by e-mail to Almudena García (almudena.garcia.fernandez at urjc.es )

== Preparation for the workshop ==

*Hardware: The workshop combines oral presentations and instructor-led hands-on sessions using the 3DSlicer software version 4.1.
All participants are required to come with their own laptop computer and install the software and datasets prior to the event. A minimum of 1 GB of RAM (4 GB is better) and a graphic accelerator with 64mb (512MB is better) of on-board graphic memory are required. Shared memory graphics boards have significantly poorer performance.

<span style="background-color: yellow">In preparation for the hands-on session, please install the following software and datasets.</span> The following OS will be supported: MacOS X SnowLeopard, Windows7 64-bit, Windows7 32-bit and Linux 64.
* '''Software''':
Please install the version of Slicer located at the link below. Note: to download the binaries, click on the link located below the URL banner.
** MacOSX [http://slicer.kitware.com/midas3/item/1470 Slicer4.1 MacOSX]
** Linux 64 [http://slicer.kitware.com/midas3/item/1469 Slicer4.1 Linux 64]
** Windows 7 64 [http://slicer.kitware.com/midas3/item/1472 Slicer4.1 Windows7 64]
** Windows 7 32 [http://slicer.kitware.com/midas3/item/1471 Slicer4.1 Windows7 32]

* '''Datasets''':
Please download the following datasets.
**[[media:3DVisualizationData.zip‎|Dataset 1: 3D Visualization]]
**[[media:DiffusionMRI_tutorialData.zip| Dataset 2: DiffusionMR]]
**[[media:WhiteMatterExplorationData.zip‎| Dataset 3: Neurosurgical Planning]]
**[[media:HelloPythonData.zip| Dataset 4: HelloPython]]

== Slicer Community ==
Participants are invited to join the [http://www.slicer.org/pages/Mailinglist Slicer user and Slicer developer mailing lists] prior to the workshop. This is a place for the Slicer community to discuss questions and feature requests related to 3D Slicer.

== Slicer4 Training Survey ==
After the workshop, participants will be invited to take the [http://www.surveymonkey.com/s/GZDXKXQ Slicer4 Training Survey] to provide feedback and suggestions.

[http://www.na-mic.org/Wiki/index.php/Events Back to NA-MIC Events]

2012 Summer Project Week:CUDA Volume Rendering Extension

2012-06-18T18:25:32Z

Finetjul: Created page with '__NOTOC__ <gallery> Image:PW-MIT2012.png|Projects List </gallery> ==Key Investigators== * Kitware: Julien Finet * Robarts: Elvis Chen <di…'

__NOTOC__
<gallery>
Image:PW-MIT2012.png|[[2012_Summer_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* Kitware: Julien Finet
* Robarts: Elvis Chen

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

<h3>Objective</h3>
* Support addition of Volume Rendering techniques as extensions
* Create a CUDA volume rendering extension
</div>

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

<h3>Approach, Plan</h3>

Redesign the VR display nodes and displayable managers
Wrap existing CUDA VR into a Slicer 4.1.1 extension.
</div>

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

<h3>Progress</h3>

</div>
</div>

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

==Delivery Mechanism==

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

#ITK Module
#Slicer Module - YES
##Built-in - NO
##Extension -- commandline
##Extension -- loadable - YES
#Other (Please specify)

==References==

</div>

2012 Summer Project Week

2012-06-18T18:14:02Z

Finetjul: /* 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)]]
|'''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:Slicer in Networked Environment|Slicer in Networked Environment]] (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''' [[2012 Summer Project Week Breakout Session:SlicerExtensions|Slicer4 Extensions]] (JC) <br>
[[MIT_Project_Week_Rooms#Grier_34-401_AB|Grier Room (Left)]]
<br>----------------------------------------<br>
'''4:30-5:30pm''' [[2012_Summer_Project_Week:LeanSlicer|Lean Slicer (round 1)]]<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><br> [[2012 Summer Project Week Breakout Session:QtTesting|QtTesting]] (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'''===

# [[Semiautomatic longitudinal segmentation of MR volumes in traumatic brain injury]] (Andrei Irimia, Micah Chambers, Bo Wang, Marcel Prastawa, Danielle Pace, Stephen Aylward, Jack van Horn, Guido Gerig)
# [[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)
# [[2012_Summer_Project_Week:Intraoperative_Tract_Detection | Intraoperative White Matter Tract Detection Module]] (Lauren O'Donnell, Isaiah Norton)
# [[2012_Summer_Project_Week:Ultrasound_Aberration_Correction | An Ultrasound-based Method for Aberration Correction in TCFUS]] (Jason White, Greg Clement)
# [[2012_Summer_Project_Week:TimeSeriesMonitoringIntracranialBones| Monitoring time series images of intracranial bones in meningioma ]] (Karl Diedrich)
# [[2012_Summer_Project_Week:Early_Dementia_Diagnostic |Early Dementia Diagnostic Tools]] (Marcel Koek, Sonia Pujol)
# [[2012_Summer_Project_Week:Radnostics |Spine Segmentation & Osteoporosis Detection In CT Imaging Studies]] (Anthony Blumfield, Ron Kikinis)

==='''Radiation Therapy'''===
#[[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:Overlapping_structures| First class structure set support in Slicer]] (Greg Sharp, James Shackleford, Steve Pieper)
#[[2012_Summer_Project_Week:PlastimatchIntegration| Plastimatch loadable module]] (James Shackleford, Greg Sharp)
#[[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:SlicerRT| Radiotherapy extensions for Slicer 4]] (Andras Lasso, Csaba Pinter, Kevin Wang)
#[[2012_Summer_Project_Week:PET_Image_Analysis | SUV Threshold Computation]] (Nadya Shusharina, Greg Sharp)

==='''Huntington's Disease'''===
# [[2012_Summer_Project_Week:DTIPrep|DTIPrep]] (David Welch, Hans Johnson)
# [[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: Software Tools]] (James Fishbaugh, Marcel Prastawa, Guido Gerig)
# [[2012_Summer_Project_Week:DTI-Reg|DTI atlas based fiber analysis]] (Francois Budin)

==='''Atrial Fibrillation'''===
# [[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)
# [[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:SlicerWeb|Web Interface to Slicer 4]] (Steve Pieper)
# [[2012_Summer_Project_Week:OpenIGTLinkIF|Improvement of OpenIGTLink IF for Slicer 4]] (Junichi Tokuda, Laurent Chauvin)
# [[2012_Summer_Project_Week:LeanSlicer|Lean Slicer to facilitate regulatory approval]] (Andras Lasso, Chris Wedlake)
# [[2012_Summer_Project_Week:LiveUltrasound|Live Ultrasound]] (Tamas Ungi, Andinet Enquobahrie, Junichi Tokuda)
# [[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:TransformRecorder|Transform Recorder and other IGT modules]] (Simrin Nagpal, Tamas Ungi)
# [[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:iGyne|iGyne for Gynecological Cancer Brachytherapy]] (Xiaojun Chen, Jan Egger, Tina Kapur, Steve Pieper)
#[[2012_Summer_Project_Week:Interactive_Needle_Segmentation|Interactive Needle Segmentation for Gynecological Cancer Brachytherapy]] (Nabgha Farhat, Neha Agrawal, Jan Egger, Tina Kapur, Steve Pieper)
# [[2012_Summer_Project_Week:VertebraCTUSReg|Single Vertebra CT-US Registration]] (Samira Sojoudi, Saman Nouranian, Simrin Nagpal, Tamas Ungi, David Welch)
# [[2012_Summer_Project_Week:Fast Fiducial Registration|Fast Fiducial Registration Module]] (David Welch, Hans Johnson, Nicole Aucoin, Ron Kikinis)
# [[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:4D_Ultrasound_Slicer4|4D Ultrasound on Slicer4]] (Laurent Chauvin, Nobuhiko Hata)
# [[2012_Summer_Project_Week:Kinect4Slicer|Kinect4Slicer]] (Laurent Chauvin, Nobuhiko Hata)
# [[2012_Summer_Project_Week:Needle Tip Tracking |Needle Tip Tracking for complex MR images]] (Atsushi Yamada, Nobuhiko Hata)

==='''General Segmentation'''===
#[[2012_Summer_Project_Week:SemiAutomatedAirwaySegmentationfrom0.64mmLungCTDatasets|Semi-automated airway segmentation from 0.64mm lung CT datasets]] (Pietro Nardelli, Padraig Cantillon-Murphy, Raul San Jose Estepar)
#[[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)
# [[2012_Summer_Project_Week:QuantitativePETImageAnalysisModule|Quantitative PET Image Analysis Module]] (Markus Van Tol)
#[[2012_Summer_Project_Week:SegmentationWithLabelFusion|Segmentation with Label Fusion]] (Ramesh Sridharan, Christian Wachinger, Polina Golland)

==='''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, Petter Risholm, 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)
# [[2012_Summer_Project_Week:Reporting|Reporting module]] (Andrey, Nicole, Steve, Ron, Pat)

==='''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, Brendan Moloney)
# [[2012_Summer_Project_Week:PythonCLIandWidget|Python CLI modules (Demian, JC, Julien, Steve)]].
# [[2012_Summer_Project_Week:Charting|Charting]] (Jim)
# [[2012_Summer_Project_Week:GPUEditor|GPU Editor Effects]] (Steve, Jim)
# [[2012_Summer_Project_Week:XTK|XTK/WebGL Exporter]] (Daniel, Nicolas - Boston Children's Hospital)
# [[2012_Summer_Project_Week:EventOptimization|Callback/Events/Observation best practice + Performance bottleneck discussion (Julien, Steve,...)]]
# [[2012_Summer_Project_Week:XNATSlicerIntegration|XNAT/Slicer Integration]] (Sunil, Dan, Steve,...)
# [[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:SimpleITK Integration|SimpleITK Integration]] (Hans Johnson, Bradley Lowekamp)
# [[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)
# [[2012_Summer_Project_Week:CUDA Volume Rendering Extension|CUDA Volume Rendering as Extension]] (J2, Elvis)

==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
#Kleper, Vladimir, Northwestern Univ, vkleper@northwestern.edu
#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
#Risholm, Petter, Harvard, pettri@bwh.harvard.edu
#San Jose, Raul, BWH, rjosest@bwh.harvard.edu
#Schroeder, William, Kitware, will.schroeder@kitware.com
#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

2012 Summer Project Week

2012-05-03T19:16:49Z

Finetjul: /* Infrastructure */

Tests of Iowa Workshop tutorials

2012-03-19T15:55:35Z

Finetjul:

[[Iowa 2012 Workshop Materials]]

<table>
{| class="wikitable sortable labelpage labelpagetable" border="1" align="left"
|-
|'''Tutorial Name'''||'''Tutorial Data'''||'''Platform'''||'''Slicer Version'''||'''Test Date'''||'''Test Author & Comments/Mantis Links'''
|-
|[[media:DTI_Analysis_Tutorial_Slicer4.1_SPujol.pdf | Slicer4.1 DTI Tutorial]]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Mac OS Lion || || ||
|-
|[[media:DTI_Analysis_Tutorial_Slicer4.1_SPujol.pdf | Slicer4.1 DTI Tutorial]]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Mac OS Snow Leopard || 2012/03/18 ||2012-03-18 (r19639) || Sonia. OK.
|-
|[[media:DTI_Analysis_Tutorial_Slicer4.1_SPujol.pdf | Slicer4.1 DTI Tutorial]]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Windows 7 32 || || ||
|-
|[[media:DTI_Analysis_Tutorial_Slicer4.1_SPujol.pdf | Slicer4.1 DTI Tutorial]]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Windows XP || 2012-03-17 || 3/18.12 || Steve<br>Everything works except turning on glyphs after label map seeding, which results in a crash due to lack of memory. Suggestion is to skip this step of the tutorial for users on win32. Another option is to only segment a single slice of the corpus in order to generate fewer tracts. Also it might help to delete the dwi volume after tensor estimation. When I did these steps I was able to complete all steps of the tutorial.
|-
|[[media:DTI_Analysis_Tutorial_Slicer4.1_SPujol.pdf | Slicer4.1 DTI Tutorial]]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Linux Unbuntu 64 || || ||
|-
|[[media:DTI_Analysis_Tutorial_Slicer4.1_SPujol.pdf | Slicer4.1 DTI Tutorial]]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Linux 64 (debug) || || ||
|-
|[http://www.na-mic.org/Wiki/images/e/e4/DTI_Analysis_Tutorial_SoniaPujol_SPIE2012.pdf Slicer4 DTI Tutorial]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Linux 64 (debug)|| r19517 || 03/07/2012 ||
Nicole: <s>[http://na-mic.org/Bug/view.php?id=1793 1793]</s>. <s>[http://na-mic.org/Bug/view.php?id=1795 1795]</s>
|-
|[http://www.na-mic.org/Wiki/images/e/e4/DTI_Analysis_Tutorial_SoniaPujol_SPIE2012.pdf Slicer4 DTI Tutorial]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Windows 7 64b (package)|| r19577 || 03/13/2012 ||
Julien <br>pdf is 95MB !?!?<br>Page 22, Popup look is now different<br>Page 23, in red slice only the popup should still be up (didn't unpin)<br>Page 25: Diffusion Tensor Estimation has been renamed into DWI to DTI estimation<br>Page 25: dwi is already selected as Input DWI<br>Page 25: Minor Bug ! It stays "scheduled" for >5secs, not sure why<br>Page 26: Popup looks different now<br>Page 30: shouldn't labda1~labda2 >> lambda3 look more like a smarties ?<br>Page 32: typo connect ->connects<br>Page 36: Need to click on ">>" button first<br>Page 41: Bug ! After apply, the foreground image is reset to none, need to manually set it back to dti<br>Page 46: After selecting FractionalAnisotropy, Auto WL is automatically selected<br>Page 48: You might want to include screenshot of Link button again<br>Page 51: No need to move the mouse in 3D view, it automatically refreshes. If not, then a bug must be reported<br>Page 57: 1 bullet point has no . at the end(for information, there is no . in the other slides.<br>Page 60: Advice to use the right/left arrow keys to slice through?<br>Page 65: No axial slice displayed in 3D<br>Page 74: explain how to rename?<br>Page 78: explain to go to Annotation module again ?<br>Page 79: no need to turn off and on, it automatically refreshed when I placed the fiducial. If not, then a bug must be reported.<br>Page 81: explain where to place fiducial.<br>Page 82: Bug, it doesn't recompute automatically
|-
|[http://www.na-mic.org/Wiki/images/e/e4/DTI_Analysis_Tutorial_SoniaPujol_SPIE2012.pdf Slicer4 DTI Tutorial]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Windows XP 32b || Slicer 4.1.0 rc1 (r19609) || 03/15/2012 ||
Julien <br>no link for the data mentioned in the tutorial<br>No mention to what Slicer version the tutorial is compatible with<br>Page1: Slicer Logo is 4.0, does it mean it's compatible with 4.0 ? no<br>Page 10: I have 100modules (from log messages dialog CTRL+0)<br>Page 19: typo: appears in the 2D viewer'''s'''<br>Page 22: Add "fit image to window" icon<br>Page 41: Odd black pixels in fa volume (see email)<br>Page 58: Add arrow to indicates how to change to yellow layout ?<br>Page 60: icon of the draw tool ? I first used the paint tool instead<br>Page 64: no "Minimum Length", only "Minimum Path Length". Bug ? why "Maximum Length" is not also "Maximum Path Length" ?<br>Page 64: Bug: why only Integration Step Length is (mm) but not others?<br>Page 66: Click on "Glyph" -> Crash (Slicer= 690Mo)
|-
|[http://www.na-mic.org/Wiki/index.php/File:HelloPython-ProgrammingTutorial_spujol-pieper-2012-03-15.pdf HelloPython Tutorial]
||[http://www.na-mic.org/Wiki/index.php/File:HelloPythonData.zip HelloPythonDataset] || Mac OS Lion || version from tutorial page || March 19 || Steve<br>Tested solution modules with sample data and all looked good.
|-
|[http://www.na-mic.org/Wiki/index.php/File:HelloPython-ProgrammingTutorial_spujol-pieper-2012-03-15.pdf HelloPython Tutorial]
||[http://www.na-mic.org/Wiki/index.php/File:HelloPythonData.zip HelloPythonDataset] || Windows 7 64 || version from tutorial page || March 19 || Steve<br>Tested solution modules with sample data and all looked good.
|-
|[http://www.na-mic.org/Wiki/index.php/File:HelloPython-ProgrammingTutorial_spujol-pieper-2012-03-15.pdf HelloPython Tutorial]
||[http://www.na-mic.org/Wiki/index.php/File:HelloPythonData.zip HelloPythonDataset]|| Windows XP 32 || version from tutorial page || March 19 || Steve<br>Tested solution modules with sample data and all looked good.
|-
|[http://www.na-mic.org/Wiki/index.php/File:HelloPython-ProgrammingTutorial_spujol-pieper-2012-03-15.pdf HelloPython Tutorial]
||[http://www.na-mic.org/Wiki/index.php/File:HelloPythonData.zip HelloPythonDataset] || Linux Ubuntu 64|| Slicer4.1rc1 || 03/16/2012 ||
Benjamin <br> p3 : Image has no link with this tutorial <br> p16 : The Directory HelloPython has two sub directories "code" and "data". Wrong path. <br> p21 : Add comment to warn the user about the indentation <br> p17 : Slicer layout change compare to the previous screenshot <br> p31 : We are not able to copy properly the text <br> p35 : helloPython sript path is ".../helloPython/code/" <br> p36: word "can" is written twice, and I already have 3 items in the sub menu "Exemples" <br> p48: The Directory HelloPython has two sub directories "code" and "data". Wrong path. <br> p50: Slicer layout change compare to the previous screenshot <br> p55: The last line should be on 1 line, or warn the user who may not know how work Python. <br> p59: Same as p48 and p16 <br> p61: Slicer layout change compare to the previous screenshot <br> p62: More explanation maybe - Up/Down - Left/Right - ?
|-
|[http://www.na-mic.org/Wiki/index.php/File:HelloPython-ProgrammingTutorial_spujol-pieper-2012-03-15.pdf HelloPython Tutorial]
||[http://www.na-mic.org/Wiki/index.php/File:HelloPythonData.zip HelloPythonDataset] || linux 64 (debug) || || ||
|-
|[http://www.na-mic.org/Wiki/index.php/File:WhiteMatterExplorationNeurosurgicalPlanning_SoniaPujol.pdf Neurosurgical Planning Tutorial]
||[[media:WhiteMatterExplorationData.zip‎| Neurosurgical Planning dataset]] || Mac OS SnowLeopard || 2012.03.18|| 2012.03.18 || Sonia. OK
|-
|[http://www.na-mic.org/Wiki/index.php/File:WhiteMatterExplorationNeurosurgicalPlanning_SoniaPujol.pdf Neurosurgical Planning Tutorial]
||[[media:WhiteMatterExplorationData.zip‎| Neurosurgical Planning dataset]] || Mac OS Lion || || ||
|-
|[http://www.na-mic.org/Wiki/index.php/File:WhiteMatterExplorationNeurosurgicalPlanning_SoniaPujol.pdf Neurosurgical Planning Tutorial]
||[[media:WhiteMatterExplorationData.zip‎| Neurosurgical Planning dataset]] || Windows 7 64|| 4.1.0-rc1-2012-03-17 r19637 || March 19 || Julien<br>Page 13: Background is already correctly set<br>Page 14: circle on screenshot where to change current volume to "BaselineVolume" (DTIVolume selected by default) (+ typo, it's "BaselineVolume" not "Baseline Volume")<br>Page 24: You might want to mention that Grow Cut works in 3D<br>Page 31: grow cut button circle is off<br>Page 39: I don't have the axial slice visible in 3D view<br>Page 40: Didn't understand why positioning the mouse in the cystic part<br>Page 46: Give description for "Output Fiber Bundle"
|-
|[http://www.na-mic.org/Wiki/index.php/File:WhiteMatterExplorationNeurosurgicalPlanning_SoniaPujol.pdf Neurosurgical Planning Tutorial]
||[[media:WhiteMatterExplorationData.zip‎| Neurosurgical Planning dataset]] || Windows XP 32|| version from tutorial page || March 19 || Steve<br>Worked as expected
|-
|[http://www.na-mic.org/Wiki/index.php/File:WhiteMatterExplorationNeurosurgicalPlanning_SoniaPujol.pdf Neurosurgical Planning Tutorial]
||[[media:WhiteMatterExplorationData.zip‎| Neurosurgical Planning dataset]] || Linux Ubuntu 64 || 4.1rc1 || March 15 || Steve - worked great - few content comments sent to Sonia
|-
|[http://www.na-mic.org/Wiki/index.php/File:WhiteMatterExplorationNeurosurgicalPlanning_SoniaPujol.pdf Neurosurgical Planning Tutorial]
||[[media:WhiteMatterExplorationData.zip‎| Neurosurgical Planning dataset]] || Linux 64 (debug) || || ||
|-
|[http://www.na-mic.org/Wiki/index.php/File:DataLoadingAndVisualizationSlicer4_SoniaPujol.pdf Data Loading and 3DVisualization ]
||[[media:‎3DVisualizationData.zip| 3D Visualization dataset]] || Mac OS SnowLeopard || 2012-03-18 || 2012-03-18 (r19639) || Sonia. OK. Note: The Save Scene doesn't save the scene with the correction orientation e.g. if the user saves the scene with 3D viewer showing the 3D models in Superior orientation, the scene gets restore in Anterior orientation.
|-
|[http://www.na-mic.org/Wiki/index.php/File:DataLoadingAndVisualizationSlicer4_SoniaPujol.pdf Data Loading and 3DVisualization]
||[[media:3DVisualizationData.zip‎|3D Visualization dataset]] || Mac OS Lion || || ||
|-
|[http://www.na-mic.org/Wiki/index.php/File:DataLoadingAndVisualizationSlicer4_SoniaPujol.pdf Data Loading and 3DVisualization]
||[[media:3DVisualizationData.zip‎| 3D Visualization dataset]] || Windows 7 64 || || || Julien<br>Page 47: Opacity could have been set from the tree view directly (last column)<br>Page 55 is a double<br>Page 56: no mention to check the Slice Intersection checkbox<br>Page 67 is a doublon<br>
|-
|[http://www.na-mic.org/Wiki/index.php/File:DataLoadingAndVisualizationSlicer4_SoniaPujol.pdf Data Loading and 3DVisualization]
||[[media:3DVisualizationData.zip‎| 3D Visualization dataset]] || Windows XP 32 || 2012-03-17 || 3/18/12 || Steve<br> Everything worked as expected (32 bit windows build)
|-
|[http://www.na-mic.org/Wiki/index.php/File:DataLoadingAndVisualizationSlicer4_SoniaPujol.pdf Data Loading and 3DVisualization]
||[[media:3DVisualizationData.zip‎| 3D Visualization dataset]] || Linux Ubuntu 64 || || ||
|-
|[http://www.na-mic.org/Wiki/index.php/File:DataLoadingAndVisualizationSlicer4_SoniaPujol.pdf Data Loading and 3DVisualization]
||[[media:3DVisualizationData.zip‎| 3D Visualization dataset]] || Linux 64 (debug) || || ||
|-

|}

* [http://www.na-mic.org/Wiki/index.php/Slicer-4.1 Back to Slicer4.1 Feb 27 page]

Tests of Iowa Workshop tutorials

2012-03-19T15:05:50Z

Finetjul:

[[Iowa 2012 Workshop Materials]]

<table>
{| class="wikitable sortable labelpage labelpagetable" border="1" align="left"
|-
|'''Tutorial Name'''||'''Tutorial Data'''||'''Platform'''||'''Slicer Version'''||'''Test Date'''||'''Test Author & Comments/Mantis Links'''
|-
|[[media:DTI_Analysis_Tutorial_Slicer4.1_SPujol.pdf | Slicer4.1 DTI Tutorial]]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Mac OS Lion || || ||
|-
|[[media:DTI_Analysis_Tutorial_Slicer4.1_SPujol.pdf | Slicer4.1 DTI Tutorial]]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Mac OS Snow Leopard || 2012/03/18 ||2012-03-18 (r19639) || Sonia. OK.
|-
|[[media:DTI_Analysis_Tutorial_Slicer4.1_SPujol.pdf | Slicer4.1 DTI Tutorial]]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Windows 7 32 || || ||
|-
|[[media:DTI_Analysis_Tutorial_Slicer4.1_SPujol.pdf | Slicer4.1 DTI Tutorial]]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Windows XP || 2012-03-17 || 3/18.12 || Steve<br>Everything works except turning on glyphs after label map seeding, which results in a crash due to lack of memory. Suggestion is to skip this step of the tutorial for users on win32. Another option is to only segment a single slice of the corpus in order to generate fewer tracts. Also it might help to delete the dwi volume after tensor estimation. When I did these steps I was able to complete all steps of the tutorial.
|-
|[[media:DTI_Analysis_Tutorial_Slicer4.1_SPujol.pdf | Slicer4.1 DTI Tutorial]]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Linux Unbuntu 64 || || ||
|-
|[[media:DTI_Analysis_Tutorial_Slicer4.1_SPujol.pdf | Slicer4.1 DTI Tutorial]]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Linux 64 (debug) || || ||
|-
|[http://www.na-mic.org/Wiki/images/e/e4/DTI_Analysis_Tutorial_SoniaPujol_SPIE2012.pdf Slicer4 DTI Tutorial]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Linux 64 (debug)|| r19517 || 03/07/2012 ||
Nicole: <s>[http://na-mic.org/Bug/view.php?id=1793 1793]</s>. <s>[http://na-mic.org/Bug/view.php?id=1795 1795]</s>
|-
|[http://www.na-mic.org/Wiki/images/e/e4/DTI_Analysis_Tutorial_SoniaPujol_SPIE2012.pdf Slicer4 DTI Tutorial]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Windows 7 64b (package)|| r19577 || 03/13/2012 ||
Julien <br>pdf is 95MB !?!?<br>Page 22, Popup look is now different<br>Page 23, in red slice only the popup should still be up (didn't unpin)<br>Page 25: Diffusion Tensor Estimation has been renamed into DWI to DTI estimation<br>Page 25: dwi is already selected as Input DWI<br>Page 25: Minor Bug ! It stays "scheduled" for >5secs, not sure why<br>Page 26: Popup looks different now<br>Page 30: shouldn't labda1~labda2 >> lambda3 look more like a smarties ?<br>Page 32: typo connect ->connects<br>Page 36: Need to click on ">>" button first<br>Page 41: Bug ! After apply, the foreground image is reset to none, need to manually set it back to dti<br>Page 46: After selecting FractionalAnisotropy, Auto WL is automatically selected<br>Page 48: You might want to include screenshot of Link button again<br>Page 51: No need to move the mouse in 3D view, it automatically refreshes. If not, then a bug must be reported<br>Page 57: 1 bullet point has no . at the end(for information, there is no . in the other slides.<br>Page 60: Advice to use the right/left arrow keys to slice through?<br>Page 65: No axial slice displayed in 3D<br>Page 74: explain how to rename?<br>Page 78: explain to go to Annotation module again ?<br>Page 79: no need to turn off and on, it automatically refreshed when I placed the fiducial. If not, then a bug must be reported.<br>Page 81: explain where to place fiducial.<br>Page 82: Bug, it doesn't recompute automatically
|-
|[http://www.na-mic.org/Wiki/images/e/e4/DTI_Analysis_Tutorial_SoniaPujol_SPIE2012.pdf Slicer4 DTI Tutorial]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Windows XP 32b || Slicer 4.1.0 rc1 (r19609) || 03/15/2012 ||
Julien <br>no link for the data mentioned in the tutorial<br>No mention to what Slicer version the tutorial is compatible with<br>Page1: Slicer Logo is 4.0, does it mean it's compatible with 4.0 ? no<br>Page 10: I have 100modules (from log messages dialog CTRL+0)<br>Page 19: typo: appears in the 2D viewer'''s'''<br>Page 22: Add "fit image to window" icon<br>Page 41: Odd black pixels in fa volume (see email)<br>Page 58: Add arrow to indicates how to change to yellow layout ?<br>Page 60: icon of the draw tool ? I first used the paint tool instead<br>Page 64: no "Minimum Length", only "Minimum Path Length". Bug ? why "Maximum Length" is not also "Maximum Path Length" ?<br>Page 64: Bug: why only Integration Step Length is (mm) but not others?<br>Page 66: Click on "Glyph" -> Crash (Slicer= 690Mo)
|-
|[http://www.na-mic.org/Wiki/index.php/File:HelloPython-ProgrammingTutorial_spujol-pieper-2012-03-15.pdf HelloPython Tutorial]
||[http://www.na-mic.org/Wiki/index.php/File:HelloPythonData.zip HelloPythonDataset] || Mac OS Lion || version from tutorial page || March 19 || Steve<br>Tested solution modules with sample data and all looked good.
|-
|[http://www.na-mic.org/Wiki/index.php/File:HelloPython-ProgrammingTutorial_spujol-pieper-2012-03-15.pdf HelloPython Tutorial]
||[http://www.na-mic.org/Wiki/index.php/File:HelloPythonData.zip HelloPythonDataset] || Windows 7 64 || version from tutorial page || March 19 || Steve<br>Tested solution modules with sample data and all looked good.
|-
|[http://www.na-mic.org/Wiki/index.php/File:HelloPython-ProgrammingTutorial_spujol-pieper-2012-03-15.pdf HelloPython Tutorial]
||[http://www.na-mic.org/Wiki/index.php/File:HelloPythonData.zip HelloPythonDataset]|| Windows XP 32 || version from tutorial page || March 19 || Steve<br>Tested solution modules with sample data and all looked good.
|-
|[http://www.na-mic.org/Wiki/index.php/File:HelloPython-ProgrammingTutorial_spujol-pieper-2012-03-15.pdf HelloPython Tutorial]
||[http://www.na-mic.org/Wiki/index.php/File:HelloPythonData.zip HelloPythonDataset] || Linux Ubuntu 64|| Slicer4.1rc1 || 03/16/2012 ||
Benjamin <br> p3 : Image has no link with this tutorial <br> p16 : The Directory HelloPython has two sub directories "code" and "data". Wrong path. <br> p21 : Add comment to warn the user about the indentation <br> p17 : Slicer layout change compare to the previous screenshot <br> p31 : We are not able to copy properly the text <br> p35 : helloPython sript path is ".../helloPython/code/" <br> p36: word "can" is written twice, and I already have 3 items in the sub menu "Exemples" <br> p48: The Directory HelloPython has two sub directories "code" and "data". Wrong path. <br> p50: Slicer layout change compare to the previous screenshot <br> p55: The last line should be on 1 line, or warn the user who may not know how work Python. <br> p59: Same as p48 and p16 <br> p61: Slicer layout change compare to the previous screenshot <br> p62: More explanation maybe - Up/Down - Left/Right - ?
|-
|[http://www.na-mic.org/Wiki/index.php/File:HelloPython-ProgrammingTutorial_spujol-pieper-2012-03-15.pdf HelloPython Tutorial]
||[http://www.na-mic.org/Wiki/index.php/File:HelloPythonData.zip HelloPythonDataset] || linux 64 (debug) || || ||
|-
|[http://www.na-mic.org/Wiki/index.php/File:WhiteMatterExplorationNeurosurgicalPlanning_SoniaPujol.pdf Neurosurgical Planning Tutorial]
||[[media:WhiteMatterExplorationData.zip‎| Neurosurgical Planning dataset]] || Mac OS SnowLeopard || 2012.03.18|| 2012.03.18 || Sonia. OK
|-
|[http://www.na-mic.org/Wiki/index.php/File:WhiteMatterExplorationNeurosurgicalPlanning_SoniaPujol.pdf Neurosurgical Planning Tutorial]
||[[media:WhiteMatterExplorationData.zip‎| Neurosurgical Planning dataset]] || Mac OS Lion || || ||
|-
|[http://www.na-mic.org/Wiki/index.php/File:WhiteMatterExplorationNeurosurgicalPlanning_SoniaPujol.pdf Neurosurgical Planning Tutorial]
||[[media:WhiteMatterExplorationData.zip‎| Neurosurgical Planning dataset]] || Windows 7 64|| 4.1.0-rc1-2012-03-17 r19637 || March 19 || Julien<br>Page 13: Background is already correctly set<br>Page 14: circle on screenshot where to change current volume to "BaselineVolume" (DTIVolume selected by default) (+ typo, it's "BaselineVolume" not "Baseline Volume")<br>Page 24: You might want to mention that Grow Cut works in 3D<br>Page 31: grow cut button circle is off<Page 39: I don't have the axial slice visible in 3D view<br>Page 40: Didn't understand why positioning the mouse in the cystic part<br>Page 46: Give description for "Output Fiber Bundle"
|-
|[http://www.na-mic.org/Wiki/index.php/File:WhiteMatterExplorationNeurosurgicalPlanning_SoniaPujol.pdf Neurosurgical Planning Tutorial]
||[[media:WhiteMatterExplorationData.zip‎| Neurosurgical Planning dataset]] || Windows XP 32|| || ||
|-
|[http://www.na-mic.org/Wiki/index.php/File:WhiteMatterExplorationNeurosurgicalPlanning_SoniaPujol.pdf Neurosurgical Planning Tutorial]
||[[media:WhiteMatterExplorationData.zip‎| Neurosurgical Planning dataset]] || Linux Ubuntu 64 || 4.1rc1 || March 15 || Steve - worked great - few content comments sent to Sonia
|-
|[http://www.na-mic.org/Wiki/index.php/File:WhiteMatterExplorationNeurosurgicalPlanning_SoniaPujol.pdf Neurosurgical Planning Tutorial]
||[[media:WhiteMatterExplorationData.zip‎| Neurosurgical Planning dataset]] || Linux 64 (debug) || || ||
|-
|[http://www.na-mic.org/Wiki/index.php/File:DataLoadingAndVisualizationSlicer4_SoniaPujol.pdf Data Loading and 3DVisualization ]
||[[media:‎3DVisualizationData.zip| 3D Visualization dataset]] || Mac OS SnowLeopard || 2012-03-18 || 2012-03-18 (r19639) || Sonia. OK. Note: The Save Scene doesn't save the scene with the correction orientation e.g. if the user saves the scene with 3D viewer showing the 3D models in Superior orientation, the scene gets restore in Anterior orientation.
|-
|[http://www.na-mic.org/Wiki/index.php/File:DataLoadingAndVisualizationSlicer4_SoniaPujol.pdf Data Loading and 3DVisualization]
||[[media:3DVisualizationData.zip‎|3D Visualization dataset]] || Mac OS Lion || || ||
|-
|[http://www.na-mic.org/Wiki/index.php/File:DataLoadingAndVisualizationSlicer4_SoniaPujol.pdf Data Loading and 3DVisualization]
||[[media:3DVisualizationData.zip‎| 3D Visualization dataset]] || Windows 7 32 || || ||
|-
|[http://www.na-mic.org/Wiki/index.php/File:DataLoadingAndVisualizationSlicer4_SoniaPujol.pdf Data Loading and 3DVisualization]
||[[media:3DVisualizationData.zip‎| 3D Visualization dataset]] || Windows XP || 2012-03-17 || 3/18/12 || Steve<br> Everything worked as expected (32 bit windows build)
|-
|[http://www.na-mic.org/Wiki/index.php/File:DataLoadingAndVisualizationSlicer4_SoniaPujol.pdf Data Loading and 3DVisualization]
||[[media:3DVisualizationData.zip‎| 3D Visualization dataset]] || Linux Ubuntu 64 || || ||
|-
|[http://www.na-mic.org/Wiki/index.php/File:DataLoadingAndVisualizationSlicer4_SoniaPujol.pdf Data Loading and 3DVisualization]
||[[media:3DVisualizationData.zip‎| 3D Visualization dataset]] || Linux 64 (debug) || || ||
|-

|}

* [http://www.na-mic.org/Wiki/index.php/Slicer-4.1 Back to Slicer4.1 Feb 27 page]

Tests of Iowa Workshop tutorials

2012-03-15T17:57:22Z

Finetjul:

<table>
{| class="wikitable sortable labelpage labelpagetable" border="1" align="left"
|-
|'''Tutorial Name'''||'''Tutorial Data'''||'''Platform'''||'''Slicer Version'''||'''Test Date'''||'''Test Author & Comments/Mantis Links'''
|-
|[http://www.na-mic.org/Wiki/images/e/e4/DTI_Analysis_Tutorial_SoniaPujol_SPIE2012.pdf Slicer4 DTI Tutorial]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Mac OS Lion || || ||
|-
|[http://www.na-mic.org/Wiki/images/e/e4/DTI_Analysis_Tutorial_SoniaPujol_SPIE2012.pdf Slicer4 DTI Tutorial]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Windows 7 32 || || ||
|-
|[http://www.na-mic.org/Wiki/images/e/e4/DTI_Analysis_Tutorial_SoniaPujol_SPIE2012.pdf Slicer4 DTI Tutorial]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Windows XP || || ||
|-
|[http://www.na-mic.org/Wiki/images/e/e4/DTI_Analysis_Tutorial_SoniaPujol_SPIE2012.pdf Slicer4 DTI Tutorial]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Linux Unbuntu 64 || || ||
|-
|[http://www.na-mic.org/Wiki/images/e/e4/DTI_Analysis_Tutorial_SoniaPujol_SPIE2012.pdf Slicer4 DTI Tutorial]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Linux 64 (debug)|| r19517 || 03/07/2012 ||
Nicole: <s>[http://na-mic.org/Bug/view.php?id=1793 1793]</s>. <s>[http://na-mic.org/Bug/view.php?id=1795 1795]</s>
|-
|[http://www.na-mic.org/Wiki/images/e/e4/DTI_Analysis_Tutorial_SoniaPujol_SPIE2012.pdf Slicer4 DTI Tutorial]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Windows 7 64b (package)|| r19577 || 03/13/2012 ||
Julien <br>pdf is 95MB !?!?<br>Page 22, Popup look is now different<br>Page 23, in red slice only the popup should still be up (didn't unpin)<br>Page 25: Diffusion Tensor Estimation has been renamed into DWI to DTI estimation<br>Page 25: dwi is already selected as Input DWI<br>Page 25: Minor Bug ! It stays "scheduled" for >5secs, not sure why<br>Page 26: Popup looks different now<br>Page 30: shouldn't labda1~labda2 >> lambda3 look more like a smarties ?<br>Page 32: typo connect ->connects<br>Page 36: Need to click on ">>" button first<br>Page 41: Bug ! After apply, the foreground image is reset to none, need to manually set it back to dti<br>Page 46: After selecting FractionalAnisotropy, Auto WL is automatically selected<br>Page 48: You might want to include screenshot of Link button again<br>Page 51: No need to move the mouse in 3D view, it automatically refreshes. If not, then a bug must be reported<br>Page 57: 1 bullet point has no . at the end(for information, there is no . in the other slides.<br>Page 60: Advice to use the right/left arrow keys to slice through?<br>Page 65: No axial slice displayed in 3D<br>Page 74: explain how to rename?<br>Page 78: explain to go to Annotation module again ?<br>Page 79: no need to turn off and on, it automatically refreshed when I placed the fiducial. If not, then a bug must be reported.<br>Page 81: explain where to place fiducial.<br>Page 82: Bug, it doesn't recompute automatically
|-
|[http://www.na-mic.org/Wiki/images/e/e4/DTI_Analysis_Tutorial_SoniaPujol_SPIE2012.pdf Slicer4 DTI Tutorial]||[http://www.na-mic.org/Wiki/index.php/File:DiffusionMRI_tutorialData.zip Diffusion Data] || Windows XP 32b || Slicer 4.1.0 rc1 (r19609) || 03/15/2012 ||
Julien <br>no link for the data mentioned in the tutorial<br>No mention to what Slicer version the tutorial is compatible with<br>Page1: Slicer Logo is 4.0, does it mean it's compatible with 4.0 ? no<br>Page 10: I have 100modules (from log messages dialog CTRL+0)<br>Page 19: typo: appears in the 2D viewer'''s'''<br>Page 22: Add "fit image to window" icon<br>Page 41: Odd black pixels in fa volume (see email)<br>Page 58: Add arrow to indicates how to change to yellow layout ?<br>Page 60: icon of the draw tool ? I first used the paint tool instead<br>Page 64: no "Minimum Length", only "Minimum Path Length". Bug ? why "Maximum Length" is not also "Maximum Path Length" ?<br>Page 64: Bug: why only Integration Step Length is (mm) but not others?<br>Page 66: Click on "Glyph" -> Crash (Slicer= 690Mo)
|-
|[http://www.na-mic.org/Wiki/index.php/File:HelloPython-ProgrammingTutorial_spujol-pieper-2012-03-15.pdf HelloPython Tutorial]
||[http://www.na-mic.org/Wiki/index.php/File:HelloPythonData.zip HelloPythonDataset] || Mac OS Lion || || ||
|-
|[http://www.na-mic.org/Wiki/index.php/File:HelloPython-ProgrammingTutorial_spujol-pieper-2012-03-15.pdf HelloPython Tutorial]
||[http://www.na-mic.org/Wiki/index.php/File:HelloPythonData.zip HelloPythonDataset] || Windows 7 32 || || ||
|-
|[http://www.na-mic.org/Wiki/index.php/File:HelloPython-ProgrammingTutorial_spujol-pieper-2012-03-15.pdf HelloPython Tutorial]
||[http://www.na-mic.org/Wiki/index.php/File:HelloPythonData.zip HelloPythonDataset]|| Windows XP || || ||
|-
|-
|[http://www.na-mic.org/Wiki/index.php/File:HelloPython-ProgrammingTutorial_spujol-pieper-2012-03-15.pdf HelloPython Tutorial]
||[http://www.na-mic.org/Wiki/index.php/File:HelloPythonData.zip HelloPythonDataset] || Linux Ubuntu 64|| || ||
|-
|[http://www.na-mic.org/Wiki/index.php/File:HelloPython-ProgrammingTutorial_spujol-pieper-2012-03-15.pdf HelloPython Tutorial]
||[http://www.na-mic.org/Wiki/index.php/File:HelloPythonData.zip HelloPythonDataset] || linux 64 (debug) || || ||
|-
|}

* [http://www.na-mic.org/Wiki/index.php/Slicer-4.1 Back to Slicer4.1 Feb 27 page]

Tests of Iowa Workshop tutorials

2012-03-13T18:01:53Z

Finetjul:

Tests of Iowa Workshop tutorials

2012-03-07T20:44:36Z

Finetjul:

Tests of Iowa Workshop tutorials

2012-03-07T20:44:24Z

Finetjul:

AHM 2012

2012-02-27T20:37:42Z

Finetjul: Add gallery for event (1 only have 1 photo :/ )

Back to [[Events]]
[[Image:PW-SLC2012.png|300px]]

<gallery>
File:AHM2012-JC.jpg|Jc talking about extensions on Tuesday morning
</gallery>

January 9-13, 2012, Salt Lake City, Utah
== Introduction ==
{| border="00" cellpadding="8" cellspacing="0"
|-
| rowspan="2" align="left" | '''This is the home page for the 2012 NA-MIC all hands meeting (AHM).''' NA-MIC participants meet for a AHM once a year. The purpose of the AHM is to coordinate, discuss plans and report to NIH officers and the external advisory board (EAB). The external advisory board meets with the NA-MIC leadership immediately after the AHM. In parallel, NA-MIC is organizing a project week. These events, with the exception of the EAB meeting, are open to collaborators and potential collaborators.

For more information about the project weeks in general, click [[Engineering:Programming_Events|'''here''']].

For information about the January 2012 project week, see below.

For information about Utah as a travel destination click [http://www.utah.com '''here'''].
| style="background: #ebeced" align="center"| [[Image:SLC.jpg|center|350px|View of the City]]
|-
| style="background: #ebeced"|The 2012 AHM, EAB and Project Week will be held <br>'''January 9-13, 2012''', in '''Salt Lake City''', Utah.
|}

== Dates, Venue, Registration ==
{|
|align="left" style="width:60%"|
'''Dates:'''
* The All Hands Meeting and External Advisory Board Meeting will be held on '''Thursday, January 12th'''.
* Project Activities will be held rest of the week between '''Monday, January 9th and Friday, January 13th'''.

'''Registration:''' Please click [http://www.sci.utah.edu/namic2012.html '''here'''] to register online before '''January 3, 2012'''. All participants must a pay registration fee ('''$200''' for AHM only, and '''$450''' for AHM+Project Week), which covers our catering and facilities costs.

'''Venue:''' The venue for the meeting is the Marriott, Salt Lake City, Utah. Please either call the hotel at +1-801-961-8700 (toll free) and mention the group code "sciscia" or book online [http://www.marriott.com/hotels/travel/slccc-salt-lake-city-marriott-city-center/ '''here''']. Please note that '''''we need attendees to use this hotel''''' in order not to incur additional charges for use of the conference rooms and keep registration fees low. The group rate is $149/night + tax and is valid for reservations made until '''December 9'''. After that it is $229/night + tax.

|style="width:40%" |[[image:Marriott-floorplan.png|thumb |250px|'''Meeting Rooms:''' See [http://www.marriott.com/hotels/event-planning/floor-plans/slccc-salt-lake-city-marriott-city-center/ here] for the web version.]]
|}

== Agenda==
{| border="1" cellpadding="5"
|- style="background:#eeeeee; font-size:125%; color:#0063B6" align="center"
| style="width:5%"| '''Time'''
| style="width:15%" | '''Monday, January 9'''
| style="width:15%" | '''Tuesday, January 10'''
| style="width:15%" | '''Wednesday, January 11'''
| style="width:35%" | '''Thursday, January 12 '''
| style="width:15%" | '''Friday, January 13'''
|-
| style="background:#eeeeee; color:black"|
| style="background:#ffffff; color:#522200"| '''[[2012_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Capitol BC)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2012_Winter_Project_Week|Project Activities]] '''<br><font color="#44AA88">''(Capitol BC)''</font>
| style="background:#dbf3ff; color:#522200"| '''[[2012_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Capitol BC)''</font>
| style="background:#F2E5D3; color:#522200"| '''AHM''' <br><font color="#44AA88">''(Capitol ABC)''</font>, '''[http://wiki.na-mic.org/Wiki/index.php/2012_EAB EAB]'''
| style="background:#dbf3ff; color:#522200"|'''[[2012_Winter_Project_Week|Project Activities]] ''' <br><font color="#44AA88">''(Capitol BC)''</font>
|-
| style="background:#eeeeee; color:black"|'''7:30-8:00'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#F2E5D3; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Breakfast <br><font color="#BB9933">''(Olympus A)''</font>
|-
| style="background:#eeeeee; color:black"|'''8:00-10:00'''
|'''9-10am''': [[AHM2012-DICOM-Huddle|DICOM General Breakout Session]] <br><font color="#9966cc">''(Amethyst)''</font>
|'''8-10am''': [[AHM2012-Slicer-Overview-and-Migration|Slicer 4: Overview and Migration]] (for Developers) <br><font color="#44AA88">''(Capitol B)''</font>
|[[AHM2012-3D-US-Slicer-Breakout|Breakout: 3D Ultrasound in Slicer]] (Noby Hata) <br><font color="#9966cc">''(Amethyst)''</font>
| '''8am''': [[AHM2012:Welcome|Welcome]] <BR>'''8:05-9am''': Keynote: iDASH: Integrating Data for Analysis, Anonymization, and Sharing, Lucila Ohno-Machado, PhD, UCSD [[media:Gabor-AHM-2012.pptx|iDASH]]<br> '''9-10am''': Algorithms Core Update [[media:NAMIC-AHM-MIT-2012.pptx|MIT]], [[media:UNC_AHM2012.pptx‎‎|UNC]], [[media:2012_01_Ross-Utah_Update.pptx|Utah I]], [[media:UtahII-AHM2012-12Min.pptx|Utah II]], [[media:Bu.namic.ahm.final.zip|BU]]
| style="background:#dbf3ff; color:#522200"|8:00-9:00 Update your wiki pages!<br>9:00 [[2012_Winter_Project_Week|Project Review]] <br><font color="#44AA88">''(Capitol BC)''</font>
|-
| style="background:#eeeeee; color:black"|'''10:00-10:30'''
| style="background:#ffffff; color:black"|
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#F2E5D3; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
|-
| style="background:#eeeeee; color:black"|'''10:30-12:00'''
| Core and Site PIs meeting with Ron <br><font color="#44AA88">''(Capitol A)''</font>
| [[2012_Winter_Project_Week_SimpleITK_and_Slicer4|Breakout: SimpleITK and Slicer 4.0]] (Hans Johnson & Bradley Lowekamp) <br><font color="#9966cc">''(Amethyst)''</font>
| [[AHM2012-3D-US-Slicer-Breakout|Breakout: 3D Ultrasound in Slicer]] (Noby Hata) <br><font color="#9966cc">''(Amethyst)''</font>
| '''10:30-11:30am''': Engineering Core Update [[media:AHM2012-Core1b-Engineering-Introduction.pptx|Introduction]], [[media:AHM2012-Core1b-Engineering-EndUserPlatform.ppt|End user platform]], [[Media:AHM2012-Core1b-Engineering-ComputationalPlatform.ppt|Computational platform]], [[media:AHM2012-Core1b-Engineering-DataManagementPlatform.ppt|Data management platform]], [[media:AHM2012-Core1b-Engineering-SoftwareEngineeringAndSoftwareQuality.ppt|Software engineering and software quality]]<br> '''11:30-12pm''': [[media:AHM2012_TrainingCore_SoniaPujol.pdf|Outreach Update]], Sonia Pujol
|
|-
| style="background:#eeeeee; color:black"|'''12:00-1:00'''
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font> <br>
| style="background:#dbf3ff; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font><br>
| style="background:#F2E5D3; color:black"| Lunch <br><font color="#BB9933">''(Olympus A)''</font>
| style="background:#dbf3ff; color:black"| Boxed Lunch and Adjourn <br><font color="#BB9933">''(Olympus A)''</font>
|-
| style="background:#eeeeee; color:black"|'''1:00-3:00'''
| style="background:#dbf3ff; color:#522200"|[[2012_Winter_Project_Week|Project Presentations]]<br><font color="#44AA88">''(Capitol BC)''</font>
| [[2012_Winter_Project_Week_Slicer4_Module_Design_Breakout|Breakout: Slicer 4 Module Design with Individual Teams]] <br><font color="#44AA88">''(Capitol A)''</font>
|'''DBP Team Meetings''' <br><font color="#44AA88">''(Capitol A)''</font> <br> '''1-2pm''': [[2012_Winter_Project_Week_DBP_MGH_Team_Meeting|DBP MGH Head and Neck Cancer]] <br>'''2-3pm''': [[2012_Winter_Project_Week_DBP_Utah_Team_Meeting|DBP Utah Atrial Fibrillation]]
| '''1-1:30pm''': International Research Organizations contribute to NA-MIC <br>'''1-1:30pm''': Best Practices from a Past DBP, Gabor Fichtinger, PhD, Queens University ([[media:Gabor-AHM-2012.pdf|slides]])<br> '''Current DBP Updates''' <br> '''1:30pm''': Huntington's Disease, Hans Johnson, U Iowa ([[media:AHM2012-Core1b-Engineering-DataManagement.ppt|slides]])<br> '''1:50pm''': Atrial Fibrillation, Rob MacLeod, CARMA, U of Utah ([[media:DBP-AF-report.pdf|slides]])<br>''' 2:10pm''': Traumatic Brain Injury, Jack Van Horn, UCLA<br> '''2:30pm''': Head and Neck Cancer, Greg Sharp, MGH ([[media:2012-01-12-sharp-2.pdf|slides]])
|
|-
| style="background:#eeeeee; color:black"|'''3:00-3:30'''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#dbf3ff; color:black"| Coffee <br>''(General area)''
| style="background:#F2E5D3; color:black"| Coffee <br>''(General area)''
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''3:00-5:00'''
|[[AHM2012-Slicer-with-Ron|Breakout: Slicer 4 with Ron (for Users)]] <br><font color="#44AA88">''(Capitol A)''</font>
| [[2012_Winter_Project_Week_DICOM_RT_Breakout|Breakout: DICOM RT]] <br><font color="#9966cc">''(Amethyst)''</font>
|'''DBP Team Meetings''' <br><font color="#44AA88">''(Capitol A)''</font> <br> '''3-4pm''': [[2012_Winter_Project_Week_DBP_UCLA_Team_Meeting|DBP UCLA Traumatic Brain Injury]] <br>'''4-5pm''': [[2012_Winter_Project_Week_DBP_Iowa_Team_Meeting|DBP Iowa Huntington's Disease]]
|'''3-4pm''': [[2012_EAB|EAB meeting]] <br><font color="#9966cc">''(Amethyst)''</font><br> '''4-5pm:''' EAB closed session <br><font color="#9966cc">''(Amethyst)''</font>
| style="background:#ffffff; color:black"|
|-
| style="background:#eeeeee; color:black"|'''05:00-07:00'''
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#dbf3ff; color:black"|
| style="background:#F2E5D3; color:black"|'''6:00''' Optional: [http://www.murphysbarandgrillut.com/ Beer at Murphy's] (like last year)
| style="background:#ffffff; color:black"|
|}

'''General Announcements:'''

**Will be added here

==Registered Attendees==

<big>'''NOTE:'''</big> <font color="maroon">The registered attendee list will be posted here by the organizers. '''DO NOT''' add your name to this list yourself.</font> To register, please click [http://www.sci.utah.edu/namic2012-registration.html here].

# Ackerman Michael , National Library of Medicine, NIH, OHPPC
# Aucoin Nicole , BWH
# Aylward Stephen , Kitware
# Baumgartner Christian , Psychiatry Neuroimaging Lab - BWH Boston
# Berger Jean-Baptiste ,
# Blezek Daniel Mayo Clinic
# Blumenfeld Morry , Brigham and Womens Hospital
# Blumfield Anthony , Radnostics
# Cates Josh , University of Utah
# Chambers Micah , UCLA
# Chapman Brian , University of California, San Diego
# Chauvin Laurent , BWH
# Chen Xiaojun , Surgical Plan Lab,Brigham Womens Hospital
# Chen Elvis , Robarts Research Institute
# Datar Manasi , SCI Institute
# Diedrich Karl , AZE Research and Development
# Egger Jan , SPL, BWH, HMS
# Fedorov Andriy , BWH
# Fichtinger Gabor , Queens University
# Fillion-Robin Jean-Christophe , Kitware
# Finet Julien , Kitware
# Fishbaugh James , SCI Institute
# Gao Yi , Brigham And Womens Hospital
# Gardner Greg , SCI Institute
# George Ashvin , SCI Institute
# Gerig Guido , SCI Institute
# Ghosh Satrajit , Isomics, Inc.
# Golland Polina , MIT
# Gouaillard Alexandre , CoSMo Software
# Grethe Jeffrey , UCSD
# Hata Nobuhiko , BWH
# Iftekharuddin Khan , Old Dominion University
# Irimia Andrei , University of California, Los Angeles
# Johnson Chris , EAB, Chair
# Johnson Hans , University of Iowa
# Kalpathy-Cramer Jayashree , MGH
# Kikinis Ron , Brigham and Womens Hospital
# Kim Eun Young Regina , University of Iowa
# Kochis Donna Kitware
# Kolesov Ivan , Georgia Institute of Technology
# Lasso Andras , Queens University
# Liang Jianming , Arizona State University
# Long Benjamin , Kitware
# Lorensen Bill , Brigham and Womens Hospital
# Lou Yifei , Georgia Tech
# Lowekamp Bradley ,
# MacLeod Rob , SCI Institute
# Marcus Daniel , Washington University
# Matsui Joy , University of Iowa
# Milchenko Mikhail , Washington University in St. Louis
# Miller James , GE Research
# Montillo Albert , GE
# Moradi Mehdi , BWH Harvard Medical School
# Morris Alan , SCI Institute
# Napel Sandy , Brigham and Womens Hospital
# Norton Isaiah , Brigham Womens Hospital
# Oguz Ipek , UNC
# Ohno-Machado Lucila , Plenary Speaker
# Pace Danielle , Kitware
# Pai Vinai , NIBIB NIH
# Paniagua Beatriz , University of North Carolina at Chapel Hill
# Patel Pratik , Brainlab
# Perry Daniel , SCI Institute
# Pieper Steve , Isomics, Inc.
# Pierpaoli Carlo , EAB
# Pinter Csaba , Queens University
# Pohl Kilian , UPEN
# Prior Fred , Brigham and Womens Hospital
# Pujol Sonia , BWH
# Roger Gwendoline , UNC
# Ryan William , Mayo Clinic
# San Jose Raul , BWH
# Savadjiev Peter , Brigham and Womens Hospital
# Schroeder William , Kitware
# Scully Mark , University of Iowa
# Shackleford James , MGH
# Sharma Anuja , SCI Institute
# Sharp Gregory , MGH
# Shusharina Nadya ,
# Sridharan Ramesh , MIT CSAIL
# Styner Martin , University of North Carolina
# Tannenbaum Allen , Boston University
# Toews Matthew , BWH HMS
# Tokuda Junichi , BWH
# Tustison Nick , University of Virginia
# Ungi Tamas , Queens University
# Vachet Clement , UNC Chapel Hill
# Van Horn John , UCLA
# Veeraraghavan Harini , General Electric Research
# Veni Gopalkrishna , SCI Institute
# Wachinger Christian , MIT CSAIL
# Wang Kevin , University Health Network
# Wang Bo , SCI Institute
# Wasem Andrew , CoSMo Software
# Wasserman Demian , Brigham and Womens Hospital
# Wedlake Chris , Robarts Research Institute
# Welch Dave , University of Iowa
# Whitaker Ross , SCI Institute
# Yarmarkovich Alexander , Isomics
# Yeniaras Erol , MD Anderson Cancer Center
# Yoo Terry , National Libraray of Medicine at NIH, OHPCC
# Zhu Liangjia , Georgia Institute of Technology
# zhu yingxuan , GE Global Research
# Zygmunt Kris , SCI Institute

as of January 12, 2012 1:00 PM MST

File:AHM2012-JC.jpg

2012-02-27T20:36:10Z

Finetjul:

Slicer-4.1

2012-02-25T00:35:13Z

Finetjul: /* Features and Responsibilities */

Target date for the code freeze is Monday. Feb. 27, 2012

=Features and Responsibilities=
*Dicom widget: Steve
**cget
**pop up reorganization
**Lollipop
*Charts: Jim
**Label statistics
*compareviews and linking: Jim
**bugs [http://www.na-mic.org/Bug/view.php?id=1526 1526], [http://www.na-mic.org/Bug/view.php?id=1598 1598], [http://www.na-mic.org/Bug/view.php?id=1495 1495], [http://www.na-mic.org/Bug/view.php?id=1583 1583], [http://www.na-mic.org/Bug/view.php?id=1607 1607], [http://www.na-mic.org/Bug/view.php?id=1632 1632], [http://www.na-mic.org/Bug/view.php?id=1631 1631], [http://www.na-mic.org/Bug/view.php?id=1686 1686] (or a subset)
*VTK GPU raycaster: J2
**[http://www.na-mic.org/Bug/view.php?id=1612 linear ramp](resolved)
**[http://na-mic.org/Mantis/view.php?id=1663 crash in transfer function editor](resolved)
* View controller cosmetics: J2
**[http://www.na-mic.org/Bug/view.php?id=1750 redesign](resolved)
**[http://www.na-mic.org/Bug/view.php?id=1751 mouse gesture for foreground/labelmap opacity] ([http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/SlicerApplication/MouseandKeyboardShortcuts#Slice_Viewer resolved])
*Brainsfit cosmetics: Hans
**[http://na-mic.org/Mantis/view.php?id=1584 feature request]
*Extensions: JC
** Refine the mechanism to build/test/upload extensions.
** Provide support to extension developers so that the following extensions are built:
*** ABC, SkullStripper, EMSegmenter, VMTK, Plastimatch, DVH/SlicerRt
*Documentation: JC
** Mechanism to easily "version" the documentation. (Easy creation of set of pages associated to release 4.1 from the pages prefixed with 4.0)
** NiceToHave:
*** Offline documentation: Mobile skin for webkit rendering of the slicer wiki documentation pages
* PythonQt: JC
** Update CTK and Slicer to consider the contributed change to PythonQt
* Annotation module bugs: [http://www.na-mic.org/Bug/view.php?id=1712 drag and drop scrolling](resolved), [http://www.na-mic.org/Bug/view.php?id=1713 deleting hierarchies](resolved), [http://www.na-mic.org/Bug/view.php?id=1715 import](resolved), ruler (crash on scene load fixed by Jim's changes), [http://www.na-mic.org/Bug/view.php?id=1717 storage nodes] - Nicole

=Bug fixes targeted for this release=
Sonia's reports on the DTI modules of the current Slicer4 release:

* Mantis Bug Reports:
** [http://www.na-mic.org/Bug/view.php?id=1722 Brain Mask] (assigned to Demian)
** [http://www.na-mic.org/Bug/view.php?id=1679 Color by Orientation] (assigned to Demian)
** [http://www.na-mic.org/Bug/view.php?id=1678 Glyphs Visualization] (assigned to Alex. fixed)
**[http://www.na-mic.org/Bug/view.php?id=1685 Fiducials Seeding ] (assigned to Alex. fixed )
** [http://www.na-mic.org/Bug/view.php?id=1684 Consistency of the GUI in the labelmap and fiducial seeding modules] (assigned to Alex, fixed)
** [http://www.na-mic.org/Bug/view.php?id=1724 Scalar Measurement computation issue (Planar measure)] : wrong window and level values in the Volumes module ( assigned to Julien Finet) iss due to extreme values in the data - can this be clamped in the scalar estimation module?
** [http://www.na-mic.org/Bug/view.php?id=1725 Scalar measurement update issue]
** DTI pipeline Windows 32 crash (Marianna's test: Mantis bug report xxx]
** [http://www.na-mic.org/Bug/view.php?id=1732 Scene Restore Issue in Slicer4] (assigned to: )
* Suggested Reorganization of the Diffusion menu (assigned to Demian)
**Diffusion Data Conversion:
***DICOM to Nrrd
***DTIimport/export
** DWI:
***Brain Mask
***Tensor Estimation
*** Denoising
** DTI
*** Scalar Measurements
*** Tractography
*** Resample

* 'DicomToNrrdConverter' should be 'DICOM To NRRD Converter', and make the parameters of the Output sections visible on the GUI (assigned to Demian)

* Use new Slicer4 QTtesting functionalities for cross-platform testing of Iowa Workshop tutorials
= Mantis issue tracking for Slicer 4.1 target =
Follow this [http://www.na-mic.org/Bug/search.php?project_id=3&sticky_issues=on&target_version=Slicer+4.1.0&sortby=last_updated&dir=DESC&hide_status_id=80 link].

= Deferred to after 4.1 freeze =
* Fix for texture resolution: Alex
** From Ron: for IGT need minimum 12Hz frame rate, maximum 200ms latency, preferred 30 hz frame rate and less than 100ms latency
* Update screenshot to reflect all possible layouts [http://www.na-mic.org/Bug/view.php?id=1662 bug 1662] - Nicole

* Is it realistic to try for SimpleITK in this release? (After discussion: no, needs more testing - aim for summer project week)
** Yes, if somebody can help with ITK 4 on windows.
** linux packaging issue:
*** (2) itkXXX.so files are missing in the Slicer package.
** linux discovering CLI:
*** (1) missing symbol on exit of CLI; in addition with a Qt bug, it fails to parse the CLI XML description
** possibly other issues on window (needs testing)
*** (3) Building SWIG for SimpleITK is the problem.
** need to try all the packaging platforms
*** packaging has never been tried on mac (J2 didn't try to compile on Mac neither)
*** packaging has never been tried on windows (because it doesn't compile)

{| style="margin: 1em auto 1em auto; border: 1px solid darkgray;"
|-
!
! scope="col" colspan="3" style="border-bottom: 1px solid grey;"| Build
! scope="col" colspan="3" style="border-bottom: 1px solid grey;"| Run
! scope="col" colspan="3" style="border-bottom: 1px solid grey;"| Package
|-
!Type
!Windows
!Linux
!Mac
!Windows
!Linux
!Mac
!Windows
!Linux
!Mac
|-
| ITKv4 in Slicer
|bgcolor="Orange" align="center"|?
|bgcolor="LightGreen" align="center"|ok
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (1)
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (2)
|bgcolor="Orange" align="center"|?
|-
| SimpleITK in Slicer
|bgcolor="#f34a33" align="center"| no (3)
|bgcolor="LightGreen" align="center"|ok
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (1)
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (2)
|bgcolor="Orange" align="center"|?
|}
[[Events|Back to events page]]

Slicer-4.1

2012-02-24T15:37:31Z

Finetjul: /* Features and Responsibilities */

Target date for the code freeze is Monday. Feb. 27, 2012

=Features and Responsibilities=
*Dicom widget: Steve
**cget
**pop up reorganization
**Lollipop
*Charts: Jim
**Label statistics
*compareviews and linking: Jim
**bugs [http://www.na-mic.org/Bug/view.php?id=1526 1526], [http://www.na-mic.org/Bug/view.php?id=1598 1598], [http://www.na-mic.org/Bug/view.php?id=1495 1495], [http://www.na-mic.org/Bug/view.php?id=1583 1583], [http://www.na-mic.org/Bug/view.php?id=1607 1607], [http://www.na-mic.org/Bug/view.php?id=1632 1632], [http://www.na-mic.org/Bug/view.php?id=1631 1631], [http://www.na-mic.org/Bug/view.php?id=1686 1686] (or a subset)
*VTK GPU raycaster: J2
**[http://www.na-mic.org/Bug/view.php?id=1612 linear ramp](resolved)
**[http://na-mic.org/Mantis/view.php?id=1663 crash in transfer function editor](resolved)
* View controller cosmetics: J2
**[http://www.na-mic.org/Bug/view.php?id=1750 redesign](resolved)
** Please consider notes here (not captured on the project wiki page, but we agreed on this redesign I think): [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.0/SlicerApplication/MouseandKeyboardShortcuts#Proposed_functionality]
*Brainsfit cosmetics: Hans
**[http://na-mic.org/Mantis/view.php?id=1584 feature request]
*Extensions: JC
** Refine the mechanism to build/test/upload extensions.
** Provide support to extension developers so that the following extensions are built:
*** ABC, SkullStripper, EMSegmenter, VMTK, Plastimatch, DVH/SlicerRt
*Documentation: JC
** Mechanism to easily "version" the documentation. (Easy creation of set of pages associated to release 4.1 from the pages prefixed with 4.0)
** NiceToHave:
*** Offline documentation: Mobile skin for webkit rendering of the slicer wiki documentation pages
* PythonQt: JC
** Update CTK and Slicer to consider the contributed change to PythonQt
* Annotation module bugs: [http://www.na-mic.org/Bug/view.php?id=1712 drag and drop scrolling](resolved), [http://www.na-mic.org/Bug/view.php?id=1713 deleting hierarchies](resolved), [http://www.na-mic.org/Bug/view.php?id=1715 import](resolved), ruler (crash on scene load fixed by Jim's changes), [http://www.na-mic.org/Bug/view.php?id=1717 storage nodes] - Nicole

=Bug fixes targeted for this release=
Sonia's reports on the DTI modules of the current Slicer4 release:

* Mantis Bug Reports:
** [http://www.na-mic.org/Bug/view.php?id=1722 Brain Mask] (assigned to Demian)
** [http://www.na-mic.org/Bug/view.php?id=1679 Color by Orientation] (assigned to Demian)
** [http://www.na-mic.org/Bug/view.php?id=1678 Glyphs Visualization] (assigned to Alex. fixed)
**[http://www.na-mic.org/Bug/view.php?id=1685 Fiducials Seeding ] (assigned to Alex. fixed )
** [http://www.na-mic.org/Bug/view.php?id=1684 Consistency of the GUI in the labelmap and fiducial seeding modules] (assigned to Alex, fixed)
** [http://www.na-mic.org/Bug/view.php?id=1724 Scalar Measurement computation issue (Planar measure)] : wrong window and level values in the Volumes module ( assigned to Julien Finet) iss due to extreme values in the data - can this be clamped in the scalar estimation module?
** [http://www.na-mic.org/Bug/view.php?id=1725 Scalar measurement update issue]
** DTI pipeline Windows 32 crash (Marianna's test: Mantis bug report xxx]
** [http://www.na-mic.org/Bug/view.php?id=1732 Scene Restore Issue in Slicer4] (assigned to: )
* Suggested Reorganization of the Diffusion menu (assigned to Demian)
**Diffusion Data Conversion:
***DICOM to Nrrd
***DTIimport/export
** DWI:
***Brain Mask
***Tensor Estimation
*** Denoising
** DTI
*** Scalar Measurements
*** Tractography
*** Resample

* 'DicomToNrrdConverter' should be 'DICOM To NRRD Converter', and make the parameters of the Output sections visible on the GUI (assigned to Demian)

* Use new Slicer4 QTtesting functionalities for cross-platform testing of Iowa Workshop tutorials
= Mantis issue tracking for Slicer 4.1 target =
Follow this [http://www.na-mic.org/Bug/search.php?project_id=3&sticky_issues=on&target_version=Slicer+4.1.0&sortby=last_updated&dir=DESC&hide_status_id=80 link].

= Deferred to after 4.1 freeze =
* Fix for texture resolution: Alex
** From Ron: for IGT need minimum 12Hz frame rate, maximum 200ms latency, preferred 30 hz frame rate and less than 100ms latency
* Update screenshot to reflect all possible layouts [http://www.na-mic.org/Bug/view.php?id=1662 bug 1662] - Nicole

* Is it realistic to try for SimpleITK in this release? (After discussion: no, needs more testing - aim for summer project week)
** Yes, if somebody can help with ITK 4 on windows.
** linux packaging issue:
*** (2) itkXXX.so files are missing in the Slicer package.
** linux discovering CLI:
*** (1) missing symbol on exit of CLI; in addition with a Qt bug, it fails to parse the CLI XML description
** possibly other issues on window (needs testing)
*** (3) Building SWIG for SimpleITK is the problem.
** need to try all the packaging platforms
*** packaging has never been tried on mac (J2 didn't try to compile on Mac neither)
*** packaging has never been tried on windows (because it doesn't compile)

{| style="margin: 1em auto 1em auto; border: 1px solid darkgray;"
|-
!
! scope="col" colspan="3" style="border-bottom: 1px solid grey;"| Build
! scope="col" colspan="3" style="border-bottom: 1px solid grey;"| Run
! scope="col" colspan="3" style="border-bottom: 1px solid grey;"| Package
|-
!Type
!Windows
!Linux
!Mac
!Windows
!Linux
!Mac
!Windows
!Linux
!Mac
|-
| ITKv4 in Slicer
|bgcolor="Orange" align="center"|?
|bgcolor="LightGreen" align="center"|ok
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (1)
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (2)
|bgcolor="Orange" align="center"|?
|-
| SimpleITK in Slicer
|bgcolor="#f34a33" align="center"| no (3)
|bgcolor="LightGreen" align="center"|ok
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (1)
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (2)
|bgcolor="Orange" align="center"|?
|}
[[Events|Back to events page]]

Slicer-4.1

2012-02-23T23:57:16Z

Finetjul: /* Features and Responsibilities */

Target date for the code freeze is Monday. Feb. 27, 2012

=Features and Responsibilities=
*Dicom widget: Steve
**cget
**pop up reorganization
**Lollipop
*Charts: Jim
**Label statistics
*compareviews and linking: Jim
**bugs [http://www.na-mic.org/Bug/view.php?id=1526 1526], [http://www.na-mic.org/Bug/view.php?id=1598 1598], [http://www.na-mic.org/Bug/view.php?id=1495 1495], [http://www.na-mic.org/Bug/view.php?id=1583 1583], [http://www.na-mic.org/Bug/view.php?id=1607 1607], [http://www.na-mic.org/Bug/view.php?id=1632 1632], [http://www.na-mic.org/Bug/view.php?id=1631 1631], [http://www.na-mic.org/Bug/view.php?id=1686 1686] (or a subset)
*VTK GPU raycaster: J2
**[http://www.na-mic.org/Bug/view.php?id=1612 linear ramp](resolved)
**[http://na-mic.org/Mantis/view.php?id=1663 crash in transfer function editor](resolved)
* View controller cosmetics: J2
**[[2012_Project_Week:ViewerControls|Redesign drafts]]
** Please consider notes here (not captured on the project wiki page, but we agreed on this redesign I think): [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.0/SlicerApplication/MouseandKeyboardShortcuts#Proposed_functionality]
*Brainsfit cosmetics: Hans
**[http://na-mic.org/Mantis/view.php?id=1584 feature request]
*Extensions: JC
** Refine the mechanism to build/test/upload extensions.
** Provide support to extension developers so that the following extensions are built:
*** ABC, SkullStripper, EMSegmenter, VMTK, Plastimatch, DVH/SlicerRt
*Documentation: JC
** Mechanism to easily "version" the documentation. (Easy creation of set of pages associated to release 4.1 from the pages prefixed with 4.0)
** NiceToHave:
*** Offline documentation: Mobile skin for webkit rendering of the slicer wiki documentation pages
* PythonQt: JC
** Update CTK and Slicer to consider the contributed change to PythonQt
* Annotation module bugs: [http://www.na-mic.org/Bug/view.php?id=1712 drag and drop scrolling](resolved), [http://www.na-mic.org/Bug/view.php?id=1713 deleting hierarchies](resolved), [http://www.na-mic.org/Bug/view.php?id=1715 import](resolved), ruler (crash on scene load fixed by Jim's changes), [http://www.na-mic.org/Bug/view.php?id=1717 storage nodes] - Nicole

=Bug fixes targeted for this release=
Sonia's reports on the DTI modules of the current Slicer4 release:

* Mantis Bug Reports:
** [http://www.na-mic.org/Bug/view.php?id=1722 Brain Mask] (assigned to Demian)
** [http://www.na-mic.org/Bug/view.php?id=1679 Color by Orientation] (assigned to Demian)
** [http://www.na-mic.org/Bug/view.php?id=1678 Glyphs Visualization] (assigned to Alex. fixed)
**[http://www.na-mic.org/Bug/view.php?id=1685 Fiducials Seeding ] (assigned to Alex. fixed )
** [http://www.na-mic.org/Bug/view.php?id=1684 Consistency of the GUI in the labelmap and fiducial seeding modules] (assigned to Alex, fixed)
** [http://www.na-mic.org/Bug/view.php?id=1724 Scalar Measurement computation issue (Planar measure)] : wrong window and level values in the Volumes module ( assigned to Julien Finet) iss due to extreme values in the data - can this be clamped in the scalar estimation module?
** [http://www.na-mic.org/Bug/view.php?id=1725 Scalar measurement update issue]
** DTI pipeline Windows 32 crash (Marianna's test: Mantis bug report xxx]
** [http://www.na-mic.org/Bug/view.php?id=1732 Scene Restore Issue in Slicer4] (assigned to: )
* Suggested Reorganization of the Diffusion menu (assigned to Demian)
**Diffusion Data Conversion:
***DICOM to Nrrd
***DTIimport/export
** DWI:
***Brain Mask
***Tensor Estimation
*** Denoising
** DTI
*** Scalar Measurements
*** Tractography
*** Resample

* 'DicomToNrrdConverter' should be 'DICOM To NRRD Converter', and make the parameters of the Output sections visible on the GUI (assigned to Demian)

* Use new Slicer4 QTtesting functionalities for cross-platform testing of Iowa Workshop tutorials
= Mantis issue tracking for Slicer 4.1 target =
Follow this [http://www.na-mic.org/Bug/search.php?project_id=3&sticky_issues=on&target_version=Slicer+4.1.0&sortby=last_updated&dir=DESC&hide_status_id=80 link].

= Deferred to after 4.1 freeze =
* Fix for texture resolution: Alex
** From Ron: for IGT need minimum 12Hz frame rate, maximum 200ms latency, preferred 30 hz frame rate and less than 100ms latency
* Update screenshot to reflect all possible layouts [http://www.na-mic.org/Bug/view.php?id=1662 bug 1662] - Nicole

* Is it realistic to try for SimpleITK in this release? (After discussion: no, needs more testing - aim for summer project week)
** Yes, if somebody can help with ITK 4 on windows.
** linux packaging issue:
*** (2) itkXXX.so files are missing in the Slicer package.
** linux discovering CLI:
*** (1) missing symbol on exit of CLI; in addition with a Qt bug, it fails to parse the CLI XML description
** possibly other issues on window (needs testing)
*** (3) Building SWIG for SimpleITK is the problem.
** need to try all the packaging platforms
*** packaging has never been tried on mac (J2 didn't try to compile on Mac neither)
*** packaging has never been tried on windows (because it doesn't compile)

{| style="margin: 1em auto 1em auto; border: 1px solid darkgray;"
|-
!
! scope="col" colspan="3" style="border-bottom: 1px solid grey;"| Build
! scope="col" colspan="3" style="border-bottom: 1px solid grey;"| Run
! scope="col" colspan="3" style="border-bottom: 1px solid grey;"| Package
|-
!Type
!Windows
!Linux
!Mac
!Windows
!Linux
!Mac
!Windows
!Linux
!Mac
|-
| ITKv4 in Slicer
|bgcolor="Orange" align="center"|?
|bgcolor="LightGreen" align="center"|ok
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (1)
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (2)
|bgcolor="Orange" align="center"|?
|-
| SimpleITK in Slicer
|bgcolor="#f34a33" align="center"| no (3)
|bgcolor="LightGreen" align="center"|ok
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (1)
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (2)
|bgcolor="Orange" align="center"|?
|}
[[Events|Back to events page]]

Slicer-4.1

2012-02-23T23:56:57Z

Finetjul:

Target date for the code freeze is Monday. Feb. 27, 2012

=Features and Responsibilities=
*Dicom widget: Steve
**cget
**pop up reorganization
**Lollipop
*Charts: Jim
**Label statistics
*compareviews and linking: Jim
**bugs [http://www.na-mic.org/Bug/view.php?id=1526 1526], [http://www.na-mic.org/Bug/view.php?id=1598 1598], [http://www.na-mic.org/Bug/view.php?id=1495 1495], [http://www.na-mic.org/Bug/view.php?id=1583 1583], [http://www.na-mic.org/Bug/view.php?id=1607 1607], [http://www.na-mic.org/Bug/view.php?id=1632 1632], [http://www.na-mic.org/Bug/view.php?id=1631 1631], [http://www.na-mic.org/Bug/view.php?id=1686 1686] (or a subset)
*VTK GPU raycaster: J2
**[http://www.na-mic.org/Bug/view.php?id=1612 linear ramp](resolved), [http://na-mic.org/Mantis/view.php?id=1663 crash in transfer function editor](resolved)
* View controller cosmetics: J2
**[[2012_Project_Week:ViewerControls|Redesign drafts]]
** Please consider notes here (not captured on the project wiki page, but we agreed on this redesign I think): [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.0/SlicerApplication/MouseandKeyboardShortcuts#Proposed_functionality]
*Brainsfit cosmetics: Hans
**[http://na-mic.org/Mantis/view.php?id=1584 feature request]
*Extensions: JC
** Refine the mechanism to build/test/upload extensions.
** Provide support to extension developers so that the following extensions are built:
*** ABC, SkullStripper, EMSegmenter, VMTK, Plastimatch, DVH/SlicerRt
*Documentation: JC
** Mechanism to easily "version" the documentation. (Easy creation of set of pages associated to release 4.1 from the pages prefixed with 4.0)
** NiceToHave:
*** Offline documentation: Mobile skin for webkit rendering of the slicer wiki documentation pages
* PythonQt: JC
** Update CTK and Slicer to consider the contributed change to PythonQt
* Annotation module bugs: [http://www.na-mic.org/Bug/view.php?id=1712 drag and drop scrolling](resolved), [http://www.na-mic.org/Bug/view.php?id=1713 deleting hierarchies](resolved), [http://www.na-mic.org/Bug/view.php?id=1715 import](resolved), ruler (crash on scene load fixed by Jim's changes), [http://www.na-mic.org/Bug/view.php?id=1717 storage nodes] - Nicole

=Bug fixes targeted for this release=
Sonia's reports on the DTI modules of the current Slicer4 release:

* Mantis Bug Reports:
** [http://www.na-mic.org/Bug/view.php?id=1722 Brain Mask] (assigned to Demian)
** [http://www.na-mic.org/Bug/view.php?id=1679 Color by Orientation] (assigned to Demian)
** [http://www.na-mic.org/Bug/view.php?id=1678 Glyphs Visualization] (assigned to Alex. fixed)
**[http://www.na-mic.org/Bug/view.php?id=1685 Fiducials Seeding ] (assigned to Alex. fixed )
** [http://www.na-mic.org/Bug/view.php?id=1684 Consistency of the GUI in the labelmap and fiducial seeding modules] (assigned to Alex, fixed)
** [http://www.na-mic.org/Bug/view.php?id=1724 Scalar Measurement computation issue (Planar measure)] : wrong window and level values in the Volumes module ( assigned to Julien Finet) iss due to extreme values in the data - can this be clamped in the scalar estimation module?
** [http://www.na-mic.org/Bug/view.php?id=1725 Scalar measurement update issue]
** DTI pipeline Windows 32 crash (Marianna's test: Mantis bug report xxx]
** [http://www.na-mic.org/Bug/view.php?id=1732 Scene Restore Issue in Slicer4] (assigned to: )
* Suggested Reorganization of the Diffusion menu (assigned to Demian)
**Diffusion Data Conversion:
***DICOM to Nrrd
***DTIimport/export
** DWI:
***Brain Mask
***Tensor Estimation
*** Denoising
** DTI
*** Scalar Measurements
*** Tractography
*** Resample

* 'DicomToNrrdConverter' should be 'DICOM To NRRD Converter', and make the parameters of the Output sections visible on the GUI (assigned to Demian)

* Use new Slicer4 QTtesting functionalities for cross-platform testing of Iowa Workshop tutorials
= Mantis issue tracking for Slicer 4.1 target =
Follow this [http://www.na-mic.org/Bug/search.php?project_id=3&sticky_issues=on&target_version=Slicer+4.1.0&sortby=last_updated&dir=DESC&hide_status_id=80 link].

= Deferred to after 4.1 freeze =
* Fix for texture resolution: Alex
** From Ron: for IGT need minimum 12Hz frame rate, maximum 200ms latency, preferred 30 hz frame rate and less than 100ms latency
* Update screenshot to reflect all possible layouts [http://www.na-mic.org/Bug/view.php?id=1662 bug 1662] - Nicole

* Is it realistic to try for SimpleITK in this release? (After discussion: no, needs more testing - aim for summer project week)
** Yes, if somebody can help with ITK 4 on windows.
** linux packaging issue:
*** (2) itkXXX.so files are missing in the Slicer package.
** linux discovering CLI:
*** (1) missing symbol on exit of CLI; in addition with a Qt bug, it fails to parse the CLI XML description
** possibly other issues on window (needs testing)
*** (3) Building SWIG for SimpleITK is the problem.
** need to try all the packaging platforms
*** packaging has never been tried on mac (J2 didn't try to compile on Mac neither)
*** packaging has never been tried on windows (because it doesn't compile)

{| style="margin: 1em auto 1em auto; border: 1px solid darkgray;"
|-
!
! scope="col" colspan="3" style="border-bottom: 1px solid grey;"| Build
! scope="col" colspan="3" style="border-bottom: 1px solid grey;"| Run
! scope="col" colspan="3" style="border-bottom: 1px solid grey;"| Package
|-
!Type
!Windows
!Linux
!Mac
!Windows
!Linux
!Mac
!Windows
!Linux
!Mac
|-
| ITKv4 in Slicer
|bgcolor="Orange" align="center"|?
|bgcolor="LightGreen" align="center"|ok
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (1)
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (2)
|bgcolor="Orange" align="center"|?
|-
| SimpleITK in Slicer
|bgcolor="#f34a33" align="center"| no (3)
|bgcolor="LightGreen" align="center"|ok
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (1)
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (2)
|bgcolor="Orange" align="center"|?
|}
[[Events|Back to events page]]

Slicer-4.1

2012-02-23T23:55:33Z

Finetjul: /* Features and Responsibilities */

Target date for the code freeze is Monday. Feb. 27, 2012

=Features and Responsibilities=
*Dicom widget: Steve
**cget
**pop up reorganization
**Lollipop
*Charts: Jim
**Label statistics
*compareviews and linking: Jim
**bugs [http://www.na-mic.org/Bug/view.php?id=1526 1526], [http://www.na-mic.org/Bug/view.php?id=1598 1598], [http://www.na-mic.org/Bug/view.php?id=1495 1495], [http://www.na-mic.org/Bug/view.php?id=1583 1583], [http://www.na-mic.org/Bug/view.php?id=1607 1607], [http://www.na-mic.org/Bug/view.php?id=1632 1632], [http://www.na-mic.org/Bug/view.php?id=1631 1631], [http://www.na-mic.org/Bug/view.php?id=1686 1686] (or a subset)
*<s>VTK GPU raycaster</s>: J2
**<s>[http://www.na-mic.org/Bug/view.php?id=1612 linear ramp]</s>, <s>[http://na-mic.org/Mantis/view.php?id=1663 crash in transfer function editor]</s>
* View controller cosmetics: J2
**[[2012_Project_Week:ViewerControls|Redesign drafts]]
** Please consider notes here (not captured on the project wiki page, but we agreed on this redesign I think): [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.0/SlicerApplication/MouseandKeyboardShortcuts#Proposed_functionality]
*Brainsfit cosmetics: Hans
**[http://na-mic.org/Mantis/view.php?id=1584 feature request]
*Extensions: JC
** Refine the mechanism to build/test/upload extensions.
** Provide support to extension developers so that the following extensions are built:
*** ABC, SkullStripper, EMSegmenter, VMTK, Plastimatch, DVH/SlicerRt
*Documentation: JC
** Mechanism to easily "version" the documentation. (Easy creation of set of pages associated to release 4.1 from the pages prefixed with 4.0)
** NiceToHave:
*** Offline documentation: Mobile skin for webkit rendering of the slicer wiki documentation pages
* PythonQt: JC
** Update CTK and Slicer to consider the contributed change to PythonQt
* Annotation module bugs: <s>[http://www.na-mic.org/Bug/view.php?id=1712 drag and drop scrolling] </s>, <s>[http://www.na-mic.org/Bug/view.php?id=1713 deleting hierarchies] </s>, <s>[http://www.na-mic.org/Bug/view.php?id=1715 import]</s>, ruler (crash on scene load fixed by Jim's changes), [http://www.na-mic.org/Bug/view.php?id=1717 storage nodes] - Nicole

=Bug fixes targeted for this release=
Sonia's reports on the DTI modules of the current Slicer4 release:

* Mantis Bug Reports:
** [http://www.na-mic.org/Bug/view.php?id=1722 Brain Mask] (assigned to Demian)
** [http://www.na-mic.org/Bug/view.php?id=1679 Color by Orientation] (assigned to Demian)
** [http://www.na-mic.org/Bug/view.php?id=1678 Glyphs Visualization] (assigned to Alex. fixed)
**[http://www.na-mic.org/Bug/view.php?id=1685 Fiducials Seeding ] (assigned to Alex. fixed )
** [http://www.na-mic.org/Bug/view.php?id=1684 Consistency of the GUI in the labelmap and fiducial seeding modules] (assigned to Alex, fixed)
** [http://www.na-mic.org/Bug/view.php?id=1724 Scalar Measurement computation issue (Planar measure)] : wrong window and level values in the Volumes module ( assigned to Julien Finet) iss due to extreme values in the data - can this be clamped in the scalar estimation module?
** [http://www.na-mic.org/Bug/view.php?id=1725 Scalar measurement update issue]
** DTI pipeline Windows 32 crash (Marianna's test: Mantis bug report xxx]
** [http://www.na-mic.org/Bug/view.php?id=1732 Scene Restore Issue in Slicer4] (assigned to: )
* Suggested Reorganization of the Diffusion menu (assigned to Demian)
**Diffusion Data Conversion:
***DICOM to Nrrd
***DTIimport/export
** DWI:
***Brain Mask
***Tensor Estimation
*** Denoising
** DTI
*** Scalar Measurements
*** Tractography
*** Resample

* 'DicomToNrrdConverter' should be 'DICOM To NRRD Converter', and make the parameters of the Output sections visible on the GUI (assigned to Demian)

* Use new Slicer4 QTtesting functionalities for cross-platform testing of Iowa Workshop tutorials
= Mantis issue tracking for Slicer 4.1 target =
Follow this [http://www.na-mic.org/Bug/search.php?project_id=3&sticky_issues=on&target_version=Slicer+4.1.0&sortby=last_updated&dir=DESC&hide_status_id=80 link].

= Deferred to after 4.1 freeze =
* Fix for texture resolution: Alex
** From Ron: for IGT need minimum 12Hz frame rate, maximum 200ms latency, preferred 30 hz frame rate and less than 100ms latency
* Update screenshot to reflect all possible layouts [http://www.na-mic.org/Bug/view.php?id=1662 bug 1662] - Nicole

* Is it realistic to try for SimpleITK in this release? (After discussion: no, needs more testing - aim for summer project week)
** Yes, if somebody can help with ITK 4 on windows.
** linux packaging issue:
*** (2) itkXXX.so files are missing in the Slicer package.
** linux discovering CLI:
*** (1) missing symbol on exit of CLI; in addition with a Qt bug, it fails to parse the CLI XML description
** possibly other issues on window (needs testing)
*** (3) Building SWIG for SimpleITK is the problem.
** need to try all the packaging platforms
*** packaging has never been tried on mac (J2 didn't try to compile on Mac neither)
*** packaging has never been tried on windows (because it doesn't compile)

{| style="margin: 1em auto 1em auto; border: 1px solid darkgray;"
|-
!
! scope="col" colspan="3" style="border-bottom: 1px solid grey;"| Build
! scope="col" colspan="3" style="border-bottom: 1px solid grey;"| Run
! scope="col" colspan="3" style="border-bottom: 1px solid grey;"| Package
|-
!Type
!Windows
!Linux
!Mac
!Windows
!Linux
!Mac
!Windows
!Linux
!Mac
|-
| ITKv4 in Slicer
|bgcolor="Orange" align="center"|?
|bgcolor="LightGreen" align="center"|ok
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (1)
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (2)
|bgcolor="Orange" align="center"|?
|-
| SimpleITK in Slicer
|bgcolor="#f34a33" align="center"| no (3)
|bgcolor="LightGreen" align="center"|ok
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (1)
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (2)
|bgcolor="Orange" align="center"|?
|}
[[Events|Back to events page]]

2012 Project Week:AutomatedTesting

2012-02-21T19:03:26Z

Finetjul: /* Key Investigators */ add link to progress page

=Key Investigators=
* Brigham and Women's Hospital: Sonia Pujol
* Isomics Inc: Steve Pieper
* Kitware: Jean-Christophe Fillon-Robin, Benjamin Long

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

<h3>Objective</h3>

The objective is to implement automated GUI testing in Slicer4 based on QtTesting, to be able to perform nightly automated tutorial testing.

</div>

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

<h3>Approach, Plan</h3>
We'll generate automated tests for the Slicer4minute tutorial, and define associated metrics to measure the outcomes.
</div>
<div style="width: 40%; float: left;">

<h3>Progress</h3>
* Implemented new translators/players files to increase widget coverage
* Discussed how scenario could be appropriately tested and/or played back in Slicer4
* Future work is tracked [http://wiki.slicer.org/slicerWiki/index.php/Documentation/Snapshot/Developers/QtTesting here]

</div>
</div>

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

</div>

Slicer-4.1

2012-02-18T00:03:30Z

Finetjul:

Target date for the code freeze is Monday. Feb. 27, 2012

=Features and Responsibilities=
*Dicom widget: Steve
**cget
**pop up reorganization
**Lollipop
*Charts: Jim
**Label statistics
*compareviews and linking: Jim
**bugs [http://www.na-mic.org/Bug/view.php?id=1526 1526], [http://www.na-mic.org/Bug/view.php?id=1598 1598], [http://www.na-mic.org/Bug/view.php?id=1495 1495], [http://www.na-mic.org/Bug/view.php?id=1583 1583], [http://www.na-mic.org/Bug/view.php?id=1607 1607], [http://www.na-mic.org/Bug/view.php?id=1632 1632], [http://www.na-mic.org/Bug/view.php?id=1631 1631], [http://www.na-mic.org/Bug/view.php?id=1686 1686] (or a subset)
*VTK GPU raycaster: J2
**linear ramp, crash in transfer function editor
* View controller cosmetics: J2
**[[2012_Project_Week:ViewerControls|Redesign drafts]]
** Please consider notes here (not captured on the project wiki page, but we agreed on this redesign I think): [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.0/SlicerApplication/MouseandKeyboardShortcuts#Proposed_functionality]
*Brainsfit cosmetics: Hans
**[http://na-mic.org/Mantis/view.php?id=1584 feature request]
*Extensions: JC
** Refine the mechanism to build/test/upload extensions.
** Provide support to extension developers so that the following extensions are built:
*** ABC, SkullStripper, EMSegmenter, VMTK, Plastimatch, DVH/SlicerRt
*Documentation: JC
** Mechanism to easily "version" the documentation. (Easy creation of set of pages associated to release 4.1 from the pages prefixed with 4.0)
** NiceToHave:
*** Offline documentation: Mobile skin for webkit rendering of the slicer wiki documentation pages
* PythonQt: JC
** Update CTK and Slicer to consider the contributed change to PythonQt
* Annotation module bugs: [http://www.na-mic.org/Bug/view.php?id=1712 drag and drop scrolling] (resolved), [http://www.na-mic.org/Bug/view.php?id=1713 deleting hierarchies] (resolved), [http://www.na-mic.org/Bug/view.php?id=1715 import] (resolved), ruler (crash on scene load fixed by Jim's changes), [http://www.na-mic.org/Bug/view.php?id=1717 storage nodes] - Nicole

=Bug fixes targeted for this release=
Sonia's reports on the DTI modules of the current Slicer4 release:

* Mantis Bug Reports:
** [http://www.na-mic.org/Bug/view.php?id=1722 Brain Mask] (assigned to Demian)
** [http://www.na-mic.org/Bug/view.php?id=1679 Color by Orientation] (assigned to Demian)
** [http://www.na-mic.org/Bug/view.php?id=1678 Glyphs Visualization] (assigned to Alex. fixed)
**[http://www.na-mic.org/Bug/view.php?id=1685 Fiducials Seeding ] (assigned to Alex. fixed )
** [http://www.na-mic.org/Bug/view.php?id=1684 Consistency of the GUI in the labelmap and fiducial seeding modules] (assigned to Alex, fixed)
** [http://www.na-mic.org/Bug/view.php?id=1724 Scalar Measurement computation issue (Planar measure)] : wrong window and level values in the Volumes module ( assigned to Julien Finet) iss due to extreme values in the data - can this be clamped in the scalar estimation module?
** [http://www.na-mic.org/Bug/view.php?id=1725 Scalar measurement update issue]
** DTI pipeline Windows 32 crash (Marianna's test: Mantis bug report xxx]
** [http://www.na-mic.org/Bug/view.php?id=1732 Scene Restore Issue in Slicer4] (assigned to: )
* Suggested Reorganization of the Diffusion menu (assigned to Demian)
**Diffusion Data Conversion:
***DICOM to Nrrd
***DTIimport/export
** DWI:
***Brain Mask
***Tensor Estimation
*** Denoising
** DTI
*** Scalar Measurements
*** Tractography
*** Resample

* 'DicomToNrrdConverter' should be 'DICOM To NRRD Converter', and make the parameters of the Output sections visible on the GUI (assigned to Demian)

* Use new Slicer4 QTtesting functionalities for cross-platform testing of Iowa Workshop tutorials
= Mantis issue tracking for Slicer 4.1 target =
Follow this [http://www.na-mic.org/Bug/search.php?project_id=3&sticky_issues=on&target_version=Slicer+4.1.0&sortby=last_updated&dir=DESC&hide_status_id=80 link].

= Deferred to after 4.1 freeze =
* Fix for texture resolution: Alex
** From Ron: for IGT need minimum 12Hz frame rate, maximum 200ms latency
* Update screenshot to reflect all possible layouts [http://www.na-mic.org/Bug/view.php?id=1662 bug 1662] - Nicole

* Is it realistic to try for SimpleITK in this release? (After discussion: no, needs more testing - aim for summer project week)
** Yes, if somebody can help with ITK 4 on windows.
** linux packaging issue:
*** (2) itkXXX.so files are missing in the Slicer package.
** linux discovering CLI:
*** (1) missing symbol on exit of CLI; in addition with a Qt bug, it fails to parse the CLI XML description
** possibly other issues on window (needs testing)
*** (3) Building SWIG for SimpleITK is the problem.
** need to try all the packaging platforms
*** packaging has never been tried on mac (J2 didn't try to compile on Mac neither)
*** packaging has never been tried on windows (because it doesn't compile)

{| style="margin: 1em auto 1em auto; border: 1px solid darkgray;"
|-
!
! scope="col" colspan="3" style="border-bottom: 1px solid grey;"| Build
! scope="col" colspan="3" style="border-bottom: 1px solid grey;"| Run
! scope="col" colspan="3" style="border-bottom: 1px solid grey;"| Package
|-
!Type
!Windows
!Linux
!Mac
!Windows
!Linux
!Mac
!Windows
!Linux
!Mac
|-
| ITKv4 in Slicer
|bgcolor="Orange" align="center"|?
|bgcolor="LightGreen" align="center"|ok
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (1)
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (2)
|bgcolor="Orange" align="center"|?
|-
| SimpleITK in Slicer
|bgcolor="#f34a33" align="center"| no (3)
|bgcolor="LightGreen" align="center"|ok
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (1)
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (2)
|bgcolor="Orange" align="center"|?
|}
[[Events|Back to events page]]

Slicer-4.1

2012-02-17T23:49:10Z

Finetjul: /* Features and Responsibilities */

Target date for the code freeze is Monday. Feb. 27, 2012

=Features and Responsibilities=
*Dicom widget: Steve
**cget
**pop up reorganization
**Lollipop
*Charts: Jim
**Label statistics
*compareviews and linking: Jim
**bugs [http://www.na-mic.org/Bug/view.php?id=1526 1526], [http://www.na-mic.org/Bug/view.php?id=1598 1598], [http://www.na-mic.org/Bug/view.php?id=1495 1495], [http://www.na-mic.org/Bug/view.php?id=1583 1583], [http://www.na-mic.org/Bug/view.php?id=1607 1607], [http://www.na-mic.org/Bug/view.php?id=1632 1632], [http://www.na-mic.org/Bug/view.php?id=1631 1631], [http://www.na-mic.org/Bug/view.php?id=1686 1686] (or a subset)
*VTK GPU raycaster: J2
**linear ramp, crash in transfer function editor
* View controller cosmetics: J2
**[[2012_Project_Week:ViewerControls|Redesign drafts]]
** Please consider notes here (not captured on the project wiki page, but we agreed on this redesign I think): [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.0/SlicerApplication/MouseandKeyboardShortcuts#Proposed_functionality]
*Brainsfit cosmetics: Hans
**[http://na-mic.org/Mantis/view.php?id=1584 feature request]
*Extensions: JC
** Refine the mechanism to build/test/upload extensions.
** Provide support to extension developers so that the following extensions are built:
*** ABC, SkullStripper, EMSegmenter, VMTK, Plastimatch, DVH/SlicerRt
*Documentation: JC
** Mechanism to easily "version" the documentation. (Easy creation of set of pages associated to release 4.1 from the pages prefixed with 4.0)
** NiceToHave:
*** Offline documentation: Mobile skin for webkit rendering of the slicer wiki documentation pages
* PythonQt: JC
** Update CTK and Slicer to consider the contributed change to PythonQt
* Annotation module bugs: [http://www.na-mic.org/Bug/view.php?id=1712 drag and drop scrolling] (resolved), [http://www.na-mic.org/Bug/view.php?id=1713 deleting hierarchies] (resolved), [http://www.na-mic.org/Bug/view.php?id=1715 import] (resolved), ruler (crash on scene load fixed by Jim's changes), [http://www.na-mic.org/Bug/view.php?id=1717 storage nodes] - Nicole

=Bug fixes targeted for this release=
Sonia's reports on the DTI modules of the current Slicer4 release:

* Mantis Bug Reports:
** [http://www.na-mic.org/Bug/view.php?id=1722 Brain Mask] (assigned to Demian)
** [http://www.na-mic.org/Bug/view.php?id=1679 Color by Orientation] (assigned to Demian)
** [http://www.na-mic.org/Bug/view.php?id=1678 Glyphs Visualization] (assigned to Alex. fixed)
**[http://www.na-mic.org/Bug/view.php?id=1685 Fiducials Seeding ] (assigned to Alex. fixed )
** [http://www.na-mic.org/Bug/view.php?id=1684 Consistency of the GUI in the labelmap and fiducial seeding modules] (assigned to Alex, fixed)
** [http://www.na-mic.org/Bug/view.php?id=1724 Scalar Measurement computation issue (Planar measure)] : wrong window and level values in the Volumes module ( assigned to Julien Finet) iss due to extreme values in the data - can this be clamped in the scalar estimation module?
** [http://www.na-mic.org/Bug/view.php?id=1725 Scalar measurement update issue]
** DTI pipeline Windows 32 crash (Marianna's test: Mantis bug report xxx]
** [http://www.na-mic.org/Bug/view.php?id=1732 Scene Restore Issue in Slicer4] (assigned to: )
* Suggested Reorganization of the Diffusion menu (assigned to Demian)
**Diffusion Data Conversion:
***DICOM to Nrrd
***DTIimport/export
** DWI:
***Brain Mask
***Tensor Estimation
*** Denoising
** DTI
*** Scalar Measurements
*** Tractography
*** Resample

* 'DicomToNrrdConverter' should be 'DICOM To NRRD Converter', and make the parameters of the Output sections visible on the GUI (assigned to Demian)

* Use new Slicer4 QTtesting functionalities for cross-platform testing of Iowa Workshop tutorials

= Deferred to after 4.1 freeze =
* Fix for texture resolution: Alex
** From Ron: for IGT need minimum 12Hz frame rate, maximum 200ms latency
* Update screenshot to reflect all possible layouts [http://www.na-mic.org/Bug/view.php?id=1662 bug 1662] - Nicole

* Is it realistic to try for SimpleITK in this release? (After discussion: no, needs more testing - aim for summer project week)
** Yes, if somebody can help with ITK 4 on windows.
** linux packaging issue:
*** (2) itkXXX.so files are missing in the Slicer package.
** linux discovering CLI:
*** (1) missing symbol on exit of CLI; in addition with a Qt bug, it fails to parse the CLI XML description
** possibly other issues on window (needs testing)
*** (3) Building SWIG for SimpleITK is the problem.
** need to try all the packaging platforms
*** packaging has never been tried on mac (J2 didn't try to compile on Mac neither)
*** packaging has never been tried on windows (because it doesn't compile)

{| style="margin: 1em auto 1em auto; border: 1px solid darkgray;"
|-
!
! scope="col" colspan="3" style="border-bottom: 1px solid grey;"| Build
! scope="col" colspan="3" style="border-bottom: 1px solid grey;"| Run
! scope="col" colspan="3" style="border-bottom: 1px solid grey;"| Package
|-
!Type
!Windows
!Linux
!Mac
!Windows
!Linux
!Mac
!Windows
!Linux
!Mac
|-
| ITKv4 in Slicer
|bgcolor="Orange" align="center"|?
|bgcolor="LightGreen" align="center"|ok
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (1)
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (2)
|bgcolor="Orange" align="center"|?
|-
| SimpleITK in Slicer
|bgcolor="#f34a33" align="center"| no (3)
|bgcolor="LightGreen" align="center"|ok
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (1)
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (2)
|bgcolor="Orange" align="center"|?
|}
[[Events|Back to events page]]

Slicer-4.1

2012-02-17T23:48:59Z

Finetjul: /* Features and Responsibilities */

Target date for the code freeze is Monday. Feb. 27, 2012

=Features and Responsibilities=
*Dicom widget: Steve
**cget
**pop up reorganization
**Lollipop
*Charts: Jim
**Label statistics
*compareviews and linking: Jim
**bugs http://www.na-mic.org/Bug/view.php?id=1526 1526], [http://www.na-mic.org/Bug/view.php?id=1598 1598], [http://www.na-mic.org/Bug/view.php?id=1495 1495], [http://www.na-mic.org/Bug/view.php?id=1583 1583], [http://www.na-mic.org/Bug/view.php?id=1607 1607], [http://www.na-mic.org/Bug/view.php?id=1632 1632], [http://www.na-mic.org/Bug/view.php?id=1631 1631], [http://www.na-mic.org/Bug/view.php?id=1686 1686] (or a subset)
*VTK GPU raycaster: J2
**linear ramp, crash in transfer function editor
* View controller cosmetics: J2
**[[2012_Project_Week:ViewerControls|Redesign drafts]]
** Please consider notes here (not captured on the project wiki page, but we agreed on this redesign I think): [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.0/SlicerApplication/MouseandKeyboardShortcuts#Proposed_functionality]
*Brainsfit cosmetics: Hans
**[http://na-mic.org/Mantis/view.php?id=1584 feature request]
*Extensions: JC
** Refine the mechanism to build/test/upload extensions.
** Provide support to extension developers so that the following extensions are built:
*** ABC, SkullStripper, EMSegmenter, VMTK, Plastimatch, DVH/SlicerRt
*Documentation: JC
** Mechanism to easily "version" the documentation. (Easy creation of set of pages associated to release 4.1 from the pages prefixed with 4.0)
** NiceToHave:
*** Offline documentation: Mobile skin for webkit rendering of the slicer wiki documentation pages
* PythonQt: JC
** Update CTK and Slicer to consider the contributed change to PythonQt
* Annotation module bugs: [http://www.na-mic.org/Bug/view.php?id=1712 drag and drop scrolling] (resolved), [http://www.na-mic.org/Bug/view.php?id=1713 deleting hierarchies] (resolved), [http://www.na-mic.org/Bug/view.php?id=1715 import] (resolved), ruler (crash on scene load fixed by Jim's changes), [http://www.na-mic.org/Bug/view.php?id=1717 storage nodes] - Nicole

=Bug fixes targeted for this release=
Sonia's reports on the DTI modules of the current Slicer4 release:

* Mantis Bug Reports:
** [http://www.na-mic.org/Bug/view.php?id=1722 Brain Mask] (assigned to Demian)
** [http://www.na-mic.org/Bug/view.php?id=1679 Color by Orientation] (assigned to Demian)
** [http://www.na-mic.org/Bug/view.php?id=1678 Glyphs Visualization] (assigned to Alex. fixed)
**[http://www.na-mic.org/Bug/view.php?id=1685 Fiducials Seeding ] (assigned to Alex. fixed )
** [http://www.na-mic.org/Bug/view.php?id=1684 Consistency of the GUI in the labelmap and fiducial seeding modules] (assigned to Alex, fixed)
** [http://www.na-mic.org/Bug/view.php?id=1724 Scalar Measurement computation issue (Planar measure)] : wrong window and level values in the Volumes module ( assigned to Julien Finet) iss due to extreme values in the data - can this be clamped in the scalar estimation module?
** [http://www.na-mic.org/Bug/view.php?id=1725 Scalar measurement update issue]
** DTI pipeline Windows 32 crash (Marianna's test: Mantis bug report xxx]
** [http://www.na-mic.org/Bug/view.php?id=1732 Scene Restore Issue in Slicer4] (assigned to: )
* Suggested Reorganization of the Diffusion menu (assigned to Demian)
**Diffusion Data Conversion:
***DICOM to Nrrd
***DTIimport/export
** DWI:
***Brain Mask
***Tensor Estimation
*** Denoising
** DTI
*** Scalar Measurements
*** Tractography
*** Resample

* 'DicomToNrrdConverter' should be 'DICOM To NRRD Converter', and make the parameters of the Output sections visible on the GUI (assigned to Demian)

* Use new Slicer4 QTtesting functionalities for cross-platform testing of Iowa Workshop tutorials

= Deferred to after 4.1 freeze =
* Fix for texture resolution: Alex
** From Ron: for IGT need minimum 12Hz frame rate, maximum 200ms latency
* Update screenshot to reflect all possible layouts [http://www.na-mic.org/Bug/view.php?id=1662 bug 1662] - Nicole

* Is it realistic to try for SimpleITK in this release? (After discussion: no, needs more testing - aim for summer project week)
** Yes, if somebody can help with ITK 4 on windows.
** linux packaging issue:
*** (2) itkXXX.so files are missing in the Slicer package.
** linux discovering CLI:
*** (1) missing symbol on exit of CLI; in addition with a Qt bug, it fails to parse the CLI XML description
** possibly other issues on window (needs testing)
*** (3) Building SWIG for SimpleITK is the problem.
** need to try all the packaging platforms
*** packaging has never been tried on mac (J2 didn't try to compile on Mac neither)
*** packaging has never been tried on windows (because it doesn't compile)

{| style="margin: 1em auto 1em auto; border: 1px solid darkgray;"
|-
!
! scope="col" colspan="3" style="border-bottom: 1px solid grey;"| Build
! scope="col" colspan="3" style="border-bottom: 1px solid grey;"| Run
! scope="col" colspan="3" style="border-bottom: 1px solid grey;"| Package
|-
!Type
!Windows
!Linux
!Mac
!Windows
!Linux
!Mac
!Windows
!Linux
!Mac
|-
| ITKv4 in Slicer
|bgcolor="Orange" align="center"|?
|bgcolor="LightGreen" align="center"|ok
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (1)
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (2)
|bgcolor="Orange" align="center"|?
|-
| SimpleITK in Slicer
|bgcolor="#f34a33" align="center"| no (3)
|bgcolor="LightGreen" align="center"|ok
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (1)
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (2)
|bgcolor="Orange" align="center"|?
|}
[[Events|Back to events page]]

Slicer-4.1

2012-02-16T20:35:53Z

Finetjul: /* Deferred to after 4.1 freeze */

Target date for the code freeze is Monday. Feb. 27, 2012

=Features and Responsibilities=
*Dicom widget: Steve
**cget
**pop up reorganization
**Lollipop
*Charts: Jim
**Label statistics
*compareviews and linking: Jim
**bugs 1526, 1598, 1495, 1583, 1607, 1632, 1631, 1686 (or a subset)
*VTK GPU raycaster: J2
**linear ramp, crash in transfer function editor
* View controller cosmetics: J2
**[[2012_Project_Week:ViewerControls|Redesign drafts]]
** Please consider notes here (not captured on the project wiki page, but we agreed on this redesign I think): [http://wiki.slicer.org/slicerWiki/index.php/Documentation/4.0/SlicerApplication/MouseandKeyboardShortcuts#Proposed_functionality]
*Brainsfit cosmetics: Hans
**[http://na-mic.org/Mantis/view.php?id=1584 feature request]
*Extensions: JC
** Refine the mechanism to build/test/upload extensions.
** Provide support to extension developers so that the following extensions are built:
*** ABC, SkullStripper, EMSegmenter, VMTK, Plastimatch, DVH/SlicerRt
*Documentation: JC
** Mechanism to easily "version" the documentation. (Easy creation of set of pages associated to release 4.1 from the pages prefixed with 4.0)
** NiceToHave:
*** Offline documentation: Mobile skin for webkit rendering of the slicer wiki documentation pages
* PythonQt: JC
** Update CTK and Slicer to consider the contributed change to PythonQt
* Update screenshot to reflect all possible layouts - Nicole
* Annotation module bugs: scrolling, deleting, import, ruler, storage nodes - Nicole

=Bug fixes targeted for this release=
Sonia's reports on the DTI modules of the current Slicer4 release:

* Mantis Bug Reports:
** [http://www.na-mic.org/Bug/view.php?id=1722 Brain Mask] (assigned to Demian)
** [http://www.na-mic.org/Bug/view.php?id=1679 Color by Orientation] (assigned to Demian)
** [http://www.na-mic.org/Bug/view.php?id=1678 Glyphs Visualization] (assigned to Alex. fixed)
**[http://www.na-mic.org/Bug/view.php?id=1685 Fiducials Seeding ] (assigned to Alex. fixed )
** [http://www.na-mic.org/Bug/view.php?id=1684 Consistency of the GUI in the labelmap and fiducial seeding modules] (assigned to Alex)
** [http://www.na-mic.org/Bug/view.php?id=1724 Scalar Measurement computation issue (Planar measure)] : wrong window and level values in the Volumes module ( assigned to Julien Finet) iss due to extreme values in the data - can this be clamped in the scalar estimation module?
** [http://www.na-mic.org/Bug/view.php?id=1725 Scalar measurement update issue]

* Suggested Reorganization of the Diffusion menu (assigned to Demian)
**Diffusion Data Conversion:
***DICOM to Nrrd
***DTIimport/export
** DWI:
***Brain Mask
***Tensor Estimation
*** Denoising
** DTI
*** Scalar Measurements
*** Tractography
*** Resample

* 'DicomToNrrdConverter' should be 'DICOM To NRRD Converter', and make the parameters of the Output sections visible on the GUI (assigned to Demian)

* Use new Slicer4 QTtesting functionalities for cross-platform testing of Iowa Workshop tutorials

= Deferred to after 4.1 freeze =
* Fix for texture resolution: Alex

* Is it realistic to try for SimpleITK in this release? (After discussion: no, needs more testing - aim for summer project week)
** Yes, if somebody can help with ITK 4 on windows.
** linux packaging issue:
*** (2) itkXXX.so files are missing in the Slicer package.
** linux discovering CLI:
*** (1) missing symbol on exit of CLI; in addition with a Qt bug, it fails to parse the CLI XML description
** possibly other issues on window (needs testing)
*** (3) Building SWIG for SimpleITK is the problem.
** need to try all the packaging platforms
*** packaging has never been tried on mac (J2 didn't try to compile on Mac neither)
*** packaging has never been tried on windows (because it doesn't compile)

{| style="margin: 1em auto 1em auto; border: 1px solid darkgray;"
|-
!
! scope="col" colspan="3" style="border-bottom: 1px solid grey;"| Build
! scope="col" colspan="3" style="border-bottom: 1px solid grey;"| Run
! scope="col" colspan="3" style="border-bottom: 1px solid grey;"| Package
|-
!Type
!Windows
!Linux
!Mac
!Windows
!Linux
!Mac
!Windows
!Linux
!Mac
|-
| ITKv4 in Slicer
|bgcolor="Orange" align="center"|?
|bgcolor="LightGreen" align="center"|ok
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (1)
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (2)
|bgcolor="Orange" align="center"|?
|-
| SimpleITK in Slicer
|bgcolor="#f34a33" align="center"| no (3)
|bgcolor="LightGreen" align="center"|ok
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (1)
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (2)
|bgcolor="Orange" align="center"|?
|}
[[Events|Back to events page]]

Slicer-4.1

2012-02-10T14:34:30Z

Finetjul: /* Open Questions */

Target date for the code freeze is Monday. Feb. 27, 2012

=Features and Responsibilities=
*Dicom widget: Steve
**cget
**pop up reorganization
**Lollipop
*Charts: Jim
**Label statistics
*compareviews and linking: Jim
**bugs 1526, 1598, 1495, 1583, 1607, 1632, 1631, 1686 (or a subset)
*VTK GPU raycaster: J2
**linear ramp, crash in transfer function editor
* View controller cosmetics: J2
**[[2012_Project_Week:ViewerControls|Redesign drafts]]
*Brainsfit cosmetics: Hans
**[http://na-mic.org/Mantis/view.php?id=1584 feature request]
*Extensions: JC
** Refine the mechanism to build/test/upload extensions.
** Provide support to extension developers so that the following extensions are built:
*** ABC, SkullStripper, EMSegmenter, VMTK, Plastimatch, DVH/SlicerRt
*Documentation: JC
** Mechanism to easily "version" the documentation. (Easy creation of set of pages associated to release 4.1 from the pages prefixed with 4.0)
** NiceToHave:
*** Offline documentation: Mobile skin for webkit rendering of the slicer wiki documentation pages
* PythonQt: JC
** Update CTK and Slicer to consider the contributed change to PythonQt
* Fix for texture resolution: Alex
* Update screen capture to reflect all possible layouts - Nicole

= Open Questions =
* Is it realistic to try for SimpleITK in this release? (After discussion: no, needs more testing - aim for summer project week)
** Yes, if somebody can help with ITK 4 on windows.
** linux packaging issue:
*** (2) itkXXX.so files are missing in the Slicer package.
** linux discovering CLI:
*** (1) missing symbol on exit of CLI; in addition with a Qt bug, it fails to parse the CLI XML description
** possibly other issues on window (needs testing)
*** (3) Building SWIG for SimpleITK is the problem.
** need to try all the packaging platforms
*** packaging has never been tried on mac (J2 didn't try to compile on Mac neither)
*** packaging has never been tried on windows (because it doesn't compile)

{| style="margin: 1em auto 1em auto; border: 1px solid darkgray;"
|-
!
! scope="col" colspan="3" style="border-bottom: 1px solid grey;"| Build
! scope="col" colspan="3" style="border-bottom: 1px solid grey;"| Run
! scope="col" colspan="3" style="border-bottom: 1px solid grey;"| Package
|-
!Type
!Windows
!Linux
!Mac
!Windows
!Linux
!Mac
!Windows
!Linux
!Mac
|-
| ITKv4
|bgcolor="Orange" align="center"|?
|bgcolor="LightGreen" align="center"|ok
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (1)
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (2)
|bgcolor="Orange" align="center"|?
|-
| SimpleITK
|bgcolor="#f34a33" align="center"| no (3)
|bgcolor="LightGreen" align="center"|ok
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (1)
|bgcolor="Orange" align="center"|?
|bgcolor="Orange" align="center"|?
|bgcolor="#f34a33" align="center"|no (2)
|bgcolor="Orange" align="center"|?
|}
[[Events|Back to events page]]

Slicer-4.1

2012-02-10T14:17:56Z

Finetjul: /* Open Questions */

Target date for the code freeze is Monday. Feb. 27, 2012

=Features and Responsibilities=
*Dicom widget: Steve
**cget
**pop up reorganization
**Lollipop
*Charts: Jim
**Label statistics
*compareviews and linking: Jim
**bugs 1526, 1598, 1495, 1583, 1607, 1632, 1631, 1686 (or a subset)
*VTK GPU raycaster: J2
**linear ramp, crash in transfer function editor
* View controller cosmetics: J2
**[[2012_Project_Week:ViewerControls|Redesign drafts]]
*Brainsfit cosmetics: Hans
**[http://na-mic.org/Mantis/view.php?id=1584 feature request]
*Extensions: JC
** Refine the mechanism to build/test/upload extensions.
** Provide support to extension developers so that the following extensions are built:
*** ABC, SkullStripper, EMSegmenter, VMTK, Plastimatch, DVH/SlicerRt
*Documentation: JC
** Mechanism to easily "version" the documentation. (Easy creation of set of pages associated to release 4.1 from the pages prefixed with 4.0)
** NiceToHave:
*** Offline documentation: Mobile skin for webkit rendering of the slicer wiki documentation pages
* PythonQt: JC
** Update CTK and Slicer to consider the contributed change to PythonQt
* Fix for texture resolution: Alex
* Update screen capture to reflect all possible layouts - Nicole

= Open Questions =
* Is it realistic to try for SimpleITK in this release? (After discussion: no, needs more testing - aim for summer project week)
** Yes, if somebody can help with ITK 4 on windows.
** linux packaging issue:
*** itkXXX.so files are missing in the Slicer package.
** linux discovering CLI:
*** missing symbol on exit of CLI; in addition with a Qt bug, it fails to parse the CLI XML description
** possibly other issues on window (needs testing)
*** Building SWIG for SimpleITK is the problem.
** need to try all the packaging platforms
*** packaging has never been tried on mac (J2 didn't try to compile on Mac neither)
*** packaging has never been tried on windows (because it doesn't compile)

[[Events|Back to events page]]

Slicer-4.1

2012-02-10T14:16:33Z

Finetjul: /* Open Questions */

Target date for the code freeze is Monday. Feb. 27, 2012

=Features and Responsibilities=
*Dicom widget: Steve
**cget
**pop up reorganization
**Lollipop
*Charts: Jim
**Label statistics
*compareviews and linking: Jim
**bugs 1526, 1598, 1495, 1583, 1607, 1632, 1631, 1686 (or a subset)
*VTK GPU raycaster: J2
**linear ramp, crash in transfer function editor
* View controller cosmetics: J2
**[[2012_Project_Week:ViewerControls|Redesign drafts]]
*Brainsfit cosmetics: Hans
**[http://na-mic.org/Mantis/view.php?id=1584 feature request]
*Extensions: JC
** Refine the mechanism to build/test/upload extensions.
** Provide support to extension developers so that the following extensions are built:
*** ABC, SkullStripper, EMSegmenter, VMTK, Plastimatch, DVH/SlicerRt
*Documentation: JC
** Mechanism to easily "version" the documentation. (Easy creation of set of pages associated to release 4.1 from the pages prefixed with 4.0)
** NiceToHave:
*** Offline documentation: Mobile skin for webkit rendering of the slicer wiki documentation pages
* PythonQt: JC
** Update CTK and Slicer to consider the contributed change to PythonQt
* Fix for texture resolution: Alex
* Update screen capture to reflect all possible layouts - Nicole

= Open Questions =
* Is it realistic to try for SimpleITK in this release? (After discussion: no, needs more testing - aim for summer project week)
** Yes, if somebody can help with ITK 4 on windows.
** linux packaging issue:
*** itkXXX.so files are missing in the Slicer package.
** linux discovering CLI: missing symbol on exit
** possibly other issues on window (needs testing)
*** Building SWIG for SimpleITK is the problem.
** need to try all the packaging platforms
*** packaging has never been tried on mac (J2 didn't try to compile on Mac neither)
*** packaging has never been tried on windows (because it doesn't compile)

[[Events|Back to events page]]

Slicer-4.1

2012-02-07T21:11:23Z

Finetjul: /* Features and Responsibilities */

Target date for the code freeze is Monday. Feb. 27, 2012

=Features and Responsibilities=
*Dicom widget: Steve
**cget
**pop up reorganization
**Lollipop
*Charts: Jim
**Label statistics
*compareviews and linking: Jim
**bugs 1526, 1598, 1495, 1583, 1607, 1632, 1631, 1686 (or a subset)
*VTK GPU raycaster: linear ramp, crash in transfer function editor: J2
* View controller cosmetic: J2
*Brainsfit cosmetics: Hans
**[http://na-mic.org/Mantis/view.php?id=1584 feature request]
*Extensions: JC
** Refine the mechanism to build/test/upload extensions.
** Provide support to extension developers so that the following extensions are built:
*** ABC, SkullStripper, EMSegmenter, VMTK, Plastimatch, DVH/SlicerRt
*Documentation: JC
** Mechanism to easily "version" the documentation. (Easy creation of set of pages associated to release 4.1 from the pages prefixed with 4.0)
** NiceToHave:
*** Offline documentation: Mobile skin for webkit rendering of the slicer wiki documentation pages
* Fix for texture resolution: Alex

= Open Questions =
* Is it realistic to try for SimpleITK in this release?
* Yes, if somebody can help with ITK 4 on windows.

[[Events|Back to events page]]

AHM2012-Slicer-Overview-and-Migration

2012-01-10T15:16:45Z

Finetjul: /* Module Creation and Migration */ Add Loadable module presentation

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

'''Tuesday, January 10, 2012 8 to 10am'''
This session is for all developers planning to migrate existing slicer3 modules to slicer4 or start a new project from scratch in slicer4.

==Overview and Architecture==
* Steve (10 minutes) [[AHM2012-Slicer-Introduction|Introduction]]
** Capabilities
** Release Schedule
** Goals
** Ongoing Slicer4 projects and collaborations (NAC, NCIGT, CTK, Supplements...)
* Jc (10 minutes) [[AHM2012-Slicer-Architecture|Architecture]]
** Modularization Object Specialization
*** Qt Widgets <- CTK Widgets <- MRML Widgets <- Slicer Widgets
*** vtkObject <- MRMLLogic <- Module Logic
** Displayable Managers
** Views and Layouts

== Module Creation and Migration ==
* Steve (5 minutes) [http://www.slicer.org/slicerWiki/index.php/Documentation/4.0/Developers/ModuleWizard Module Wizard]
* Jim (10 minutes)
** [[Media:Slicer4 CLI.ppt|CLI Modules]]
** Creating a CLI from existing C++ code
** Migrating CLI Modules to ITK version 4
* J2: Loadable Modules [[File:LoadableModules.pptx]] (20 minutes)
** Structure of a Loadable Module
** Specialization of Module Classes
** Integration with Designer
* Steve: [[AHM2012-Slicer-Python|Scripted Modules and Python Console]] (20 minutes)
** What is accessible via python
** Using the console (See [http://vimeo.com/33236047 J2's excellent demo video])
** Writing a Scripted Module
*** PythonQt interface
*** Logic with vtk/vtkITK/CLI Modules
*** Accessing MRML Data via numpy
** Refining the code and UI with slicerrc
** Limitations of python
* Demian: [[Whole-Brain-Tractography-Wizard|Whole Brain Tractography]] (10 minutes)
** Python wizard example
** Discussion of interactions among modules
** How to build on the dMRI module

== Testing Infrastructure ==
* Benjamin (20 minutes)
** What is QtTesting/How it work.
** Tests for each widgets
** Limits : RenderWindow and GUI Testing
** Slicer integration
** What's next ?

== Documentation ==
* Jc (10 minutes) [[AHM2012-Slicer-Documentation|Documentation]]
** How to write end user documentation for your module
** Source code naming and documentation style
** CMake documentaiton

== Extensions ==
* Jc (20 minutes) [[AHM2012-Slicer-Extension|Extension]]
** Writing an s4ext file
** Testing your extension
** How users will access your extension

File:LoadableModules.pptx

2012-01-10T15:01:39Z

Finetjul:

Engineering:TCON 2012

2012-01-05T20:31:06Z

Finetjul: python demo link for 2012_01_05

Back to [[TCON:Main|TCON:Main]], [[Events]]

__TOC__

==2012-01-05==

Attendees: Jim, Steve, Nicole, Mark, Mehdi, Julien, Tina

Agenda:
* Project week preparation: [[2012_Winter_Project_Week#Projects | Project List]]
* Python demo: http://vimeo.com/33236047

2012 Project Week:GeneralGUI

2011-12-22T22:58:48Z

Finetjul:

* Current GUI (as of Slicer 4.0.1)
**[[Image:Slicer_With_Large_Icons.png|500px|Large Icons]] [[Image:Slicer_With_Small_Icons.png|500px|Small Icons]]
* Move the Module selector from the toolbar to the "Module panel"
** Motivations
*** Saves horizontal space in the toolbar
*** Visually links the module selector with the module panel
*** Possibility to save some screen real estate
**** By reusing the empty module panel dock title
**** By moving the Slicer logo
*** Allows multiple module panels open at the same time (1 module selector per module panel).
** Suggestion 1
***[[Image:ModuleTitleSuggestion-LargeIcons.png|500px|Large Icons]] [[Image:ModuleTitleSuggestion-SmallIcons.png|500px|Small Icons]]
* Simplify Picking toolbar
** http://www.na-mic.org/Bug/view.php?id=1593

File:Slicer With Small Icons.png

2011-12-22T22:55:14Z

Finetjul:

File:Slicer With Large Icons.png

2011-12-22T22:52:55Z

Finetjul:

2012 Project Week:GeneralGUI

2011-12-22T22:48:45Z

Finetjul: Created page with '* Move the Module selector from the toolbar to the "Module panel" ** Motivations *** Saves horizontal space in the toolbar *** Visually links the module selector with the module …'

* Move the Module selector from the toolbar to the "Module panel"
** Motivations
*** Saves horizontal space in the toolbar
*** Visually links the module selector with the module panel
*** Possibility to save some screen real estate
**** By reusing the empty module panel dock title
**** By moving the Slicer logo
*** Allows multiple module panels open at the same time (1 module selector per module panel).
** Suggestion 1
***[[Image:ModuleTitleSuggestion-LargeIcons.png|500px|Large Icons]] [[Image:ModuleTitleSuggestion-SmallIcons.png|500px|Small Icons]]

File:ModuleTitleSuggestion-SmallIcons.png

2011-12-22T22:43:06Z

Finetjul:

File:ModuleTitleSuggestion-LargeIcons.png

2011-12-22T22:41:27Z

Finetjul:

2012 Winter Project Week

2011-12-22T22:35:37Z

Finetjul: /* NA-MIC Kit Internals */ Add GeneralGUI

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

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

== Dates.Venue.Registration ==

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

== Agenda and Project List==

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

==Background==

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

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

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

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

==Projects==

===Traumatic Brain Injury ===

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

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

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

===Head and Neck Cancer ===
* [[2012_Winter_Project_Week:PatchBased|A patch-based approach to the segmentation of organs of risk]] (Christian Wachinger, Polina Golland)
* [[2012_Winter_Project_Week:PairwiseLF|Label fusion with pairwise interactions]] (Ramesh Sridharan, Christian Wachinger, Polina Golland)
* RT dose comparison tool for Slicer (Nadya Shusharina, Greg Sharp)
* [[2012_Winter_Project_Week:InteractiveSegmentation|Interactive editing tools for segmentation]] (Greg Sharp, Steve Pieper)
* [[2012_Winter_Project_Week:UserInTheLoop_InteractiveSegmn|Interactive 3D Level-Set Segmentation]] (Peter Karasev, Karl Fritscher, Ivan Kolesov, Allen Tannenbaum)

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

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

===Registration===
* [[2012_Winter_Project_Week:CMFreg|Framework for Cranio-Maxillo Facial registration in Slicer3]] (Beatriz Paniagua, Lucia Cevidanes, Martin Styner)
* [[2012_Winter_Project_Week:SlidingOrgans|Registration in the presence of sliding between organs (Danielle Pace, Marc Neithammer, Stephen Aylward)]]
* [[2012_Winter_Project_Week:GeometricMetamorphosis|Estimating the infiltration / recession of pathologies independent of background deformations (Danielle Pace, Stephen Aylward, Marc Niethammer)]]
* [[2012_Winter_Project_Week:FastInterpolation|Fast Image Interpolation Give Parameterized Deformations For Image Registration (Ivan Kolesov, Greg Sharp, Allen Tannenbaum)]]

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

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

=== Preparation ===

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

Engineering:TCON 2011

2011-12-08T20:56:12Z

Finetjul: /* 2011-12-08 */

Back to [[TCON:Main|TCON:Main]], [[Events]]

__TOC__

==2011-12-08==
Attendees: Hans, Ron, Jim, Steve, JC, J2, Tina, Stephen

* ITK v4 transition
** 1) Replace ITKv4 git repo from Hans's to the official ITK repo - Jc, done
*** ITK v4 has an official tag in December 20th, however the code is already stable
** 2) Slicer fails to build with ITKv4 - Hans, in progress
*** SkullStripper fails to build with ITKv4
** 3) Setup factory to re-upload unofficial ITK v4 slicer packages for 1/2 weeks - J2, in progress
*** Slicer packages need to be tested
** 4) Make ITKv4 the official version for Slicer - J2, on hold
*** Move the ITKv4 nightly reports up in CDash
*** ITKv4 packages being the only ones uploaded
* AHM planning

==2011-12-01==
Attendees: Ron, Jim, Jan, Sharif, Tamas, Tina, Nicole, Mark, Steve,

* RSNA feedback [http://www.flickr.com/photos/mergehealthcare/6428093295/sizes/o/in/set-72157628213067019/ (it was fun)]
* AHM planning
*Sharif's project

==2011-11-24==
Thanksgiving. No tcon.

==2011-11-17==
Attendees: Jack van horn, marcel prastawa, stephen, tina, fabiola, nicole, mark

*TBI DBP projects added to project week:
**http://wiki.na-mic.org/Wiki/index.php/2012_Winter_Project_Week#Traumatic_Brain_Injury_DBP
**Recent Publications:
***Geometric metamorphosis. Niethammer M, Hart GL, Pace DF, Vespa PM, Irimia A, Van Horn JD, Aylward SR. Med Image Comput Comput Assist Interv. 2011;14(Pt 2):639-46. PMID: 21995083 [PubMed - indexed for MEDLINE] http://cismm.cs.unc.edu/wp-content/uploads/2011/07/2011_Niethammer_Hart_Geometric-Metamorphosis.pdf
***Comparison of Acute and Chronic Traumatic Brain Injury Using Semi-Automatic Multimodal Segmentation of MR Volumes. Irimia A, Chambers MC, Alger JR, Filippou M, Prastawa MW, Wang B, Hovda DA, Gerig G, Toga AW, Kikinis R, Vespa PM, Van Horn JD. J Neurotrauma. 2011 Nov;28(11):2287-306. Epub 2011 Sep 21. http://www.liebertonline.com/doi/abs/10.1089/neu.2011.1920

==2011-11-10==
Attendees: Jim, Tina, Andrey, Ron, Fabiola, Anthony B, Nicole, Mark, Stephen, Steve

Agenda
*Project Week
**Atrial Fibrillation DBP (Utah) - Josh Cates will join
**Projects should be added here: http://wiki.na-mic.org/Wiki/index.php/2012_Winter_Project_Week#Projects
**Engineering Projects
*RSNA Prep - any questions?

==2011-11-03==
Attendees: Ron, Ross, Hans, Martin, Jim, Tina, Steve, J2, JC, Kilian, Clement, Polina

Agenda:
*Iowa DBP projects update by Hans
**DTIPrep with Martin Styner is on target.
**Data Sharing: 15 different projects have requested access to and have downloaded parts of data.
*List hypotheses by biomarker for hd
**eg. quantification of caudate shape/size
*Project Week projects for HD should be added here:
**http://wiki.na-mic.org/Wiki/index.php/2012_Winter_Project_Week#Projects

==2011-10-27==
Attendees: Jack, Greg Sharp, Nicole, JC, J2, Steve, Tina, Hans, Mike Ackermann, Polina, Elvis

Agenda:
* Project Week Kick off TCON
* MGH DBP (Head and Neck Cancer). Greg Sharp.
**Subsequent calls:
***Iowa DBP (Huntington's) Nov 3
***Utah DBP (Atrial Fibrillation)
***UCLA DBP (TBI)
* [[RSNA_2011|RSNA Plans]]
*Suggestion to add SimpleITK tutorial at AHM. Planned for Tuesday. Hans to do it with help from Brad/NIH.

==2011-10-20==
Attendees: Sonia, Jim, Demian, Nicole, Jc, J2, Mark, Tina

Agenda:
* Slicer4 [http://www.na-mic.org/Wiki/index.php/Events:Slicer4-Review-07-2011 status of items for RSNA]
** Welcome module
** Volume Rendering
** Moving crosshairs to toolbar
** integrating external module (Brains, change tracker, ABC, Skull Stripper)
** [http://www.commontk.org/index.php/Documentation/Widget_testing Widget testing]
* [[RSNA_2011|RSNA Plans]]

==2011-10-13==
Attendees: Jim, Nicole, Mark, Hans, Steve

Agenda:
* DisplayableManagers link against CTK? CrosshairDisplayableManager needs access to the LightBoxRendererManager which is down in CTK.
* Speed. Mouse events handled in one queue and application events are handled in a separate queue.

==2011-10-06==
Attendees: Jim, Tina, Nicole, Jeff, Nicole, Jeremy, Mark

Agenda:
*Slicer user experience in AMIGO has been positive. When can we plan to start using Slicer4?
**Dec 1st is when we should try out Slicer4 in AMIGO and specify which features are missing
**Feb 1st is the target date for adding those features by (pending Steve weighing in)
*Nicole and Jim discussed crosshairs in Slicer4, wrt displayable managers (see Annotations/MRMLDisplayableManager for some more examples) (look in qSlicerMainWindow for examples of connect)
*next thursday is the NCIGT workshop in Arlington VA.

== 2011-09-29 ==

Attendees: Jim, Nicole, Mark

Agenda:

Everyone else must be finishing their Slicer4 issues...

== 2011-09-22 ==

Attendees: Jim, Steve, Tina, Mark, Jeff

Agenda:

*Slicer Tutorials scheduled for Szeged, Hungary next week (Steve)
*[http://www.ncigt.org/pages/IGT_Workshop_2011 IGT workshop in Arlington, VA October 12-13, 2011]
*MICCAI Update (from anyone who attended)

== 2011-09-15 ==
Attendees: Jim, Ron, Steve, J2, Nicole, Mark, Jeff, Tina

== 2011-09-08 ==
Attendees: Ron, Steve, Stephen, Mark, Nicole, JC, J2, Tina, Dominik, Zach Mullen,
*Status Update on Extensions
*[[Events:_DTI_Tractography_Challenge_MICCAI_2011|Tractography Workshop at MICCAI]]
* Documentation
** CLI's XML
** ITK Modules
** [[2011_Slicer4-Documentation-Sprint|Oct 20 documentation event]]
* Data Transfer
** DICOM Module (in experimental)
** Data consolidation
*** Tutorials (powerpoint)
*** Image (non-dicom)
*** Upload/download
** DICOM Load Speeds
<pre>
MANIX CASE 40

DICOM Load 60 10

NRRD Load 4 2

Slicer 4 nightly mac 2011-09-02 (release build)
</pre>

==2011-09-01==

* Attendees: Mark, Jim, Nicole, Steve, Hans, Stephen

* ITKv4 DICOM. DCMTK plan. Extend schedule. Get DCMTK to build as an external project. SCU and SCP classes have been added to DCMTK 3.6. Make ITK examples that would listen using DCMTK and the process data with ITK. They are not taking on the ownership of DicomToNrrd.
* What about DicomToNrrd? Should it be cleaned up using straight ITK, GDCM, DCMTK, CTK, ...? Hans and Mark will reassess and report back.
* Python mmap availability in Slicer is a blocker for Nipype

==2011-08-25==

* Attendees: Ron, Steve, Daniel, Mark, Jim, Nicole, Julien, Hans

* Topics:
** Review the status of [[Events:Slicer4-Review-07-2011#RSNA_2011_Targeted_Objectives|RSNA targeted action items for Slicer 4]]
** Annotations module goals
** (if time allows) Review of new wiki-module documentation process proposed by JC.
* Notes: (One month until RSNA freeze happens)
** GUI: Need to agree on moc-up of Slicer Views
** Volume Rendering: Started. Working on GPU Memory and Transfer Function.
** Models: Mostly done.
** Editor: "Seems straightforward"
** Welcome Module: Not yet started
** Volumes Module: Can drop some features. Still slow. Unknown time required - risks.
** Tractography: Going well - done, but tweaks
** Sceneview: Might not be possible as scoped - Ron/Nicole to discuss offline
** Annotation: Appearance of annotations, appearance of module, ... - may need to scale-back. Limited resources>
*** See [[Projects:ARRA:miAnnotation:Feedback#General_Changes_.28Target_for_RSNA_release.29 | notes from related meeting]]
** Documentation: JC
** Linking and compare view: Linking - Base behavior in-place; spreading capabilities. Compare-view
** ROIs: going well
** Diffusion MRI: Making good progress
** Hierarchies: Dealing with Qt bug. Annotations need work.
** VTK Bug Fixes: Fixes are in VTK. Remaining aren't critical now (text and bi-dim dropped for RSNA release).
** CTK-DICOM Widget: Data - Almost (3/4 done) Widget - needs testing and packaging
** Optimized displayable manager: Progress being made - backburner project
** Brainsfit: Being integrated. Doesn't work on windows (dll weirdness). Bundling on mac - installation not working.
*** Too complex/unclear how to build external module that doesn't become locked to Slicer
** Annotation Speedup: Coming along - keeping it simple for first implementation
** Extensions: Keeping the number small - enabled on dashboard - just waiting for green dashboard
** Web infrastructure and documentation: wiki templates

==2011-08-18==

Attendees:

*Slicer 4 documentation: [http://wiki.slicer.org/slicerWiki/index.php/Documentation-4.0 See here] and [http://wiki.slicer.org/slicerWiki/index.php/Module:EndUserDocumentationTemplate-4.0 here].
* tables and charts in Slicer (Ron)
**We need a viewer as a container for spreadsheets and charts.
**three initial use case scenarios:
# sampling across time in a time series: single pixel, small area
# label statistics: simple descriptive statistics derived from the gray scale image underlying a label map with multiple labels
#statistics along tracts in tractography
* mrml nodes for workflows (Stephen)
** perhaps a mrml node that contains a database.

* Discussion
** For now we will try using the scripted module node and rely on the keyword/value (where value is a string)
** beyond that there are several options for structuring data, but they may need to be driven by concrete use cases
*** possibly HDF5, sqlite, or other bulk data storage data structures
* Volume rendering transfer function - needs antialiasing

==2011-08-11==

Attendees: Ron, Steve, Stephen, Tina, Nicole, Daniel, Mark

*http://www.slicer.org/slicerWiki/index.php/Documentation-4.0

==2011-08-04==

Attendees: Stephen, Mark, Nicole, Tina, Ron

Agenda:
* hans' request re. github/svn pull. (nicole). supported way to do is an svn checkin (Stephen).

==2011-07-28==
Attendees:

Jean-Christophe Fillion-Robin, Sharp, Gregory C., Bill Lorensen, Andriy Fedorov, Dominik Meier, Dominique Belhachemi, Matt McCormick, Mark Scully, Ron Kikinis, Steve Pieper, Demian Wassermann, Tina Kapur, Luping Fang, Hans Johnson

Agenda:
*Moving from ITK3 to [http://www.vtk.org/Wiki/ITK#ITK_Version_4 ITK4]
**Impact to the developer community by the changes in features, API, algorithms
**[[Events:Slicer4-Review-07-2011#RSNA_2011_Targeted_Objectives|Planned Slicer 4.0 release at RSNA 2011]]
**Brainsfit in Slicer4
**[[2011_Winter_Project_Week:_Slicer4-ITK4_Continuous_Integration|Continous Integration of Slicer 4 and ITK 4]]: Some existing work by Bill Lorensen

Decisions:
*RSNA version of Slicer4 will be be based on ITKv3
*January version of Slicer4 will be based on ITKv4
*A parallel build of Slicer4 will be possible during this time frame. There is a possibility that staticly linked executables based on ITKv4 will be made available even when Slicer4 is built with ITKv3
*Ron confirmed his desire to reduce the amount of redundancy in the modules that are available in Slicer4. Hans offered to find redundant versions of tools, and reduce the redundancy.
*There was a discussion about revisiting the IO enhancement that would help reduce memory copy in ITK for performance reasons. There may be other benefits in to the NRRD/NiFTi and other image IO readers that currently copy memory.
**See: [https://github.com/Slicer/ITK/commit/12349021b152ac6546c2caf09bbbee4266baddad]
**See also [http://www.slicer.org/slicerWiki/index.php/ITKv4_Migration_plan#Custom_MetaIO_in_SlicerITK]

==2011-07-15==
Agenda:

* Open Source Software Competition in Korea: http://www.ossaward.org/index.php
* SPL-related web services will be down until tomorrow (mailing lists, sites, wikis, bug tracker...). Slicer svn will remain up (it is hosted at Kitware)

==2011-07-07==
Attendees: Steve, Ron, Luping, Jim, Stephen

* Jim is meeting with Andrey at GE about the prostate compare view use cases
* Discussion of ongoing slicer4 porting issues
** packaging on mac
** scripted displayble manager

==2011-06-30==
Attendees: Steve, Stephen, Tina, Nicole, Daniel, JC, J2, Ron

* Discuss Slicer release schedule (slicer4 and [http://www.slicer.org/slicerWiki/index.php/Slicer3:3.6_Final_Issues slicer 3.6.4])
**Target Slicer product release for RSNA
**That means end of September at latest, so that there is time to work on documentation, training modules and testing/debugging.
**[[Events:Slicer4-Review-07-2011|Slicer4 Sprint planned for July 19-20 in Boston]]

==2011-06-23==

No phone call due to [[2011_Summer_Project_Week|Project Week]].

==2011-06-16==
Attendees: Xiadong, Tina, Marc, Nicole, Daniel (UPenn), Mohasen, Luping (SPL)

*Working meeting to do documentation: http://www.slicer.org/slicerWiki/index.php/Slicer4:Developers
** [http://www.slicer.org/slicerWiki/index.php/Slicer4:SceneViewsModule Scene Views] updated
** [http://www.slicer.org/slicerWiki/index.php/Slicer4:EMSegment EMSegment] updated
** [http://www.slicer.org/slicerWiki/index.php/Slicer4:VMTK VMTK] updated

==2011-06-09==
Attendees: Jim, Xiadong, Sonia, Dominik, Dominique, Andreas, Ron, Tina, Nicole, Stephen, Mohasen, Mark Scully, Drew Rotham, Steve Pieper

Agenda:
*[http://www.na-mic.org/Wiki/index.php/Summer_2011_Tutorial_Contest 2011 Summer 2011 Tutorial contest ]dead-line extended until June 13
*DICOM projects at summer project week:
** Networking: putting ctk/dcmtk into slicer4; use case scenarios (Nicole, Steve, Noby, +?)
** ITKv4 DICOM Support: what features will be available? (Drew, Steve, Dan, Bill, +?)
** DICOMRT: mapping between RT/ITK/Slicer datastructures (Greg, Steve, Luis)
** DWI DICOM: what will we do without Xiaodong?!? (Xiaodong, Jim, Hans, Demian)
** other topics?
*Discuss the structure of Slicer 4 documentation in preparation for next week [http://wiki.slicer.org/slicerWiki/index.php/Documentation-4.0 Slicer 4 documentation placeholder]
*Agenda for next week will be to have a working meeting where appropriate people join the call and spend the hour on Slicer 4 documentation in preparation for project week http://www.slicer.org/slicerWiki/index.php/Slicer4:Developers

==2011-06-02==

Attendees: Jim, Tina, Steve, Stephen, Demian, Szymon, Anthony Blumsfield, Xiaodong, Nicole, Julien, Suarez, Hans Johnson, Mohasen (VA Hospital), Lauren O'Donnell

Agenda:
*DTI projects at summer project week:
**Tractography Projects: http://wiki.slicer.org/slicerWiki/index.php/Slicer4:Diffusion#Features_to_be_addressed_before_the_Summer_NA-MIC_meeting
**http://wiki.na-mic.org/Wiki/index.php/2011_Summer_Project_Week#Projects
*Szymon (EPFL)
**OpenIGT interface Slicer and lab robot
*Anthony
**Spine segmentation project
*Mohasen
**

== 2011-05-26==

Attendees: Junichi, Tina, Tamas, Tamas, Stephen, Jim, Noby, Peter Kazanzies, Ehsan Azimi, Greg Fischer, Hao, Suarez, Csaba

* OpenIGTLink at Project Week

==2011-05-19==
Attendee: Jim, Steve, Dominik, Nicole, Xiaodong, Ross, Marc, Tina, Chiara Carminati (Milan), Adrian(MIT), Ramesh(MIT), Clement (UNC), Nadya (MGH)

Agenda:

*http://wiki.na-mic.org/Wiki/index.php/2011_Summer_Project_Week
*openIGTLink discussion next week.

==2011-05-12==

Attendees: Tina, Steve, Allen, Clement, Yi, Ivan, Yi Fi Lou, Jim, Stephen, Mark, Nicole,

Algorithm core participants discuss project week.
* RSS as Editor module
* Mass Spect for Brain Tumors (GaTech, NCIGT, BWH collaboration)
* Head and Neck cancer bone registration
* Multi-modality image registration

==2011-05-05==

No t-con.

==2011-04-28==

Agenda:

*Summer Project Week Kickoff -- Engineering Projects
**http://wiki.na-mic.org/Wiki/index.php/2011_Summer_Project_Week

==2011-04-21==
Attendees: Steve, Tina, Julien, Xiaodong, Dominik, Marc, Nicole, Dan, Danielle

Agenda:
*Slicer4 windows build question (Steve)
*MGH DBP discussion with Greg Sharp about multilayer treatment plans (Steve).
*visualizing deformation fields via RGB or vector fields via tensor image (Dominik, Steve)
*Since we had some time today, we did a pre-kickoff discussion of engineering projects: [[2011_Summer_Project_Week#Projects]]

==2011-04-14==
Attendees:

Agenda:

* Continue Slicer4 discussion
** Can schedule another call with Extension developers once the Factory is up and running with example extensions - http://www.na-mic.org/Wiki/index.php/2011_Winter_Project_Week:Breakout_Slicer#Extensions
** Any objection to removing all KWWidget code from slicer4 svn?
*** Jc: Option Slicer_BUILD_KWWIDGETS is not supported anymore (it means the build system has been cleaned already) Module and GUI folder code are still here though
** Wrapping Module code (MRML and Logic) in python
*** Jc: Already functional. Need to make wrapping works when module are build as extension
*** VTK classes associated with module should be properly exposed in python.
** Check out "what changed?" and "multivolume containers" in the [http://www.slicer.org/slicerWiki/index.php/Slicer4:Developers#Projects list of Slicer 4 projects].
** Speed, Speed, Speed
*http://wiki.slicer.org/slicerWiki/index.php/Slicer4:VisualBlog

==2011-04-07==
Attendees: Jim, Steve, Tina, Dominik, Daniel, Nicole, JC, Suares, Demian, Kilian, Stephen, Andras, Tamas, Marc, Julien Finet, Danielle P.

Agenda:

* Slicer4
** Progress on Modules? Review and update of: http://www.na-mic.org/Wiki/index.php/2011_Winter_Project_Week:Breakout_Slicer
*** See comments associated with each modules on 2011_Winter_Project_Week:Breakout_Slicer page
** Any objection to removing all KWWidget code from slicer4 svn?
*** Jc: Option Slicer_BUILD_KWWIDGETS is not supported anymore (it means the build system has been cleaned already) Module and GUI folder code are still here though
** Wrapping Module code (MRML and Logic) in python
*** Jc: Already functional. Need to make wrapping works when module are build as extension
*** VTK classes associated with module should be properly exposed in python.
** Check out "what changed?" and "multivolume containers" in the [http://www.slicer.org/slicerWiki/index.php/Slicer4:Developers#Projects list of Slicer 4 projects].
** Speed, Speed, Speed

==2011-03-24==
Attendees: Steve, Jim, Ann, Tina, Daniel, Suares, Marc, Jack, Nicole, Dominique, Ron

Agenda:

*Scientific Progress Report Discussion (Ann Adams will join at 3pm for 20 minutes)
* http://wiki.na-mic.org/Wiki/index.php/2011-Challenge:Segment-a-spine

==2011-03-24==
Attendees: Jim, Ron, Tina, Dominik, Dominique, Marc, Hans, Daniel, Nicole, Curt, Julien

* Slicer4 layouts - [[Media:FirstCompareViewInSlicer4.png|Hey a CompareView]]
* http://wiki.slicer.org/slicerWiki/index.php/Slicer3:UIDesign:WorkingProblems:LinkedControls
* http://wiki.slicer.org/slicerWiki/index.php/Slicer4:MultiVolumeContainer
* Licensing Question: CMTK/Brainsfit/

==2011-03-17==
Attendees: Jim, Ron, Marc, Tina, Nicole, Xiaodong, Greg, Dave Partika, Julien Finet

Agenda:
*Slicer 3.6.3: 64 bit versions, extensions
*the default location for a lot of slicer things is the user home directory. This should be changed. It causes problems in the SPL.
**where to put it, how to initiate?
*saving Slicer 4 mrml scenes as secondary capture (Ron)
**I would like to be able to save an entire scene as a [http://www.medicalconnections.co.uk/wiki/Creating_Secondary_Capture_Images dicom secondary capture]. This would allow to use accessible pacs systems as repositories for slicer scenes
**is there a way to incorporate thumbnails and descriptions from the new sceneviews?
*Slicer3 linked controls
** [http://www.slicer.org/slicerWiki/index.php/Slicer3:UIDesign:WorkingProblems:LinkedControls#cite_note-0 Jim's notes]
** [http://www.na-mic.org/Bug/view.php?id=1117 bug 117]

Notes:
* Dave P will build Windows builds of Slicer and extensions (a version without numpy, make a release note) and Steve will upload. Also the darwin, need to match svn version
* Default location: ask user for not home dir directory if default is not set
** related bugs: [http://www.na-mic.org/Bug/view.php?id=598 598]
* Secondary capture to interact with PACS
** tcon before project week with Jim, Nicole, Wendy, Steve to talk about infrastructure
* Linked controls
** Scroll wheel and arrows after Steve/Nicole's implementation of the link/orientation flag only scroll the current slice viewer and the other viewers with the same orientation, need more feedback from users/Andrey
** use cases between move all slices by copying this slices's RAS matrix to the other slice nodes, and linked increment slice that moves the other slices by an incremental distance
** reformat mode and linking. If in compare view mode and change one of multiple reformat slices, the other reformatted slice views will jump to that
** proposal: link some mode, so have more granularity than all or none (currently do have a one slice link toggle key)
*** reserve some link states so can by default link certain slices
* Ron to Xiaodong: use HAMMER on new brain atlas? not tried yet

==2011-03-10==

Attendees: Jim, Steve, Mark S., Nicole, Tina

Agenda:
* 3.6.4 release planning discussion [http://www.slicer.org/slicerWiki/index.php/Slicer3:3.6_Final_Issues]
** In particular, fix for the linked slice views [http://www.na-mic.org/Bug/view.php?id=1115] (see also [http://www.na-mic.org/Bug/view.php?id=1003 1003])
** pan mode resets slice orientation ([http://www.na-mic.org/Bug/view.php?id=1117 bug #1117])
** What steps should be used for testing fixes for these bugs?
*** Are all use cases covered in currently [http://www.slicer.org/slicerWiki/index.php/Modules:MainApplicationGUI-Documentation-3.6#Linking_Control_of_Slice_Viewers documented behavior]?
***Show hide reformat widget behavior should incorporate the Michal Depa/Steve Pieper modifcations for linked views with reformat widget.
*** What optimizations (delayed updates) are we expected in for situations like compare view?
**when linked views are in the same location and visible, there are artifacts in the 3d viewer.
* More flexibility in the names of the results of CLI's. It would be good to have the ability to incorporate:
**Source volume name
**Module name
**some important parameters

Notes:
* linked slice views: Jim will write up a wiki page describing the expected behaviour, Steve and Nicole will debug
* CLI names: Jim says "yes"
* CLI compilation with separated header files: Jim, Steve, Mark to look into this via webex

==2011-03-03==

Attendees: Steve, Nicole, Jim, Andrey, Suarez, Ron, Stephen A., Daniel H, Dominique B., Xioadong, Greg Sharp, Mark S, Dominik, Hans

Agenda:
* C++/C wrapping of modules
** Hans and Greg figured out what was going wrong. In BRAINS tools they did a trick to get around Bill's trick. It takes 8 minutes to build BRAINSfit, to break it down into smaller compilation units and test it using ITK testing framework. It has a thin wrapper around program to add comparator functions. BRAINSfit is a small 3 line wrapper around BRAINS fit primary that takes argc and argv and includes generated header file. You can't include CLP header file in both compilation units since functions are defined in header file. See error at link time. If you put the right ifdef compiling for slicer and module description is defined you can make it work. Hans would like to see the CLP broken apart into a compile until and a header unit. Jim: harder to build and link - but is done through macros. Could have a test before include CLP.h. Hans: wants to be able to include the .h file in every file. Change: now would have to write a programCLP.h and programCLP.cxx.
** definitely needs to be done in Slicer4, tbd in Slicer3 (Hans using Slicer3 in his class).
*** the add executable, add library lines macros would need to be touched, need to link new object file
*** before when build both a shared and a command line module it would have to rebuild all the itk stuff twice, Casey made the change to not require it
*** Steve: came up wrt diffusion modules because they're using vtk nrrd readers that don't know about shared memory pointers
*** Hans: was building itk files three times for exec, lib, testing
** Jim will take a look at what breaks when try to split it out, code generation is easy, the add_executable will be a bit tricky
** Hans: suggests adding the .cxx to the GenerateCLP macro that defines the .h, to use in the CMakeLists. Hans will do the changes to all the execution modules that need to be changed once the infrastructure is changed (or not).
** One BRAINSfit test failing: any multi threaded mutual information code is suspect to the bug that they found. Quick fix: restrict to one thread, huge slow down (2-4x). Bug is in the Mattes mutual information optimize metric (?) in the registration framework for certain number of threads (4,7, etc). Stephen A will look at it after March 9.
* Annotation module widget priority for ROI nodes
** Ron, Daniel agrees to put it as higher than the bidimensional widget
** ROI widget is in the critical path for the volume rendering module, as well as others
** Reformat widget to priority list? will require taking something out. Will is working on a new widget, wait on that. Andrey says the reformat widget will be useful in crop volume as well. General Slicer4 widget (was integrated in the 3d viewer in Slicer3). Nicole is taking on the integration of the vtk widgets.
* Contributing modules to Slicer4 (policy review)
** by default new modules should got to an external repository (NITRC, external module) and remain there for a while until whole module goes into Slicer4 if it's determined to be core functionality
** Slicer4 core to remail lean, but external modules to be first class citizens.
** Documentation requirements, building and testing on the factory machine every night.
** If a new module fails it shouldn't break Slicer4 building or running
** Timeline on extension mechanism in Slicer4?
*** Steve wanted to get the base nightly builds working first, but need to get the extensions built nightly asap
*** new feature in next release of cdash and cmake, ctest upload command to upload binaries, can get a list of uploads from dashboard
*** harvest the information from the cdash dashboard and make it available to the extension manager rather than have the extension manager communicate directly with the (sometimes slow) dashboards. Only let uploads come from factory machines. Use VMs to run test code.
*** Steve will be the gatekeeper to allow code to be built and tested on the factory for now
**** flag for if it gets redistributed, critical/non critical build
**** allow to build locally but submit to main slicer dashboard (no code upload), already supported via Experimental
** Greg: wants to be able to build a bug fixed version of an extension for an old release (limited support for it)

==2011-02-10==

Attendees: Jim, Mark, Tina, Nicole, Dan

Agenda:
*Updates from ITK meeting
*http://wiki.na-mic.org/Wiki/index.php/2011_Progress_Report#Scientific_Report_Timeline
**Heads up given to everyone that progress report is due on wiki by mid April

==2011-02-03==
Attendees: Suares, Dominik, Kilian, Dominique, Nicole, Daniel, Stephen, Tina, Xiaodong

Agenda:
*ITK meeting in progress in Boston. Steve and Jim attending it.
*http://wiki.slicer.org/slicerWiki/index.php/Documentation-4.0
**Automatic documentation generation options are being explored at Kitware. Stephen will report as progress is made.
*http://wiki.na-mic.org/Wiki/index.php/2011_Progress_Report#Scientific_Report_Timeline
**Heads up given to everyone that progress report is due on wiki by mid April

==2011-01-27==

No tcon today.

==2011-01-20==

Attendees: Xiaodong, Wendy, Tina, Mark, Nicole, Dominik, Daniel,

Agenda

* [http://www.slicer.org/slicerWiki/index.php/Slicer3:3.6_Final_Issues Slicer 3.6.3]
* http://wiki.na-mic.org/Wiki/index.php/2011_Winter_Project_Week
* http://wiki.na-mic.org/Wiki/index.php/Resources#Active_Job_Openings

==2011-01-06==

Attendees: Steve, Stephen, Jim, Ron, Tina, Dan Marcus, Xiaodong

Agenda:

*News: DCMTK 3.6 was released today
* http://wiki.na-mic.org/Wiki/index.php/2011_Winter_Project_Week#Projects
* Command line module logic, supporting multiple argument for images in Slicer3/4
* Discussion of ITK support for large (greater than 4Gig) image volumes on win64. This will be further investigated at project week. It is only one of several issues to be researched as part of porting slicer3 and slicer4 to win64. Dave Partyka has a [[2011_Winter_Project_Week:64bit_Windows_Builds|project to work on this]] at project week.

Projects:ARRA:SlicerUI

2011-11-05T22:23:04Z

Finetjul: /* Progress */

[[Projects:ARRASuplements|Back to Slicer ARRA home page]]
= Aim =
The effective visualization, data processing, analysis and interaction of medical images and ancillary data is a complex process requiring sophisticated and efficient software tools. Further, the development of new tools requires a productive and widely supported software environment. In such an environment, the human-computer interface plays a critical role in the overall effectiveness of the software tools. To this end, the Slicer graphical user interface (GUI) is to be significantly enhanced by the adoption of the standard and widely used Qt GUI toolkit. Qt has recently changed its licensing terms, meaning that it is now compatible with Slicer's commitment to open systems. Further, Qt is now recognized as the defacto standard, cross-platform GUI toolkit, offering superior performance, capability and productivity.

= Research Plan =
Slicer currently has an extensive GUI that consists of three major, logical parts: 1) the core, 2) command-line modules, and 3) modules. The research plan recognizes this organization, and will address the GUI development accordingly.
* The first step is to replace the core GUI with Qt. This will demand some initial design and planning, including integration of various Qt tools such as Qt Designer.
* Second, the command-line modules automatically generate their GUI from an XML description of the module. This will require modification so that Qt GUIs are generated (instead of the current KWWidgets).
* Finally, select, critical modules such as EM Segmenter will be reworked to use Qt widgets.
*Most of this work will occur in the first year, with completion of the critical modules expected early in the first quarter of the second year.
*After this, the research plan switches to training and dissemination of Qt-related technology so that the broader Slicer community can participate in the transition of modules to the Qt GUI.
*The key to this plan is to switch the core and command-line modules as fast as possible since we want to minimize disruption to the Slicer community, and to support continued Slicer development.
=Key Personnel=
* William Schroeder, Ph.D., 8%
* Stephen Aylward, Ph.D., 5%
* Jean-Christophe FILLION-ROBIN, 50%
* Julien Finet, 50%

=Meetings=
* Regular meeting TCons every other Tuesday at 2:00pm

=Links=
*[http://wiki.slicer.org/slicerWiki/index.php/Slicer4:QtPort QtSlicer Wiki]
*[http://wiki.slicer.org/slicerWiki/index.php/Slicer4:QtPort/Gallery QtSlicer Gallery]
*[http://www.slicer.org/slicerWiki/index.php/Qt_in_Slicer3 Preliminary work]

=Progress=
* November 2nd, 2011
** Look&Feel improvements
*** Improve rendering update frame rate
** Under the hood
*** Cleanup volume rendering code
* October 26th, 2011
** Look&Feel improvements
*** Add option to synchronize volume rendering transfer functions with Volumes module
** Under the hood
*** Redesign API for logics and diplayable managers
** Extensions
*** Support BrainsTools as loadable modules.
* October 19th, 2011
** Look&Feel improvements
*** Add threshold sliders in volume rendering module
** Under the hood
*** Scene models don't require instantaneous synchronization of mrml scene.
** Extensions
*** Support EMSegment as loadable modules.
* October 12th, 2011
** Look&Feel improvements
*** Better support for level of detail(LOD) with volume rendering
*** More user-friendly transfer function editor
* October 5th, 2011
** Look&Feel improvements
** Under the hood
*** Automatic loading of python libraries (part 2)
*** Volume Rendering face-lift
** Extensions
*** Integrate new ChangeTracker module
* September 28th, 2011
** Look&Feel improvements
*** Add [http://www.commontk.org/index.php/File:ExpandButton.png expand button] to show/hide more buttons
*** Improve color transfer function editor
*** Support for color gradients in 3D view
** Under the hood
*** Automatic loading of python libraries (part 2)
** Extensions
*** Add access of Slicer environment to CLIs
* September 21th, 2011
** Look&Feel improvements
*** Improve the screenshot dialogs (no blinking, dynamic preview...)
*** Add favorites in file dialogs
*** Cleanup menu (File/Edit/Views/Help)
** Under the hood
*** Support gcc 4.6
*** Read .vp files
* September 14th, 2011
** Look&Feel improvement
*** Facelift for the central views layout
*** Transfer function editors usability (add borders to select points)
** Under the hood
*** Fasten annotation rendering
*** Stabilize demand driven filter pipeline
* September 7th, 2011
** Under the hood
*** Fix demand driven pipeline when combining polydata filters with image data filters
** Look&Feel improvement
*** Reorganize icons in the slice view controller
*** Work on the transfer function editor
** Extensions
*** Support EMSegment extension
* August 31st, 2011
** Look&Feel improvement:
*** Ability to select multiple files in the "Add Volume" dialog
*** Improve [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerModuleSelectorToolBar-SearchModule.png module search] in the module search bar
* August 24th, 2011
** Under the hood:
*** Use a true VTK demand driven pipeline architecture. It makes the code more stable and robust
** Look&Feel improvement:
*** Add search bar in the [http://wiki.slicer.org/slicerWiki/index.php/File:QMRMLColorPickerDialog.png color picker dialog]
** Modules
*** Added Volume Rendering settings page
* August 17th, 2011
** Look&Feel improvement:
*** Blue title bar for 3D views
*** Searchable module selector
* August 10th, 2011
** Look&Feel improvement:
*** Color and Opacity column in Models module
** Under the hood:
*** Reorganize Qt Scene models
*** Various bug fixes
* August 3rd, 2011
** Look&Feel improvement:
*** [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerModelsModule.png Models module] facelift
*** Slice/3D view popup
** Fixing mac build of DCMTK and tweaking GUI
* July 27th, 2011
** Support extensions with Superbuild
** Look&Feek improvement:
*** Slice/3D view popup
** Debugging DCMTK and numerous reports from users
* July 20th, 2011
** Event: [[Events:Slicer4-Review-07-2011|Sprint review]] event attendance
* July 13th, 2011
** Build system
*** Fix BFD dependency issues
** Look&Feel improvement:
*** Work on prototype for Slice view controller toolbar.
* July 6th, 2011
** Speed improvement for slice sliders in Windows
** Look&Feel improvement:
*** Transfer function editors
*** Popup menu in the Window/Level widget
*** Color dialog
* June 29th, 2011
** Widgets
*** New: [http://wiki.slicer.org/slicerWiki/index.php/File:qSlicerPresetComboBox.png Preset selector]
** Model visibility can now be controlled from the tree view (Models module).
* June 22th, 2011
** Release: [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:QtPort/Releases#Slicer_4.0_gamma Slicer 4.0 gamma RC2]
** Event: [http://www.na-mic.org/Wiki/index.php/2011_Summer_Project_Week NA-MIC 2011 Summer Project week]
** Modules:
*** New: EventBroker module for debug purpose
*** Editor: Support extensions
* June 15th, 2011
** Release: [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:QtPort/Releases#Slicer_4.0_gamma Slicer 4.0 gamma RC1]
** Speed improvement for color table generations
* June 8th, 2011
** Work on Module Extension retrieval from CDash
** Add [http://wiki.slicer.org/slicerWiki/index.php/File:SlicerWithVolumeRendering.png Volume Rendering] module.
*** Support generalized [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerVolumeRenderingModule-DualView.png Dual-View]
** Preparation for Slicer 4.0 gamma RC1
* June 1st, 2011
** More work on the Mac bundle
** Work on the Volume Rendering module
** Widgets:
*** Add [http://www.commontk.org/index.php/File:CtkCheckableComboBox.png ctkCheckableComboBox] and [http://wiki.slicer.org/slicerWiki/index.php/File:QMRMLCheckableComboBox.png qMRMLCheckableComboBox]
* May 26th, 2011
** Reviewing 64bit Windows and Mac packaging code (WIP)
** Participated in release of MIDAS Desktop which has hooks for Slicer (WIP)
* May 19th, 2011
** Updated CTK-based launcher for Macs
* May 11th, 2011
** Updated CDash for managing disk usage (purging old packages) and for providing easy access to uploaded packages
* May 4th, 2011
** Enable 64bit packages on Mac (WIP)
** Export Slicer libraries information for external module configuration
** Widgets:
*** Add [http://www.commontk.org/index.php/File:CtkVTKMagnifyView.png ctkVTKMagnifyView] to magnify the area under the mouse cursor in 2D slices
** Work on Transfer Function editor
* April 27, 2011
** Find_Package(Slicer) is now available
** Finalize work on Magnify view
** Work on the Qt wrapper around the VTK transfer function editor
* April 20, 2011
** Work on external modules build system (FIND_PACKAGE(Slicer))
** Work on Magnify view of area under mouse cursor for 2D slice views
** Work on Transfer Function editor
* April 13, 2011
** Improvement of slicer automatic build submission system:
*** Installers can be generated on a daily basis and be available for download without tedious system administration work ..
** "Cleaning and simplification" of slicer build system so that Slicer extension could be built and tested.
** Add [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerDiffusionWeightedVolumeDisplayWidget.png Diffusion Weighted Volume display properties panel]
* April 06, 2011
** Add dynamic property support to layout mechanism
** Tune and redesign the logics behaviors and displayable managers
** Fixup documentation and packages
* March 30, 2011
** Integration of the [http://www.commontk.org/index.php/File:CtkErrorLogWidget.png errors & logs dialog]
** Add progress when loading files
** Bug fixes and preparation of a new release
* March 23, 2011
** Added support for [http://wiki.slicer.org/slicerWiki/index.php/File:SlicerWithDTI.png DTI display] in the Volumes Module
** Widgets
*** [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerDiffusionTensorVolumeDisplayWidget.png Diffusion Tensor Volume Display widget]
*** [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerDTISliceDisplayWidget.png Diffusion Tensor Slice Display widget]
** Work on the error/status/log dialog
* March 17, 2011
** Work on the DTI display properties in the Volumes module
* March 10, 2011
** Assisting on Slicer 3.6.3 release
** Support multiple 3D views in the layouts
* March 3, 2011
** Assisting on Slicer 3.6.3 release
** Add new layouts
* February 23, 2011
** Support Command line executables
** Work on an Error Log dialog to redirect all the outputs generated by Slicer or CLIs
* February 16, 2011
** Redesign the layout mechanism in Slicer (XML based).
* February 9, 2011
** [http://www.commontk.org/index.php/CTK-Hackfest-Feb-2011 CTK hackfest]: DICOM Query/Retrieve widgets, application hosting, event bus...
* February 2, 2011
** Preparing for CTK hackfest: tcons, presentations, and packaging for CTK
** Upgrading Slicer4 dashboards with Dave P in support of testing modules
** Investigating automated binary upload
* January 28, 2011
** Extending support for modules and workflows based on Python
** Assisting in the integration of the Annotation module into Slicer4
* January 19, 2011
** Bug fixing based on feedbacks from [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:QtPort/Releases Slicer 4.0 beta-2]
* January 12, 2011
** Released [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:QtPort/Releases Slicer 4.0 beta2]
** [[AHM_2011|All Hands Meeting 2011]] in Salt Lake City
** Presentation of [[2011_Winter_Project_Week:Breakout_Slicer|the status of the port]] and [[2011_Winter_Project_Week:Breakout_Slicer#Afternoon_Qt_Loadable_Module_Tutorial|step-by-step tutorials]]
* January 5, 2011
** Tweaking and bug fixing based on feedbacks from Slicer 4.0 beta
** Preparation for Slicer 4.0 beta-2 and [[All Hands Meeting 2011]]
** New settings: Select "Home" module, show text under toolbar icons
** Widgets: Rename nodes from node selector, delete nodes from Data module, corner annotations.
* December 29, 2010
** Holiday break
* December 22, 2010
** Holiday break
* December 15, 2010
** Bug fixing and packaging for Slicer 4.0 beta release
* December 8, 2010
** Support Scripted (Python) modules
** New module: Endoscopy
** New dialogs
*** [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerSettingsDialog.png Application settings]
*** [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerExtensionsWizard.png Extensions Management]
* December 1, 2010
** New module: [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerModelsModule.png Models module]
** New widget
***[http://wiki.slicer.org/slicerWiki/index.php/File:QMRMLModelInfoWidget.png Model info widget]
***[http://www.commontk.org/index.php/File:CtkMaterialPropertyWidget.png Material property widget]
***[http://wiki.slicer.org/slicerWiki/index.php/File:QMRMLDisplayNodeWidget.png Display node widget]
***[http://wiki.slicer.org/slicerWiki/index.php/File:QMRMLModelDisplayNodeWidget.png Model display node widget]
* November 24, 2010
** New widget: [http://wiki.slicer.org/slicerWiki/index.php/File:QMRMLVolumeInfoWidget.png Volume information widget]
** New dialog: [http://wiki.slicer.org/slicerWiki/index.php/File:QMRMLColorPickerDialog.png Color dialog]
* November 17, 2010
** New widget: [http://wiki.slicer.org/slicerWiki/index.php/File:QMRMLColorTableView.png Color table view]
** New module: [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerColorModuleWidget.png Color module]
* November 10, 2010
** Work on Python scripting
** Add range control and symmetric moves capability in the [http://wiki.slicer.org/slicerWiki/index.php/File:qMRMLWindowLevelWidget.png window level range widget] and threshold widget
** Add [http://www.commontk.org/index.php/File:CtkVTKThumbnailView.png navigation view]
* November 3, 2010
** Add snapshot feature in [http://wiki.slicer.org/slicerWiki/index.php/File:qMRMLThreeDViewsWidget.png Manipulate 3D View toolbar]
** Finished redesign of the internal structure of MRML to Qt scene interface
* October 27, 2010
** Add [http://www.commontk.org/index.php/File:CtkScreenshotDialog.png screenshot dialog]
** Add [http://www.commontk.org/index.php/File:CtkAxesWidget.png axes selection widget]
* October 20, 2010
** Dashboard cleaning (fixed and added more tests)
** Redesign of internal structures (layout manager, scene model...)
* October 13, 2010
** Launcher application: Add support for Macs
** Slicer module description parser ported to Qt (CTK)
* October 6, 2010
** Updating and integrating launcher application
** Revising dashboards to use launcher application
** Continuing to establish tasks and assign priorities for this and related NA-MIC funding
** Collecting bug reports, etc from user community regarding Alpha Release
** Planning vtkWidget and other organizational meetings
* September 29, 2010
** Revising dashboards to use new Slicer4 repository
** Establishing priorities for year 2
* September 22, 2010
** Planned: Re-evaluate priorities for editor module. Perhaps it should go in an earlier release.
** Planned: Host design discussion for vtkWidgets, Editor Module, and CUDA in Slicer Qt for interactive segmentation
** Planned: Consider interactions that can provide intuitive and precise manipulation of and direct the processing of data that spans a wide range of scales in time and space.
* September 15, 2010
** Attending CTK Hackfest in Spain
** Assisting in the integration of Qt Widgets developed for Slicer into the main CTK trunk
** Providing tutorials on software engineering practices used in Slicer Qt development
* September 8, 2010
** Alpha release of Slicer Qt 4 is being packaged
** Final tests being added to improve coverage
** Backporting final set of changes to ITK and VTK releases
* September 1, 2010
** Preparation for Slicer 4.0 alpha: bug fixes, [http://wiki.slicer.org/slicerWiki/index.php/File:SlicerQT-2009-12-10.png cosmetic changes], dashboard cleaning
** Modules
*** Add more features ([http://wiki.slicer.org/slicerWiki/index.php/File:QMRMLColorTableNodeComboBox.png color table chooser], preset buttons) to the [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerVolumesModule.png Volumes module]
** Widgets
*** Added [http://wiki.slicer.org/slicerWiki/index.php/File:QMRMLColorTableNodeComboBox.png a color table node combo box]
** Widgets
*** Add the [http://wiki.slicer.org/slicerWiki/index.php/File:QMRMLThreeDViewsWidget.png toolbar] to control 3D views
* August 25, 2010
*** Support [http://wiki.na-mic.org/Wiki/index.php/File:QMRMLSliceWidget.png Lightbox] in 2D slice views
** Tcl is now interfaced with Python
** Widgets
*** support for [http://www.commontk.org/index.php/File:CtkVTKScalarsToColorsView.png VTK charts with Qt]
*** Add advanced menu in the [http://wiki.slicer.org/slicerWiki/index.php/File:QMRMLSliceWidget.png 2D slice Views]
* August 18, 2010
** Event: Review of the state of Slicer port to Qt: [[QtAugust2010]]
* August 11, 2010
** Integration: Full support of PythonQt (wrapping of custom classes)
** Widgets: Dynamically support sets of different icon size
* August 4, 2010
** ToolBar:
*** Added [http://wiki.slicer.org/slicerWiki/index.php/File:QMRMLSlicesControllerToolBar.png qMRMLSlicesControllerToolBar] to control the red/yellow/green slice displays.
*** Added [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerMouseModeToolBar.png qSlicerMouseModeToolBar] to control the mouse mode (first draft).
*** Added Undo/Redo toolbar
*** Added links Slicer documentation into the menu bar
** Dialogs: Added [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerActionsDialog.png qSlicerActionsDialog] to show the application shortcuts
* July 28, 2010
** Work on improving the design of the interaction between MRML and vtk rendering
** Application: Tweak UI/Style (support smalllarge fonts)
** ToolBar: Added [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerModuleSelectorToolBar.png qSlicerModuleSelectorToolBar]
** Modules: new [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerSliceControllersModule.png qSlicerSliceControllersModule]
* July 21, 2010
** Work on improving the design of the interaction between MRML and vtk rendering
** Application: A big step forward the integration of the [http://wiki.slicer.org/slicerWiki/index.php/File:SlicerQT-2009-12-10.png 3D/2D views in SlicerQT]
** Modules: Added Acknowledgement tab to modules
** Widgets: improved [http://wiki.slicer.org/slicerWiki/index.php/File:QMRMLThreeDView.png qMRMLThreeDView] and [http://wiki.slicer.org/slicerWiki/index.php/File:SlicerQT-2009-12-10.png qMRMLSliceViewWidget]
* July 14, 2010
** Work on improving the design of the interaction between MRML and vtk rendering
** Widgets: Preliminary work on qMRMLColorTableNodeComboBox
** Widgets: Added colors to the slider handles of the [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerROIModule.png ROI module] widgets
* July 7, 2010
** Work on improving the design of the interaction between MRML and vtk rendering
** Modules: [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerDataModule.png Data module] (new)
** Widgets: [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerVolumesIODialog.png ctkFileDialog] to customize QFileDialog
** Dialogs: Added support for selecting files for volumes, models, scalar overlay, color table, fiducial lists and fiber bundles
* June 30, 2010
** Work on improving the design of the interaction between MRML and vtk rendering
** Modules: [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerROIModule.png ROI module] (new) (Data module: WIP)
** Widgets: [http://wiki.slicer.org/slicerWiki/index.php/File:QMRMLROIWidget.png ROI widget] (new)
* June 23, 2010
** [[2010_Summer_Project_Week|2010 Summer Project Week]] ([http://wiki.slicer.org/slicerWiki/index.php/File:QtPortInSlicer.ppt Presentation])
* June 16, 2010
** Preparation for [[2010_Summer_Project_Week|2010 Summer Project Week]]
** Work on the 3D and 2D render widgets
* June 9, 2010
** Work on Slicer Superbuild
** Work on Slicer launcher
*** New launcher (http://github.com/jcfr/CTKAppLauncher)
*** [http://my.cdash.org/index.php?project=CTK&subproject=ctkAppLauncher Dashboard] is setup
*** Code coverage is >85%
** Modules
*** [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerVolumesModule.png qSlicerVolumesModule] integrated an histogram widget (WIP)
* June 2, 2010
** Work on Slicer Superbuild
** Work on Slicer launcher
** Panels
*** [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerSaveDataDialog.png qSlicerSaveDataDialog] now saves scene + data
** Widgets
*** [http://www.commontk.org/index.php/File:CtkRangeSlider.png ctkRangeWidget]: new property - [http://www.commontk.org/docs/html/classctkRangeWidget.html spinBoxAlignment]
*** [http://www.commontk.org/index.php/File:CtkRangeSlider.png ctkRangeWidget]: new feature - the slider between the 2 handles can be drag/drop, it moves both handles at a time.
* May 26, 2010
** Work on Slicer superbuild
** New widgets
*** [http://www.commontk.org/index.php/File:CtkTransferFunctionHistogramItem.png Histogram widget] (still need to be integrated into Slicer)
* May 19, 2010
** Participation of the [http://www.commontk.org/index.php/CTK-Hackfest-May-2010 CTK Meeting]
*** Work on a launcher for Slicer Qt
*** Work on [http://www.commontk.org/index.php/Documentation/ctkTransferFunctionWidget transfer function widget] editors.
* May 12, 2010
** Slicer4 branch has been merged into the trunk (after Slicer3.6 has been created)
** Integration: Superbuild is now working on Windows/Linux for Slicer Qt
** Widgets
***Layout Manager (WIP)
***3D Render View (WIP)
***Slicer View (WIP)
** Dialogs
*** Settings Manager (WIP)
* May 05, 2010
** Integration: Slicer with Qt now supports CMake 2.9 (patch had to be send to the CMake community)
** Widgets
*** 3D Render View (WIP)
*** Minor bug fixes (qMRMLNodeComboBox, ctkSliderSpinboxWidget, ...)
* Apr 28, 2010
** Integration: PythonQt functionality has been ported into CTK (moved out of Slicer)
** Modules
*** WIP: Command Line Modules
** File Dialogs
*** WIP: [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerSaveDataDialog.png qSlicerSaveDataDialog] to save the scene data (UI is complete, logic is missing).
** Widgets
*** NEW: [http://wiki.slicer.org/slicerWiki/index.php/File:CtkDirectoryButton.png ctkDirectoryButton] a button tied to a directory path selector dialog
*** WIP: Render widget
* Apr 21, 2010
** Integration: 100% of CTK widgets have been moved out of Slicer.
** Widgets
*** WIP: [http://wiki.slicer.org/slicerWiki/index.php/File:CtkTransferFunctionWidget.png ctkTransferFunctionWidget] a color transfer function widget editor
* Apr 14, 2010
** Integration: CTK is now linked by Slicer Superbuild (CTK widgets are still in Slicer though).
** File Dialogs
*** [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerDataDialog.png qSlicerDataDialog] has been updated to support specific type options and checkable headers
** Widgets
*** New widgets: [http://wiki.slicer.org/slicerWiki/index.php/File:QCTKCheckableHeaderView.png qCTKCheckableHeaderView] a checkable QHeaderView
* Apr 7, 2010
** File Dialogs
*** New dialog: [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerDataDialog.png qSlicerDataDialog]
** File Readers: more work done in the direction of a flexible IO plugin mechanism
* Apr 1, 2010
** Integration: More work done to move CTK widgets into the CTK repository
** File Dialogs: Preliminary work to port the KWWidgets dialogs to Qt. New dialog: [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerStandardFileDialog.png qSlicerStandardFileDialog].
** File Readers: New architecture to register readers/writers from loadable modules
*** Supported files: *.mrml, *.xml, volumes, models...
* Mar 24, 2010
** Integration: Preparation to move CTK widgets into the [http://github.com/pieper/CTK CTK repository] and link against it
** Widgets
*** New widgets: [http://wiki.slicer.org/slicerWiki/index.php/File:qCTKRangeSlider.png qCTKDoubleRangeSlider], a range slider that supports doubles. [http://wiki.slicer.org/slicerWiki/index.php/File:qCTKRangeWidget.png qCTKRangeWidget], a ready to use qCTKDoubleRangeSlider with linked spinboxes.
* Mar 17, 2010
** Integration: Work on CTK for a smooth integration with Slicer
** Modules: a new module has been ported to Qt: [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerVolumesModule.png Volumes module] (WIP)
** Widgets
*** New widgets: [http://wiki.slicer.org/slicerWiki/index.php/File:QMRMLThresholdVolumeWidget.png qMRMLVolumeThresholdWidget] a widget to select a threshold, [http://wiki.slicer.org/slicerWiki/index.php/File:ctkDICOMModel.png ctkDICOMModel] a model to represents a DICOM database (SQLite).
* Mar 10, 2010
** Integration: CTK now has its own repository, CTK widgets will be moved from Slicer to git CTK
** Widgets:
*** New widgets: [http://wiki.slicer.org/slicerWiki/index.php/File:QCTKNodeComboBox.png qCTKNodeComboBox] replaces qMRMLNodeSelector, [http://wiki.slicer.org/slicerWiki/index.php/File:QMRMLWindowLevelWidget.png qMRMLWindowLevelWidget] to select window/level values
* Mar 03, 2010
** Integration: PythonQt is integrated into Slicer (partial support of Qt widgets)
** Qt Designer: [http://wiki.slicer.org/slicerWiki/index.php/File:Screenshot-Qt_Designer.png added icons to the qCTKWidgets & qMRMLWidgets plugins] to quickly find the right widgets
** Widgets:
*** New widgets: [http://wiki.slicer.org/slicerWiki/index.php/File:QCTKRangeSlider.png qCTKRangeSlider] a slider with 2 handles, qMRMLNodeComboBox replaces qMRMLNodeSelector (no +, - or edit icons) (WIP)
* Feb 24, 2010
** Integration: PythonQt (WIP)
** Widgets:
***Redesign qMRMLNodeSelector to use qMRMLSceneModel (WIP)
***Move the Add/Remove/Edit push buttons of qMRMLNodeSelector under the popup list of nodes (WIP)
** Bug fixes, code cleanup
* Feb 17, 2010
** Integration: Preliminary work for integrating PythonQt
** Widgets:
*** new features: qCTKSliderSpinBoxWidget has a tracking property (valueIsChanging), qCTKMenuButton now directly uses the QMenu from QPushButton
*** new tools: qCTKGroupButton (exclusive button group allowing no button to be selected), qCTKDynamicSpacer (sizePolicy controlled by a slot)
** Bug fixes, code cleanup
* Feb 10, 2010
** Integration of Qt designer into Slicer: the qt application to design module UIs (designer) can now be launch through Slicer: "Slicer3 --launch designer"
** Arguments/Settings: qCTKSettings can store application settings, added classes to parse the application command line arguments: qVTKCommandOptions, qSlicerCoreCommandOptions, qSlicerCommandOptions
** Some module logics have been separated from the KWWidgets modules to be reused by Qt modules: ModelMirror, AtlasCreator, MRAblation, FetchMI...
** Widgets:
*** ported more features from the KWWidgets : qMRMLNodeSelector (support multi node types, attributes, ...),
*** tuned behavior of some widgets, i.e. qCTKSliderSpinBoxWidget:size synchronization of the spinboxes, text right aligned ...
** Testing: qCTKAddRemoveComboBox, qCTKTestApplication, qVTKObject...
* Feb 03, 2010
** Style: QCleanLooksStyle has been choosen to be the default Slicer style
** The module logics in KWWidgets modules can now be reused in Qt modules
** New widgets: [http://wiki.slicer.org/slicerWiki/index.php/File:QCTKMenuButton.png qCTKMenuButton], qMRMLSceneFactoryWidget (for testing MRML widgets in Designer)
** New module ported to Qt: Tractography
* Jan 27, 2010
** Command line modules: finalizing the integration with Slicer.
** Render Widget: Preliminary work has been started (qVTKRenderView)
** New widgets: qMRMLEventLoggerWidget logs all the events generated by a vtkMRMLScene (for debugging only).
** Design improvement: Using feedbacks from slicer developers, we applied changes to correct heavy/unfriendly designs.
** Testing: Added qCTKModelTester, a QT object that can test the correctness of any class deriving from QAbstractItemModel.
* Jan 20, 2010
** New widget: a generic framework for handling MRML objects in list/table/tree widgets has been developped( drag/drop supported, reparenting, scene observers...)
** Quality: compilation warnings have been removed.
** Testing: a skeleton for unit test has been written for each classes
* Jan 13, 2010
** Outcome of the [[AHM_2010|NAMIC All Hands meeting]]
*** 2 new tutorials: [http://wiki.slicer.org/slicerWiki/index.php/File:QtPortInSlicer.ppt Port of Slicer to Qt], [http://wiki.slicer.org/slicerWiki/index.php/File:FirstStepsInQt.ppt First steps with Qt]
*** Slicer with Qt has been successfully compiled on several machines under Linux, Windows and Mac. The [http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Developers:Projects:QtSlicer/Tutorials/CompileWithQt building instructions] have been updated.
*** A few [http://www.cdash.org/CDash/index.php?project=Slicer3 dashboards] have been setup to compile with Qt. We count on you to submit more dashboards.
*** More unit tests have been written
*** 2 new modules have been created with Qt
*** A lot of installation bugs/problems have been resolved
* Jan 07, 2010
** Setup [http://cdash.org/CDash/index.php?project=Slicer3 dashboards] in Qt (Nightly, Continuous and Experimental builds)
** More unary tests added
** [[AHM_2010|NAMIC All Hands meeting]]
*** Presentation of [http://wiki.slicer.org/slicerWiki/index.php/File:QtPortInSlicer.ppt Port of Slicer to Qt] to the Slicer community
*** Workshop provided to help slicer developers to setup a Slicer environment running with Qt.
*** First modules developed by the community
* Dec 30, 2009
** Added support for modules with no corresponding KWWidgets modules: New modules in QT only can now be created.
** Bug fixes on Windows.
* Dec 22, 2009
** Added tests
** Tree widgets: WIP
** Command Line modules: WIP
* Dec 16, 2009
** Modules can now be ported into Qt by the Slicer community. Presentation: [http://wiki.slicer.org/slicerWiki/index.php/File:QtPortInSlicer.ppt Port of Slicer to Qt]
* Dec 9, 2009
** New widgets: [http://wiki.slicer.org/slicerWiki/index.php/File:QMRMLItemModel.png qMRMLItemModel, qMRMLListWidget, qMRMLTreeWidget]
** Screen-casts: [http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Developers:Projects:QtSlicer/Documents videos made for RSNA]
** More work on the CLI modules, [http://wiki.slicer.org/slicerWiki/index.php/File:SlicerQT-2009-12-10.png Slicer Qt only], now compiles on MAC OS X,
* Dec 2, 2009
** Command Line modules integration: First results (UI only)
** Interface between MRML Scene and the Qt (tree, list, table...) widgets: WIP
* Nov 25, 2009
** New Module: [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerWelcomeModule.png Welcome Module]
** New tutorial: [http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Developers:Projects:QtSlicer/Tutorials/QtDesigner Using Qt Designer with CTK & MRML widgets]
** Command Line modules integration: WIP.
* Nov 18, 2009
**New widgets: [http://wiki.slicer.org/slicerWiki/index.php/File:qCTKTreeComboBox.png Tree Combo Box], [http://wiki.slicer.org/slicerWiki/index.php/File:qCTKTreeComboBox.png Node Tree Selector]
**New feature: Support for help: [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerTransformsModuleUI.png example of an help section automatically added into a module]
**Command Line modules integration: WIP.
* Nov 13, 2009
**rework on the [http://wiki.slicer.org/slicerWiki/index.php/File:2009_11_10-qSlicerTransformsModuleUI.png Transforms Module]
**started to work on the Command Line modules integration.
* Nov 6, 2009
** Loadable Modules are now supported.
** Added [http://wiki.slicer.org/slicerWiki/index.php/File:2009_11_06-qCamerasModule.png Cameras Module]
* Oct 30, 2009
** The entire Qt-Slicer code architecture has been reviewed, factorized and simplified. Coding rules have been chosen (not documented yet).
** Documentation: Added a [http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Developers:Projects:QtSlicer/Tutorials/WidgetWriting tutorial to write custom widgets]
* Oct 23, 2009
** New widgets: [http://wiki.slicer.org/slicerWiki/index.php/File:2009_10_23-QCTKCollapsibleWidget.png Collapsible widget], [http://wiki.slicer.org/slicerWiki/index.php/File:2009_10_23-QCTKColorPickerButton.png Color Picker button]
* Oct 16, 2009
** Synchronization between Qt widgets and KWWidget. Move the qt panels when the application is moved on the desktop.
** New widgets: [http://wiki.slicer.org/slicerWiki/index.php/File:2009_10_16-QCTKCoordinatesWidget.png Coordinates widget], [http://wiki.slicer.org/slicerWiki/index.php/File:2009_10_16-QCTKCollapsibleGroupBox.png Collapsible groupbox]
* Oct 9, 2009
** TCon with Julien Finet (J2), Jean-Christophe (JC), Steve, Will, Seb, Stephen, Wendy, Nicole to discuss progress
** Demonstrated new software architecture that simplifies building new modules
** Addressed issues of background color, etc previously raised by Dr. Kikinis [http://wiki.slicer.org/slicerWiki/index.php/File:2009_10_02-QtTransformModule-v2.png QtTransformModule-v2.png]
** New widgets: [http://wiki.slicer.org/slicerWiki/index.php/File:2009_10_09-QMRMLMatrixItem.png Matrix Widget], [http://wiki.slicer.org/slicerWiki/index.php/File:2009_10_09-QMRMLTransformSliders.png Transform Sliders]
* Oct 2, 2009
** TCon with JC, Steve, Will, Seb, Stephen, Wendy, Nicole
** Demonstrated initial software architecture
** Uploaded screenshot of first module and received feedback from Dr. Kikinis [http://wiki.slicer.org/slicerWiki/index.php/File:QtSlicer-2009_10_02-QtTransformModule.png QtTransformModule.png]
** Designed basic widgets: [http://wiki.slicer.org/slicerWiki/index.php/File:2009_10_02-QCTKLinearTransformSlider.png Linear Transform Slider], [http://wiki.slicer.org/slicerWiki/index.php/File:2009_10_02-QMRMLNodeSelector.png Node Selector]
* Sept 25, 2009
** [[Events:CTK-Workshop-September-2009 | One day meeting with CTK community September 25, 2009]]
* Sept 22, 20009
** TCon with JC, Will, Sebastien, Steve
** Added [http://wiki.slicer.org/slicerWiki/index.php/File:QtSlicer-2009_09_16-DoubleSliderExample.png Qt dual-slider] into Slicer
* September 16-17, 2009
** [[Sept-2009-SlicerWidgetsBrainstorm | Two-day planning meeting]]

2011 Slicer4-PreRSNAHackFest

2011-11-03T17:10:38Z

Finetjul:

=What=
Slicer 4 PreRSNA Sprint.

Since neither mantis or a high-level phone call really captures the kinds of issues we are currently facing.
The core developers need to be looking at the code and errors together to understand issues and implement the appropriate solutions.

=Who=
Core developers

=Where=
Google hangouts with extra - https://plus.google.com/hangouts/extras/talk.google.com/slicer

=When=
November 3rd, starting at 2pm EST, 1pm CST. See [http://www.worldtimeserver.com/convert_time_in_US-IA.aspx?y=2011&mo=11&d=3&h=13&mn=0 TimeZone converter]

=Participants=


{|class="wikitable alternance" style="text-align:left; width:100%; border:1px solid black;"
|+ '''''Participants'''''
|-
! scope=col style="background:#cde6f8;"| Name
! scope=col style="background:#cde6f8;"| Available Operating System
! scope=col style="background:#cde6f8;"| Remarks
|-
| Nicole Aucoin
| {{Not Done}}
|
|-
| Jean-Christophe Fillion-Robin
| Workstation(s): [[Image:Os_linux_small.png]] Ubuntu 10.04, ''Slow'' remote access: [[Image:Os_win_small.png]] Windows7 (VS2008 32bits, VS2008 64bits), [[Image:Os_macosx_small.png]] MacOSX 10.?
|
|-
| Julien Finet
| Workstation(s): [[Image:Os_linux_small.png]] Ubuntu 10.04, [[Image:Os_win_small.png]] Windows7 (VS2008 32bits, VS2008 64bits) ''Slow'' remote access: [[Image:Os_win_small.png]] Windows7 (VS2008 32bits, VS2008 64bits), [[Image:Os_macosx_small.png]] MacOSX 10.?
|
|-
| Hans Johnson
| {{Not Done}}
|
|-
| Jim Miller
| Mac 64bit 10.7
|
|-
| Steve Pieper
| [[Image:Os_win_small.png]] Windows 7 64 bit (debug mode, python 2.7, cannot package), [[Image:Os_win_small.png]] windows XP x64 (run only, not compile), [[Image:Os_macosx_small.png]] mac osx 10.5, [[Image:Os_macosx_small.png]] 10.6, [[Image:Os_macosx_small.png]] 10.7, [[Image:Os_linux_small.png]] ubuntu 10.10 x86_64
|
|-
| Kilian Pohl
| Ubuntu 11.10 64 bit trunk
|
|}

=Issues=
{{note}}''Describe the issue shortly and add the corresponding mantis link.''

{|class="wikitable alternance" style="text-align:left; width:100%; border:1px solid black;"
|+ '''''Issues'''''
|-
! scope=col style="background:#cde6f8;"| Progress
! scope=col style="background:#cde6f8;"| Issue#
! scope=col style="background:#cde6f8;"| Developer
! scope=col style="background:#cde6f8;"| Short description / Notes
|-
| {{Not Done}} 
| [http://na-mic.org/Mantis/view.php?id=1375 1375]
| Jc
| QT_PLUGIN_PATH not set right on windows install
|-
| {{Not Done}}
| [http://na-mic.org/Mantis/view.php?id=1464 1464]
| Jc
| Slicer crash while trying to call CLI module from python
|-
| {{Not Done}}
| [http://na-mic.org/Mantis/view.php?id=1498 1498]
| KP
| EMSegmenter Tasks are not found in Windows build
|-
| {{Not Done}}
| [http://na-mic.org/Mantis/view.php?id=1506 1506]
| HJ
| BRAINS not available in MAC package
|-
| {{Not Done}}
| [http://na-mic.org/Mantis/view.php?id=1513 1513]
| KP
| EMSegmenter Fast: Incorrect labels in Step 3
|-
| {{Not Done}}
| [http://na-mic.org/Mantis/view.php?id=1515 1515]
| SP
| Labelmaps generated by EMSegmenter Fast cannot be edited
|-
| {{Not Done}}
| [http://na-mic.org/Mantis/view.php?id=1516 1516]
| JC
| ctkVTKErrorLogMessageHandler crashes
|-
| {{Not Done}}
| [http://na-mic.org/Mantis/view.php?id=1517 1517]
| KP
| Preprocessing returns inconsistent scalar volume
|-
| {{Not Done}}
| [http://na-mic.org/Mantis/view.php?id=1518 1518]
| HJ
| BRAINS is called but nothing happens
|}

Projects:ARRA:SlicerUI

2011-10-02T22:47:40Z

Finetjul: /* Progress */ Add September 2011

[[Projects:ARRASuplements|Back to Slicer ARRA home page]]
= Aim =
The effective visualization, data processing, analysis and interaction of medical images and ancillary data is a complex process requiring sophisticated and efficient software tools. Further, the development of new tools requires a productive and widely supported software environment. In such an environment, the human-computer interface plays a critical role in the overall effectiveness of the software tools. To this end, the Slicer graphical user interface (GUI) is to be significantly enhanced by the adoption of the standard and widely used Qt GUI toolkit. Qt has recently changed its licensing terms, meaning that it is now compatible with Slicer's commitment to open systems. Further, Qt is now recognized as the defacto standard, cross-platform GUI toolkit, offering superior performance, capability and productivity.

= Research Plan =
Slicer currently has an extensive GUI that consists of three major, logical parts: 1) the core, 2) command-line modules, and 3) modules. The research plan recognizes this organization, and will address the GUI development accordingly.
* The first step is to replace the core GUI with Qt. This will demand some initial design and planning, including integration of various Qt tools such as Qt Designer.
* Second, the command-line modules automatically generate their GUI from an XML description of the module. This will require modification so that Qt GUIs are generated (instead of the current KWWidgets).
* Finally, select, critical modules such as EM Segmenter will be reworked to use Qt widgets.
*Most of this work will occur in the first year, with completion of the critical modules expected early in the first quarter of the second year.
*After this, the research plan switches to training and dissemination of Qt-related technology so that the broader Slicer community can participate in the transition of modules to the Qt GUI.
*The key to this plan is to switch the core and command-line modules as fast as possible since we want to minimize disruption to the Slicer community, and to support continued Slicer development.
=Key Personnel=
* William Schroeder, Ph.D., 8%
* Stephen Aylward, Ph.D., 5%
* Jean-Christophe FILLION-ROBIN, 50%
* Julien Finet, 50%

=Meetings=
* Regular meeting TCons every other Tuesday at 2:00pm

=Links=
*[http://wiki.slicer.org/slicerWiki/index.php/Slicer4:QtPort QtSlicer Wiki]
*[http://wiki.slicer.org/slicerWiki/index.php/Slicer4:QtPort/Gallery QtSlicer Gallery]
*[http://www.slicer.org/slicerWiki/index.php/Qt_in_Slicer3 Preliminary work]

=Progress=
* October 5th, 2011
** Look&Feel improvements
** Under the hood
*** Automatic loading of python libraries (part 2)
*** Volume Rendering face-lift
** Extensions
*** Integrate new ChangeTracker module
* September 28th, 2011
** Look&Feel improvements
*** Add [http://www.commontk.org/index.php/File:ExpandButton.png expand button] to show/hide more buttons
*** Improve color transfer function editor
*** Support for color gradients in 3D view
** Under the hood
*** Automatic loading of python libraries (part 2)
** Extensions
*** Add access of Slicer environment to CLIs
* September 21th, 2011
** Look&Feel improvements
*** Improve the screenshot dialogs (no blinking, dynamic preview...)
*** Add favorites in file dialogs
*** Cleanup menu (File/Edit/Views/Help)
** Under the hood
*** Support gcc 4.6
*** Read .vp files
* September 14th, 2011
** Look&Feel improvement
*** Facelift for the central views layout
*** Transfer function editors usability (add borders to select points)
** Under the hood
*** Fasten annotation rendering
*** Stabilize demand driven filter pipeline
* September 7th, 2011
** Under the hood
*** Fix demand driven pipeline when combining polydata filters with image data filters
** Look&Feel improvement
*** Reorganize icons in the slice view controller
*** Work on the transfer function editor
** Extensions
*** Support EMSegment extension
* August 31st, 2011
** Look&Feel improvement:
*** Ability to select multiple files in the "Add Volume" dialog
*** Improve [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerModuleSelectorToolBar-SearchModule.png module search] in the module search bar
* August 24th, 2011
** Under the hood:
*** Use a true VTK demand driven pipeline architecture. It makes the code more stable and robust
** Look&Feel improvement:
*** Add search bar in the [http://wiki.slicer.org/slicerWiki/index.php/File:QMRMLColorPickerDialog.png color picker dialog]
** Modules
*** Added Volume Rendering settings page
* August 17th, 2011
** Look&Feel improvement:
*** Blue title bar for 3D views
*** Searchable module selector
* August 10th, 2011
** Look&Feel improvement:
*** Color and Opacity column in Models module
** Under the hood:
*** Reorganize Qt Scene models
*** Various bug fixes
* August 3rd, 2011
** Look&Feel improvement:
*** [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerModelsModule.png Models module] facelift
*** Slice/3D view popup
** Fixing mac build of DCMTK and tweaking GUI
* July 27th, 2011
** Support extensions with Superbuild
** Look&Feek improvement:
*** Slice/3D view popup
** Debugging DCMTK and numerous reports from users
* July 20th, 2011
** Event: [[Events:Slicer4-Review-07-2011|Sprint review]] event attendance
* July 13th, 2011
** Build system
*** Fix BFD dependency issues
** Look&Feel improvement:
*** Work on prototype for Slice view controller toolbar.
* July 6th, 2011
** Speed improvement for slice sliders in Windows
** Look&Feel improvement:
*** Transfer function editors
*** Popup menu in the Window/Level widget
*** Color dialog
* June 29th, 2011
** Widgets
*** New: [http://wiki.slicer.org/slicerWiki/index.php/File:qSlicerPresetComboBox.png Preset selector]
** Model visibility can now be controlled from the tree view (Models module).
* June 22th, 2011
** Release: [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:QtPort/Releases#Slicer_4.0_gamma Slicer 4.0 gamma RC2]
** Event: [http://www.na-mic.org/Wiki/index.php/2011_Summer_Project_Week NA-MIC 2011 Summer Project week]
** Modules:
*** New: EventBroker module for debug purpose
*** Editor: Support extensions
* June 15th, 2011
** Release: [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:QtPort/Releases#Slicer_4.0_gamma Slicer 4.0 gamma RC1]
** Speed improvement for color table generations
* June 8th, 2011
** Work on Module Extension retrieval from CDash
** Add [http://wiki.slicer.org/slicerWiki/index.php/File:SlicerWithVolumeRendering.png Volume Rendering] module.
*** Support generalized [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerVolumeRenderingModule-DualView.png Dual-View]
** Preparation for Slicer 4.0 gamma RC1
* June 1st, 2011
** More work on the Mac bundle
** Work on the Volume Rendering module
** Widgets:
*** Add [http://www.commontk.org/index.php/File:CtkCheckableComboBox.png ctkCheckableComboBox] and [http://wiki.slicer.org/slicerWiki/index.php/File:QMRMLCheckableComboBox.png qMRMLCheckableComboBox]
* May 26th, 2011
** Reviewing 64bit Windows and Mac packaging code (WIP)
** Participated in release of MIDAS Desktop which has hooks for Slicer (WIP)
* May 19th, 2011
** Updated CTK-based launcher for Macs
* May 11th, 2011
** Updated CDash for managing disk usage (purging old packages) and for providing easy access to uploaded packages
* May 4th, 2011
** Enable 64bit packages on Mac (WIP)
** Export Slicer libraries information for external module configuration
** Widgets:
*** Add [http://www.commontk.org/index.php/File:CtkVTKMagnifyView.png ctkVTKMagnifyView] to magnify the area under the mouse cursor in 2D slices
** Work on Transfer Function editor
* April 27, 2011
** Find_Package(Slicer) is now available
** Finalize work on Magnify view
** Work on the Qt wrapper around the VTK transfer function editor
* April 20, 2011
** Work on external modules build system (FIND_PACKAGE(Slicer))
** Work on Magnify view of area under mouse cursor for 2D slice views
** Work on Transfer Function editor
* April 13, 2011
** Improvement of slicer automatic build submission system:
*** Installers can be generated on a daily basis and be available for download without tedious system administration work ..
** "Cleaning and simplification" of slicer build system so that Slicer extension could be built and tested.
** Add [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerDiffusionWeightedVolumeDisplayWidget.png Diffusion Weighted Volume display properties panel]
* April 06, 2011
** Add dynamic property support to layout mechanism
** Tune and redesign the logics behaviors and displayable managers
** Fixup documentation and packages
* March 30, 2011
** Integration of the [http://www.commontk.org/index.php/File:CtkErrorLogWidget.png errors & logs dialog]
** Add progress when loading files
** Bug fixes and preparation of a new release
* March 23, 2011
** Added support for [http://wiki.slicer.org/slicerWiki/index.php/File:SlicerWithDTI.png DTI display] in the Volumes Module
** Widgets
*** [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerDiffusionTensorVolumeDisplayWidget.png Diffusion Tensor Volume Display widget]
*** [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerDTISliceDisplayWidget.png Diffusion Tensor Slice Display widget]
** Work on the error/status/log dialog
* March 17, 2011
** Work on the DTI display properties in the Volumes module
* March 10, 2011
** Assisting on Slicer 3.6.3 release
** Support multiple 3D views in the layouts
* March 3, 2011
** Assisting on Slicer 3.6.3 release
** Add new layouts
* February 23, 2011
** Support Command line executables
** Work on an Error Log dialog to redirect all the outputs generated by Slicer or CLIs
* February 16, 2011
** Redesign the layout mechanism in Slicer (XML based).
* February 9, 2011
** [http://www.commontk.org/index.php/CTK-Hackfest-Feb-2011 CTK hackfest]: DICOM Query/Retrieve widgets, application hosting, event bus...
* February 2, 2011
** Preparing for CTK hackfest: tcons, presentations, and packaging for CTK
** Upgrading Slicer4 dashboards with Dave P in support of testing modules
** Investigating automated binary upload
* January 28, 2011
** Extending support for modules and workflows based on Python
** Assisting in the integration of the Annotation module into Slicer4
* January 19, 2011
** Bug fixing based on feedbacks from [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:QtPort/Releases Slicer 4.0 beta-2]
* January 12, 2011
** Released [http://wiki.slicer.org/slicerWiki/index.php/Slicer4:QtPort/Releases Slicer 4.0 beta2]
** [[AHM_2011|All Hands Meeting 2011]] in Salt Lake City
** Presentation of [[2011_Winter_Project_Week:Breakout_Slicer|the status of the port]] and [[2011_Winter_Project_Week:Breakout_Slicer#Afternoon_Qt_Loadable_Module_Tutorial|step-by-step tutorials]]
* January 5, 2011
** Tweaking and bug fixing based on feedbacks from Slicer 4.0 beta
** Preparation for Slicer 4.0 beta-2 and [[All Hands Meeting 2011]]
** New settings: Select "Home" module, show text under toolbar icons
** Widgets: Rename nodes from node selector, delete nodes from Data module, corner annotations.
* December 29, 2010
** Holiday break
* December 22, 2010
** Holiday break
* December 15, 2010
** Bug fixing and packaging for Slicer 4.0 beta release
* December 8, 2010
** Support Scripted (Python) modules
** New module: Endoscopy
** New dialogs
*** [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerSettingsDialog.png Application settings]
*** [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerExtensionsWizard.png Extensions Management]
* December 1, 2010
** New module: [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerModelsModule.png Models module]
** New widget
***[http://wiki.slicer.org/slicerWiki/index.php/File:QMRMLModelInfoWidget.png Model info widget]
***[http://www.commontk.org/index.php/File:CtkMaterialPropertyWidget.png Material property widget]
***[http://wiki.slicer.org/slicerWiki/index.php/File:QMRMLDisplayNodeWidget.png Display node widget]
***[http://wiki.slicer.org/slicerWiki/index.php/File:QMRMLModelDisplayNodeWidget.png Model display node widget]
* November 24, 2010
** New widget: [http://wiki.slicer.org/slicerWiki/index.php/File:QMRMLVolumeInfoWidget.png Volume information widget]
** New dialog: [http://wiki.slicer.org/slicerWiki/index.php/File:QMRMLColorPickerDialog.png Color dialog]
* November 17, 2010
** New widget: [http://wiki.slicer.org/slicerWiki/index.php/File:QMRMLColorTableView.png Color table view]
** New module: [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerColorModuleWidget.png Color module]
* November 10, 2010
** Work on Python scripting
** Add range control and symmetric moves capability in the [http://wiki.slicer.org/slicerWiki/index.php/File:qMRMLWindowLevelWidget.png window level range widget] and threshold widget
** Add [http://www.commontk.org/index.php/File:CtkVTKThumbnailView.png navigation view]
* November 3, 2010
** Add snapshot feature in [http://wiki.slicer.org/slicerWiki/index.php/File:qMRMLThreeDViewsWidget.png Manipulate 3D View toolbar]
** Finished redesign of the internal structure of MRML to Qt scene interface
* October 27, 2010
** Add [http://www.commontk.org/index.php/File:CtkScreenshotDialog.png screenshot dialog]
** Add [http://www.commontk.org/index.php/File:CtkAxesWidget.png axes selection widget]
* October 20, 2010
** Dashboard cleaning (fixed and added more tests)
** Redesign of internal structures (layout manager, scene model...)
* October 13, 2010
** Launcher application: Add support for Macs
** Slicer module description parser ported to Qt (CTK)
* October 6, 2010
** Updating and integrating launcher application
** Revising dashboards to use launcher application
** Continuing to establish tasks and assign priorities for this and related NA-MIC funding
** Collecting bug reports, etc from user community regarding Alpha Release
** Planning vtkWidget and other organizational meetings
* September 29, 2010
** Revising dashboards to use new Slicer4 repository
** Establishing priorities for year 2
* September 22, 2010
** Planned: Re-evaluate priorities for editor module. Perhaps it should go in an earlier release.
** Planned: Host design discussion for vtkWidgets, Editor Module, and CUDA in Slicer Qt for interactive segmentation
** Planned: Consider interactions that can provide intuitive and precise manipulation of and direct the processing of data that spans a wide range of scales in time and space.
* September 15, 2010
** Attending CTK Hackfest in Spain
** Assisting in the integration of Qt Widgets developed for Slicer into the main CTK trunk
** Providing tutorials on software engineering practices used in Slicer Qt development
* September 8, 2010
** Alpha release of Slicer Qt 4 is being packaged
** Final tests being added to improve coverage
** Backporting final set of changes to ITK and VTK releases
* September 1, 2010
** Preparation for Slicer 4.0 alpha: bug fixes, [http://wiki.slicer.org/slicerWiki/index.php/File:SlicerQT-2009-12-10.png cosmetic changes], dashboard cleaning
** Modules
*** Add more features ([http://wiki.slicer.org/slicerWiki/index.php/File:QMRMLColorTableNodeComboBox.png color table chooser], preset buttons) to the [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerVolumesModule.png Volumes module]
** Widgets
*** Added [http://wiki.slicer.org/slicerWiki/index.php/File:QMRMLColorTableNodeComboBox.png a color table node combo box]
** Widgets
*** Add the [http://wiki.slicer.org/slicerWiki/index.php/File:QMRMLThreeDViewsWidget.png toolbar] to control 3D views
* August 25, 2010
*** Support [http://wiki.na-mic.org/Wiki/index.php/File:QMRMLSliceWidget.png Lightbox] in 2D slice views
** Tcl is now interfaced with Python
** Widgets
*** support for [http://www.commontk.org/index.php/File:CtkVTKScalarsToColorsView.png VTK charts with Qt]
*** Add advanced menu in the [http://wiki.slicer.org/slicerWiki/index.php/File:QMRMLSliceWidget.png 2D slice Views]
* August 18, 2010
** Event: Review of the state of Slicer port to Qt: [[QtAugust2010]]
* August 11, 2010
** Integration: Full support of PythonQt (wrapping of custom classes)
** Widgets: Dynamically support sets of different icon size
* August 4, 2010
** ToolBar:
*** Added [http://wiki.slicer.org/slicerWiki/index.php/File:QMRMLSlicesControllerToolBar.png qMRMLSlicesControllerToolBar] to control the red/yellow/green slice displays.
*** Added [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerMouseModeToolBar.png qSlicerMouseModeToolBar] to control the mouse mode (first draft).
*** Added Undo/Redo toolbar
*** Added links Slicer documentation into the menu bar
** Dialogs: Added [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerActionsDialog.png qSlicerActionsDialog] to show the application shortcuts
* July 28, 2010
** Work on improving the design of the interaction between MRML and vtk rendering
** Application: Tweak UI/Style (support smalllarge fonts)
** ToolBar: Added [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerModuleSelectorToolBar.png qSlicerModuleSelectorToolBar]
** Modules: new [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerSliceControllersModule.png qSlicerSliceControllersModule]
* July 21, 2010
** Work on improving the design of the interaction between MRML and vtk rendering
** Application: A big step forward the integration of the [http://wiki.slicer.org/slicerWiki/index.php/File:SlicerQT-2009-12-10.png 3D/2D views in SlicerQT]
** Modules: Added Acknowledgement tab to modules
** Widgets: improved [http://wiki.slicer.org/slicerWiki/index.php/File:QMRMLThreeDView.png qMRMLThreeDView] and [http://wiki.slicer.org/slicerWiki/index.php/File:SlicerQT-2009-12-10.png qMRMLSliceViewWidget]
* July 14, 2010
** Work on improving the design of the interaction between MRML and vtk rendering
** Widgets: Preliminary work on qMRMLColorTableNodeComboBox
** Widgets: Added colors to the slider handles of the [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerROIModule.png ROI module] widgets
* July 7, 2010
** Work on improving the design of the interaction between MRML and vtk rendering
** Modules: [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerDataModule.png Data module] (new)
** Widgets: [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerVolumesIODialog.png ctkFileDialog] to customize QFileDialog
** Dialogs: Added support for selecting files for volumes, models, scalar overlay, color table, fiducial lists and fiber bundles
* June 30, 2010
** Work on improving the design of the interaction between MRML and vtk rendering
** Modules: [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerROIModule.png ROI module] (new) (Data module: WIP)
** Widgets: [http://wiki.slicer.org/slicerWiki/index.php/File:QMRMLROIWidget.png ROI widget] (new)
* June 23, 2010
** [[2010_Summer_Project_Week|2010 Summer Project Week]] ([http://wiki.slicer.org/slicerWiki/index.php/File:QtPortInSlicer.ppt Presentation])
* June 16, 2010
** Preparation for [[2010_Summer_Project_Week|2010 Summer Project Week]]
** Work on the 3D and 2D render widgets
* June 9, 2010
** Work on Slicer Superbuild
** Work on Slicer launcher
*** New launcher (http://github.com/jcfr/CTKAppLauncher)
*** [http://my.cdash.org/index.php?project=CTK&subproject=ctkAppLauncher Dashboard] is setup
*** Code coverage is >85%
** Modules
*** [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerVolumesModule.png qSlicerVolumesModule] integrated an histogram widget (WIP)
* June 2, 2010
** Work on Slicer Superbuild
** Work on Slicer launcher
** Panels
*** [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerSaveDataDialog.png qSlicerSaveDataDialog] now saves scene + data
** Widgets
*** [http://www.commontk.org/index.php/File:CtkRangeSlider.png ctkRangeWidget]: new property - [http://www.commontk.org/docs/html/classctkRangeWidget.html spinBoxAlignment]
*** [http://www.commontk.org/index.php/File:CtkRangeSlider.png ctkRangeWidget]: new feature - the slider between the 2 handles can be drag/drop, it moves both handles at a time.
* May 26, 2010
** Work on Slicer superbuild
** New widgets
*** [http://www.commontk.org/index.php/File:CtkTransferFunctionHistogramItem.png Histogram widget] (still need to be integrated into Slicer)
* May 19, 2010
** Participation of the [http://www.commontk.org/index.php/CTK-Hackfest-May-2010 CTK Meeting]
*** Work on a launcher for Slicer Qt
*** Work on [http://www.commontk.org/index.php/Documentation/ctkTransferFunctionWidget transfer function widget] editors.
* May 12, 2010
** Slicer4 branch has been merged into the trunk (after Slicer3.6 has been created)
** Integration: Superbuild is now working on Windows/Linux for Slicer Qt
** Widgets
***Layout Manager (WIP)
***3D Render View (WIP)
***Slicer View (WIP)
** Dialogs
*** Settings Manager (WIP)
* May 05, 2010
** Integration: Slicer with Qt now supports CMake 2.9 (patch had to be send to the CMake community)
** Widgets
*** 3D Render View (WIP)
*** Minor bug fixes (qMRMLNodeComboBox, ctkSliderSpinboxWidget, ...)
* Apr 28, 2010
** Integration: PythonQt functionality has been ported into CTK (moved out of Slicer)
** Modules
*** WIP: Command Line Modules
** File Dialogs
*** WIP: [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerSaveDataDialog.png qSlicerSaveDataDialog] to save the scene data (UI is complete, logic is missing).
** Widgets
*** NEW: [http://wiki.slicer.org/slicerWiki/index.php/File:CtkDirectoryButton.png ctkDirectoryButton] a button tied to a directory path selector dialog
*** WIP: Render widget
* Apr 21, 2010
** Integration: 100% of CTK widgets have been moved out of Slicer.
** Widgets
*** WIP: [http://wiki.slicer.org/slicerWiki/index.php/File:CtkTransferFunctionWidget.png ctkTransferFunctionWidget] a color transfer function widget editor
* Apr 14, 2010
** Integration: CTK is now linked by Slicer Superbuild (CTK widgets are still in Slicer though).
** File Dialogs
*** [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerDataDialog.png qSlicerDataDialog] has been updated to support specific type options and checkable headers
** Widgets
*** New widgets: [http://wiki.slicer.org/slicerWiki/index.php/File:QCTKCheckableHeaderView.png qCTKCheckableHeaderView] a checkable QHeaderView
* Apr 7, 2010
** File Dialogs
*** New dialog: [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerDataDialog.png qSlicerDataDialog]
** File Readers: more work done in the direction of a flexible IO plugin mechanism
* Apr 1, 2010
** Integration: More work done to move CTK widgets into the CTK repository
** File Dialogs: Preliminary work to port the KWWidgets dialogs to Qt. New dialog: [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerStandardFileDialog.png qSlicerStandardFileDialog].
** File Readers: New architecture to register readers/writers from loadable modules
*** Supported files: *.mrml, *.xml, volumes, models...
* Mar 24, 2010
** Integration: Preparation to move CTK widgets into the [http://github.com/pieper/CTK CTK repository] and link against it
** Widgets
*** New widgets: [http://wiki.slicer.org/slicerWiki/index.php/File:qCTKRangeSlider.png qCTKDoubleRangeSlider], a range slider that supports doubles. [http://wiki.slicer.org/slicerWiki/index.php/File:qCTKRangeWidget.png qCTKRangeWidget], a ready to use qCTKDoubleRangeSlider with linked spinboxes.
* Mar 17, 2010
** Integration: Work on CTK for a smooth integration with Slicer
** Modules: a new module has been ported to Qt: [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerVolumesModule.png Volumes module] (WIP)
** Widgets
*** New widgets: [http://wiki.slicer.org/slicerWiki/index.php/File:QMRMLThresholdVolumeWidget.png qMRMLVolumeThresholdWidget] a widget to select a threshold, [http://wiki.slicer.org/slicerWiki/index.php/File:ctkDICOMModel.png ctkDICOMModel] a model to represents a DICOM database (SQLite).
* Mar 10, 2010
** Integration: CTK now has its own repository, CTK widgets will be moved from Slicer to git CTK
** Widgets:
*** New widgets: [http://wiki.slicer.org/slicerWiki/index.php/File:QCTKNodeComboBox.png qCTKNodeComboBox] replaces qMRMLNodeSelector, [http://wiki.slicer.org/slicerWiki/index.php/File:QMRMLWindowLevelWidget.png qMRMLWindowLevelWidget] to select window/level values
* Mar 03, 2010
** Integration: PythonQt is integrated into Slicer (partial support of Qt widgets)
** Qt Designer: [http://wiki.slicer.org/slicerWiki/index.php/File:Screenshot-Qt_Designer.png added icons to the qCTKWidgets & qMRMLWidgets plugins] to quickly find the right widgets
** Widgets:
*** New widgets: [http://wiki.slicer.org/slicerWiki/index.php/File:QCTKRangeSlider.png qCTKRangeSlider] a slider with 2 handles, qMRMLNodeComboBox replaces qMRMLNodeSelector (no +, - or edit icons) (WIP)
* Feb 24, 2010
** Integration: PythonQt (WIP)
** Widgets:
***Redesign qMRMLNodeSelector to use qMRMLSceneModel (WIP)
***Move the Add/Remove/Edit push buttons of qMRMLNodeSelector under the popup list of nodes (WIP)
** Bug fixes, code cleanup
* Feb 17, 2010
** Integration: Preliminary work for integrating PythonQt
** Widgets:
*** new features: qCTKSliderSpinBoxWidget has a tracking property (valueIsChanging), qCTKMenuButton now directly uses the QMenu from QPushButton
*** new tools: qCTKGroupButton (exclusive button group allowing no button to be selected), qCTKDynamicSpacer (sizePolicy controlled by a slot)
** Bug fixes, code cleanup
* Feb 10, 2010
** Integration of Qt designer into Slicer: the qt application to design module UIs (designer) can now be launch through Slicer: "Slicer3 --launch designer"
** Arguments/Settings: qCTKSettings can store application settings, added classes to parse the application command line arguments: qVTKCommandOptions, qSlicerCoreCommandOptions, qSlicerCommandOptions
** Some module logics have been separated from the KWWidgets modules to be reused by Qt modules: ModelMirror, AtlasCreator, MRAblation, FetchMI...
** Widgets:
*** ported more features from the KWWidgets : qMRMLNodeSelector (support multi node types, attributes, ...),
*** tuned behavior of some widgets, i.e. qCTKSliderSpinBoxWidget:size synchronization of the spinboxes, text right aligned ...
** Testing: qCTKAddRemoveComboBox, qCTKTestApplication, qVTKObject...
* Feb 03, 2010
** Style: QCleanLooksStyle has been choosen to be the default Slicer style
** The module logics in KWWidgets modules can now be reused in Qt modules
** New widgets: [http://wiki.slicer.org/slicerWiki/index.php/File:QCTKMenuButton.png qCTKMenuButton], qMRMLSceneFactoryWidget (for testing MRML widgets in Designer)
** New module ported to Qt: Tractography
* Jan 27, 2010
** Command line modules: finalizing the integration with Slicer.
** Render Widget: Preliminary work has been started (qVTKRenderView)
** New widgets: qMRMLEventLoggerWidget logs all the events generated by a vtkMRMLScene (for debugging only).
** Design improvement: Using feedbacks from slicer developers, we applied changes to correct heavy/unfriendly designs.
** Testing: Added qCTKModelTester, a QT object that can test the correctness of any class deriving from QAbstractItemModel.
* Jan 20, 2010
** New widget: a generic framework for handling MRML objects in list/table/tree widgets has been developped( drag/drop supported, reparenting, scene observers...)
** Quality: compilation warnings have been removed.
** Testing: a skeleton for unit test has been written for each classes
* Jan 13, 2010
** Outcome of the [[AHM_2010|NAMIC All Hands meeting]]
*** 2 new tutorials: [http://wiki.slicer.org/slicerWiki/index.php/File:QtPortInSlicer.ppt Port of Slicer to Qt], [http://wiki.slicer.org/slicerWiki/index.php/File:FirstStepsInQt.ppt First steps with Qt]
*** Slicer with Qt has been successfully compiled on several machines under Linux, Windows and Mac. The [http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Developers:Projects:QtSlicer/Tutorials/CompileWithQt building instructions] have been updated.
*** A few [http://www.cdash.org/CDash/index.php?project=Slicer3 dashboards] have been setup to compile with Qt. We count on you to submit more dashboards.
*** More unit tests have been written
*** 2 new modules have been created with Qt
*** A lot of installation bugs/problems have been resolved
* Jan 07, 2010
** Setup [http://cdash.org/CDash/index.php?project=Slicer3 dashboards] in Qt (Nightly, Continuous and Experimental builds)
** More unary tests added
** [[AHM_2010|NAMIC All Hands meeting]]
*** Presentation of [http://wiki.slicer.org/slicerWiki/index.php/File:QtPortInSlicer.ppt Port of Slicer to Qt] to the Slicer community
*** Workshop provided to help slicer developers to setup a Slicer environment running with Qt.
*** First modules developed by the community
* Dec 30, 2009
** Added support for modules with no corresponding KWWidgets modules: New modules in QT only can now be created.
** Bug fixes on Windows.
* Dec 22, 2009
** Added tests
** Tree widgets: WIP
** Command Line modules: WIP
* Dec 16, 2009
** Modules can now be ported into Qt by the Slicer community. Presentation: [http://wiki.slicer.org/slicerWiki/index.php/File:QtPortInSlicer.ppt Port of Slicer to Qt]
* Dec 9, 2009
** New widgets: [http://wiki.slicer.org/slicerWiki/index.php/File:QMRMLItemModel.png qMRMLItemModel, qMRMLListWidget, qMRMLTreeWidget]
** Screen-casts: [http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Developers:Projects:QtSlicer/Documents videos made for RSNA]
** More work on the CLI modules, [http://wiki.slicer.org/slicerWiki/index.php/File:SlicerQT-2009-12-10.png Slicer Qt only], now compiles on MAC OS X,
* Dec 2, 2009
** Command Line modules integration: First results (UI only)
** Interface between MRML Scene and the Qt (tree, list, table...) widgets: WIP
* Nov 25, 2009
** New Module: [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerWelcomeModule.png Welcome Module]
** New tutorial: [http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Developers:Projects:QtSlicer/Tutorials/QtDesigner Using Qt Designer with CTK & MRML widgets]
** Command Line modules integration: WIP.
* Nov 18, 2009
**New widgets: [http://wiki.slicer.org/slicerWiki/index.php/File:qCTKTreeComboBox.png Tree Combo Box], [http://wiki.slicer.org/slicerWiki/index.php/File:qCTKTreeComboBox.png Node Tree Selector]
**New feature: Support for help: [http://wiki.slicer.org/slicerWiki/index.php/File:QSlicerTransformsModuleUI.png example of an help section automatically added into a module]
**Command Line modules integration: WIP.
* Nov 13, 2009
**rework on the [http://wiki.slicer.org/slicerWiki/index.php/File:2009_11_10-qSlicerTransformsModuleUI.png Transforms Module]
**started to work on the Command Line modules integration.
* Nov 6, 2009
** Loadable Modules are now supported.
** Added [http://wiki.slicer.org/slicerWiki/index.php/File:2009_11_06-qCamerasModule.png Cameras Module]
* Oct 30, 2009
** The entire Qt-Slicer code architecture has been reviewed, factorized and simplified. Coding rules have been chosen (not documented yet).
** Documentation: Added a [http://wiki.slicer.org/slicerWiki/index.php/Slicer3:Developers:Projects:QtSlicer/Tutorials/WidgetWriting tutorial to write custom widgets]
* Oct 23, 2009
** New widgets: [http://wiki.slicer.org/slicerWiki/index.php/File:2009_10_23-QCTKCollapsibleWidget.png Collapsible widget], [http://wiki.slicer.org/slicerWiki/index.php/File:2009_10_23-QCTKColorPickerButton.png Color Picker button]
* Oct 16, 2009
** Synchronization between Qt widgets and KWWidget. Move the qt panels when the application is moved on the desktop.
** New widgets: [http://wiki.slicer.org/slicerWiki/index.php/File:2009_10_16-QCTKCoordinatesWidget.png Coordinates widget], [http://wiki.slicer.org/slicerWiki/index.php/File:2009_10_16-QCTKCollapsibleGroupBox.png Collapsible groupbox]
* Oct 9, 2009
** TCon with Julien Finet (J2), Jean-Christophe (JC), Steve, Will, Seb, Stephen, Wendy, Nicole to discuss progress
** Demonstrated new software architecture that simplifies building new modules
** Addressed issues of background color, etc previously raised by Dr. Kikinis [http://wiki.slicer.org/slicerWiki/index.php/File:2009_10_02-QtTransformModule-v2.png QtTransformModule-v2.png]
** New widgets: [http://wiki.slicer.org/slicerWiki/index.php/File:2009_10_09-QMRMLMatrixItem.png Matrix Widget], [http://wiki.slicer.org/slicerWiki/index.php/File:2009_10_09-QMRMLTransformSliders.png Transform Sliders]
* Oct 2, 2009
** TCon with JC, Steve, Will, Seb, Stephen, Wendy, Nicole
** Demonstrated initial software architecture
** Uploaded screenshot of first module and received feedback from Dr. Kikinis [http://wiki.slicer.org/slicerWiki/index.php/File:QtSlicer-2009_10_02-QtTransformModule.png QtTransformModule.png]
** Designed basic widgets: [http://wiki.slicer.org/slicerWiki/index.php/File:2009_10_02-QCTKLinearTransformSlider.png Linear Transform Slider], [http://wiki.slicer.org/slicerWiki/index.php/File:2009_10_02-QMRMLNodeSelector.png Node Selector]
* Sept 25, 2009
** [[Events:CTK-Workshop-September-2009 | One day meeting with CTK community September 25, 2009]]
* Sept 22, 20009
** TCon with JC, Will, Sebastien, Steve
** Added [http://wiki.slicer.org/slicerWiki/index.php/File:QtSlicer-2009_09_16-DoubleSliderExample.png Qt dual-slider] into Slicer
* September 16-17, 2009
** [[Sept-2009-SlicerWidgetsBrainstorm | Two-day planning meeting]]

Events:Slicer4-Review-07-2011

2011-10-01T06:30:20Z

Finetjul: /* UI */

==RSNA 2011 Targeted Objectives==
*Roadmap for the Slicer 4 release for the [http://www.na-mic.org/Wiki/index.php/RSNA2011_Planning Nov 27-Dec.2 RSNA demos at the 3DSlicer Booth]
*Most tasks need to be ready by end of September, to leave time to update tutorials, test and debug.
* List of [http://www.na-mic.org/Bug/search.php?project_id=3&sticky_issues=on&target_version=Slicer+4.0+RSNA&sortby=last_updated&dir=DESC&hide_status_id=80 open Mantis issues] with RSNA Target
===UI===
{|
|align="left"|
* [http://www.na-mic.org/Bug/view.php?id=1337 Main GUI Cosmetics]
** % face lift for the Slice viewers: reduce permanent non-image components. Reduce the number and depth of submenus. (J2) '''done'''
** % Main Gui 3D viewers should have similar appearance to slice viewers (J2) '''done'''
** % scenview and screensnapshot icons move to the icon bar at the top of the main gui. (J2-> Nicole) '''done'''
* Module Cosmetics
** % [http://www.na-mic.org/Bug/view.php?id=1252 Volume Rendering] (J2) (in progress)
** % [http://www.na-mic.org/Bug/view.php?id=1242 Models module] (J2) '''done'''
** % [http://www.na-mic.org/Bug/view.php?id=1281 Editor], see picture to the right (Steve) (Done)
** % [http://www.na-mic.org/Bug/view.php?id=1293 Welcome Module] (Wendy)
** % [http://www.na-mic.org/Bug/view.php?id=1295 Volumes Module] (J2)
*** Not part of the original plan, will be done if time permits (nice to have, low priority for RSNA), not a show stopper.
** % [http://www.na-mic.org/Bug/view.php?id=1296 Tractography Display Module] (Isaiah) '''done'''
** % [http://www.na-mic.org/Bug/view.php?id=1299 Sceneviews module] (Nicole)
* % Stabilize annotations module (Nicole, Daniel, Alex)
* Update tutorials (Sonia)
* % Volume rendering transfer function
** %% Mac crash in transfer functions (J2) (in progress)
** stability and usability such as jittery, and gradient banding on MAC (J2) (gradient banding not started yet)
** %Threshold feature ->offset slider(J2) (in progress)
** % Level of Detail (interrupt CPU VR when accessing the transfer function editor) + progress indicator during long renders (J2)
* % Documentation on wiki (at least stubs)
* % Linking and CompareView (Jim)
* ROI Slice Displayable Manager '''done'''
** % Centering on the slice (Alex) '''done''' (Now implemented even better with ROI widget in slice view)
* % Updated Icons (Annotations, HotLink, cursors, new layouts) (Wendy) all '''done''' except hotlink
* % Revised colors for ROI widget (Wendy) '''done'''
* % Reorganization of the dMRI sections (Demian)
|[[image:EditorFacelift-2011-07.png|300px|right|thumb|Mock-up of redesigned editor interface]]
|-
|}

===Under the hood===
*hierarchies
** % Collapsing Model Hierarchies controls display of children (Nicole) '''done'''
** % Collapsing Annotation Hierarchies controls display of children (Nicole and Daniel)
* % Annotations (Nicole, Daniel)
** vtkWidgets - bug fixes (Will)
*** 2D ruler tick spacing '''done'''
*** 3D ruler tick marks '''done'''
*** Widget performance (Michael) '''done'''
** % 3D Representations for all (ruler, bidimensional and maybe fiducials/caption) (Will, Nicole)
* % CTK DICOM widget (Steve, Nicole) - interface done, some debugging to do.
**% Implement Slicer Data Bundle (SDB a.k.a. lollipop): put the entire scene into a single folder, zip the folder, add a proper DICOM secondary capture header, which exposes the scenesnapshots. This should be the default save option. Everything else should be accessible through an "advanced" button. (Nicole) - prototype done, but not integrated with app. Zip is done by Nicole, Steve did secondary capture dicom.
** % Listener, Query, Retrieve, Send (Steve) - done except for Send (which is grayed out for now)
* % Optimize Model Displayable Manager (Alex)
* % Brainsfit: the slicer 3 brainsfit will be available in slicer 4 (Hans)
* % Fix resize crash due to extent problem in reslice mask (J2) '''done'''

===Infrastructure===
{|
|align="left" rowspan="2"|
* Tk/Tcl
** % Annotation/main interaction speedup (Steve) - replace SliceSWidget::updateAnnotation(s) with vtkMRMLSliceInformationDisplayableManager and vtkMRMLSliceLogic::CalculateInformationText - done as Data Probe - need to check windows performance
* Extensions
** % ABC, SkullStripper, EMSegmenter, VMTK (?), Plastimatch, [[2011_Summer_Project_Week_DVH|DVH extension]] (Jc)
** % Support for superbuild (Jc)
* Web: minor updates and tweaks
** % mobile skin for webkit rendering of the slicer wiki documentation pages (JC, Zack, others)
** % Statistics on packages and on individual extensions (Jc with input from Zack)
** % redirect links to slicer 4 dashboard (slicer.org download page, developer pages,....)
** % Slicer 4 nightlies, snapshots (monthly) and stable versions are pulled from the factory machine
** % Template for Slicer 4 documentation (JC)
|[[image:2011-08-04-MainGuiViewerInfo.png|400px|right|thumb|ViewerInformation mock-up [http://www.na-mic.org/Bug/view.php?id=1317]]]
|-
|[[image:SliceAnnotations-2011-07.png|300px|right|thumb|Snapshot of SliceAnnotationTree]]
|-
|}

===Beginning Of The Rest===

=What=
Slicer 4 review and programming sprint
=When=
July 19, 10 am -21, 4pm 2011

=Who=
Slicer 4 core programmers
=Where=
Demo room, 2nd floor, 1249 Boylston Street, Boston, MA
=Why=
*Identify roadmap for a Slicer 4 product release for the [http://www.na-mic.org/Wiki/index.php/RSNA2011_Planning Nov 27-Dec.2 RSNA demos at the 3DSlicer Booth]
**Main GUI and UI changes first, so that tutorial porting can begin
**debugging the features used in the RSNA tutorials

=Work on=
== Full List ==
Below is the complete list of items discussed. Items that are targeted for the RSNA 2011 events are preceded by a % sign, the person responsible is identified in parenthesis

===UI===
[[image:SlicerColorSelector.PNG|400px|right|thumb|SlicerColorSelector using CTK color dialog]]
* Reformat capabilities: We need a widget and possibly a slider based interface. (Nicole, Will)
*Cosmetics
** % [http://www.na-mic.org/Bug/view.php?id=1252 Volume Rendering] (J2)
** % [http://www.na-mic.org/Bug/view.php?id=1242 Models module] (J2)
** % [http://www.na-mic.org/Bug/view.php?id=1281 Editor] (Steve)
** % Main GUI face lift for the Slice viewers: reduce permanent non-image components. Reduce the number and depth of submenus. (J2)
** % Main Gui 3D viewers should have similar appearance to slice viewers (J2)
** % Stabilize annotations module (Nicole)
* Update tutorials (Sonia)
** After Facelift of Main Gui and some core modules
** Using GUI Testing?
* % Volume rendering transfer function (J2)
** %% Mac crash in transfer functions
** stability
** Jittery, and banding on MAC
** %Threshold
** Better appearance of the elements of the transfer function. They look ugly and are not antialiased. Check the graph in [https://www.ohloh.net/p/slicer Ohloh] and mouse over it. Looks much nicer! (according to the page source, the charts are made with [http://www.highcharts.com/ HighCharts])
** Level of Detail (interrupt CPU VR when accessing the transfer function editor) + progress indicator during long renders
** Group selection and shifting
* % Color selector
** % the default color selector should be THE CTK color dialog (see picture to the right). (J2)
** add search function to the labels (J2)
* % Documentation on wiki (at least stubs)
* % Linking and CompareView (Jim)
* ROI Slice Displayable Manager
** % Centering on the slice (Alex)
* % Updated Icons (Annotations, HotLink, cursors, new layouts) (Wendy)

===Under the hood===
[[image:Treeview-2011-07.png|160px|right|thumb|Possible Treeview variation]]
* GPU Volume Rendering
** Support for ATI and MAC
** How many GPU render engines to support/provide?
***Ron says: I just need a single one that works for flythroughs and can handle the combination of volume rendering, cross-sections, surface models, annotations
*hierarchies
**display: the current display is confusing. Image shows a possible modification
** % Collapsing Model Hierarchies controls display of children (Nicole)
** % Collapsing Annotation Hierarchies controls display of children (Nicole and Daniel)
**drag and drop capability
* % Annotations (Nicole, Daniel)
** vtkWidgets - bug fixes (Will)
** GUI layout (Nicole)
** compositing with volume rendering does not work properly
*** % 3D Representations for all (ruler, bidimensional and maybe fiducials/caption) (Will, Nicole)
* % CTK DICOM widget (Steve, Nicole)
**% Implement Slicer Data Bundle (SDB a.k.a. lollipop): put the entire scene into a single folder, zip the folder, add a proper DICOM secondary capture header, which exposes the scenesnapshots. (Nicole)
** % Listener, Query, Retrieve, Send (Steve)
**use DICOM widget local database as default mechanism for load/save
**everything else is import/export
**Slicer should have a single location for these operations
*DisplayModule
**[http://www.slicer.org/slicerWiki/index.php/Slicer4:DisplayModule Draft of the DisplayModule]
* % Optimize Model Displayable Manager (Alex)

===Infrastructure===
* Move to git/gerrit (TBD - can it be used with git-svn or is the suggestion to retire svn?)
* GUI Testing
** Instrumenting CTK widgets
** Conversion of tutorials to tests
** What will this provide that [http://sikuli.org/ Sikuli] does not? Sonia is ready to use Sikuli unless there is a good reason not to.
* Tk/Tcl
** Removing the last dependencies in core interaction loops - see [[Slicer4:SliceInteractions]]
** % Annotation/main interaction speedup (Steve)
** Maintain improve/functionality for Editor
* Performance optimization
** Module for profiling events
* Extensions
** % ABC, EMSegmenter, VMTK (Jc)
** % Support for superbuild (Jc)
** Requirements for testing, documentation, tutorials, and continued support from developers
*** How to name different levels of compliance
* Downloads
** % Statistics on packages and on individual extensions (Jc)
** Web pages
** Technologies
* Charts
** Reference Implementation (Marcus)
* MIDAS
** sceneviews support
* Interactive CLI modules

=== Compilation ===
* issues with win64 debug build - these impact developers more than users - we will prioritize getting nightly binary builds working on all platforms for RSNA before streamlining the developer process
** Fix numpy builds on win64
*** Need to embed manifests in numpy pyd files
** Fix win64 tcl version
*** currently permission issue with dlls in win64 slicerlib mirror
*** currently using tcl8.4 on win32 and elsewhere but tcl8.5 on win64 (should use the same everywhere if possible - we may want to switch to the [http://tcl.activestate.com active tcl pre-built distributions for windows])

* Slicer4 dashboard

=Agenda=

=Attending=
#Ron Kikinis
#Steve Pieper
#Nicole Aucoin
#Julien Finet
#Daniel Haehn (only 07/19)
#Jean-Christophe Fillion-Robin
#Stephen Aylward
#Will Schroeder
#Jim Miller
#Suares Tamekue Tatuebu
#Luping Fang
#Mike Halle
#Andrey Fedorov