NAMIC Wiki - User contributions [en]

File:DTIPrep TutorialContestSummer2011.pptx

2011-06-30T20:07:42Z

Matsuij: uploaded a new version of "File:DTIPrep TutorialContestSummer2011.pptx"

File:DTIPrep TutorialContestSummer2011.pdf

2011-06-30T20:07:11Z

Matsuij: uploaded a new version of "File:DTIPrep TutorialContestSummer2011.pdf"

DTIPrep Tutorial

2011-06-13T16:44:42Z

Matsuij:

[[File: DTIPrep_TutorialContestSummer2011.pptx|DTIPrep_TutorialContestSummer2011.pptx]]

[[File: DTIPrep_TutorialContestSummer2011.pdf|DTIPrep_TutorialContestSummer2011.pdf]]

[[File: DTIPrep_TutorialContestSummer2011.tar.gz|DTIPrep_TutorialContestSummer2011.tar.gz]]

DTIPrep Tutorial

2011-06-13T16:43:13Z

Matsuij:

[[PPT: DTIPrep_TutorialContestSummer2011.pptx|DTIPrep_TutorialContestSummer2011.pptx]]

[[PDF: DTIPrep_TutorialContestSummer2011.pdf|DTIPrep_TutorialContestSummer2011.pdf]]

[[Test Data: DTIPrep_TutorialContestSummer2011.tar.gz|DTIPrep_TutorialContestSummer2011.tar.gz]]

File:DTIPrep TutorialContestSummer2011.tar.gz

2011-06-13T16:41:59Z

Matsuij:

DTIPrep Tutorial

2011-06-04T04:26:35Z

Matsuij:

[[File:DTIPrep_TutorialContestSummer2011.pptx|DTIPrep_TutorialContestSummer2011.pptx]]

[[File:DTIPrep_TutorialContestSummer2011.pdf|DTIPrep_TutorialContestSummer2011.pdf]]

DTIPrep Tutorial

2011-06-04T04:24:10Z

Matsuij:

[[File:DTIPrep_TutorialContestSummer2011.ppt]]

[[File:DTIPrep_TutorialContestSummer2011.pdf]]

DTIPrep Tutorial

2011-06-04T04:23:03Z

Matsuij: Created page with 'File:DTIPrep_TutorialContestSummer2011.ppt File:DTIPrep_TutorialContestSummer2011.pdf'

[[File:DTIPrep_TutorialContestSummer2011.ppt]]
[[File:DTIPrep_TutorialContestSummer2011.pdf]]

File:DTIPrep TutorialContestSummer2011.pdf

2011-06-04T04:21:47Z

Matsuij:

File:DTIPrep TutorialContestSummer2011.pptx

2011-06-04T04:20:28Z

Matsuij:

Summer 2011 Tutorial Contest

2011-06-04T04:18:41Z

Matsuij: /* List of submitted tutorials */

=Background=

[http://www.slicer.org Slicer3] is used to perform meaningful research tasks. As part of the NA-MIC Training Core activities we are building a curated portfolio of tutorials for the basic functions and specialized functionality available in Slicer. Our current portfolio of tutorials as well as tutorials that were developed in past contests are posted on the [http://www.slicer.org/slicerWiki/index.php/Slicer3.6:Training#Software_tutorials| NA-MIC training compendium].

=Tutorial Contest Goal=
The primary purpose of this contest is to enrich the training materials that are available to end-users and developers using 3D Slicer and the NA-MIC kit. We believe contestants will be motivated to participate to enhance the dissemination of their own algorithms that they have incorporated into the Slicer3 platform and/or to enhance training of Slicer3 functionality for their own laboratory groups.

There will be three categories:
*Category 1: '''END TO END SOLUTION TUTORIAL''' <br> In this category, the tutorial will teach a user how to solve a particular clinical problem using the NA-MIC Kit. <br> Examples: [[Slicer3:ProstateNav_TutorialContestSummer2010| Robot-assisted MRI-guided prostate biopsy]], [http://www.slicer.org/slicerWiki/images/3/37/WhiteMatterExplorationNeurosurgicalPlanning_JHU2011_SoniaPujol.pdf White Matter Exploration for Neurosurgical Planning]
*Category 2: '''ALGORITHM TUTORIAL:''' In this category the tutorial will teach a user how to make an algorithm work on their data.<br> Examples: [http://www.slicer.org/slicerWiki/images/4/4e/EMSegmenterTutorialAdvancedMode-Slicer-3.6.3-2.pdf EM Segmenter Advanced Mode]<br>
*Category 3: '''METHODOLOGY TUTORIAL'''. Application-level tutorials for users and developers.<br> Examples:[[Slicer3:Fiducials_TutorialContestSummer2010 | '''Fiducials''']]

Entries in each category require the following material:
* scientific background and application motivation
* step-by-step instructions
* anonymized sampel dataset

=Rules=
*Tutorial must be based on the '''Slicer3.6.3 release''' or on '''Slicer4'''.
*To enter the contest, you must provide '''a version of the tutorial that works on all supported platforms (Mac,Windows,Linux)+'''.
*Tutorial and all of its components (data, powerpoints/pdfs, additional modules etc.) must be released under the [http://www.slicer.org/slicerWiki/index.php/Slicer:license Slicer license]
*Tutorial data must be anonymized
*Tutorial must include contact information of the primary author (e-mail and phone number)
*Tutorial must follow the guidelines specified above and use the [[Media:TutorialContest_Template_2011.ppt‎ | tutorial template]].
*If applicable, the tutorial must provide clear directions for downloading and installing additional modules <br>
+Applicants will work with the NA-MIC Training and Dissemination Cores in advance to do the multi-platform testing.

=Submission Dead-line and Presentation=

'''<span style="background-color: yellow"> Submission dead-line: Friday June 3, 2011'''</span>
* '''Submission process''': to enter the contest, please follow the 5 steps below:
**1. Create a wiki page for your tutorial on the NA-MIC wiki.
**2. Upload your slides and tutorial dataset. Your tutorial and data must be named as 'TutorialName_TutorialContestSummer2011.pdf' and 'TutorialData_TutorialContestSummer2011.zip'
**3. Add a link to the uploaded tutorial and datasets on your tutorial page.
**4. Enter the results of your tests in the [http://wiki.na-mic.org/Wiki/index.php/Training:Summer_2011_Contest_Table Summer 2011 test table ]
**5. Once you have completed step 1-4, add a link to your tutorial page in the list below and send a notification email to Sonia Pujol (spujol at bwh.harvard.edu) and to Katie Hayes( hayes at nmr.mgh.harvard.edu) to receive a confirmation of your submission.

* '''Presentation at the NA-MIC Project week''': Brief highlights of tutorials will be presented by the authors at 3 pm on Tuesday June 21 at the Summer 2011 Project Week. Each presentation should be 10-minute summary of the submission.

= List of submitted tutorials=

[[TBISegmentation_TutorialContestSummer2011|UCLA Automatic Segmentation of Traumatic Brain Injury MRI volumes using Atlas Based Classification and 3D Slicer]]

[[UNC SPHARM-PDM Tutorial| UNC ShapeAnalysisModule]]

[[UNC MANCOVA Tutorial| UNC shapeAnalysisMANCOVA_Wizard]]

[[Plastimatch Dose Warping]]

[[BRAINSCut_Tutorial_NAMIC2011SummerConstest|BRAINSCut Tutorial for human brain sub-cortical segmentation]]

[[Non-rigid MR-CT Image Registration|Non-rigid_MR-CT_Image_Registration]]

[[DTIPrep Tutorial|DTIPrep Tutorial]]

To see the list of Summer 2010 Tutorial Contest Winners, please follow this
[http://www.na-mic.org/Wiki/index.php/Events:TutorialContestJune2010 link]

2011 Winter Project Week:DTIPrepDocumentation

2011-01-14T15:30:52Z

Matsuij: /* Key Investigators */

__NOTOC__
<gallery>
Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
</gallery>

==Key Investigators==
* UIowa: Hans Johnson, Mark Scully, Joy Matsui
* UNC: Martin Styner, Clement Vachet, Cheryl Dietrich

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

<h3>Objective</h3>
Improve the DTIPrep documentation and create a 1st draft tutorial for DTIPrep

</div>

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

<h3>Approach, Plan</h3>
Update the NITRC media wiki pages for DTIPrep to match the current version of the program. Use the updated wiki as a basis for a tutorial.
Coordinate efforts with Cheryl Dietrich at UNC.
</div>

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

<h3>Progress</h3>
A detailed pdf on DTIPrep documentation has been uploaded from UNC. Work has started on creating a NAMIC-style ppt tutorial and will be completed soon. This tutorial will be submitted for the June tutorial contest.

</div>
</div>

2011 Winter Project Week

2011-01-11T17:15:37Z

Matsuij: /* Diffusion */

Back to [[Project Events]], [[Events]]
Back to [[Project Events]], [[AHM_2011]], [[Events]]

__NOTOC__
[[image:PW-SLC2011.png|300px]]

== Dates.Venue.Registration ==

Please [[AHM_2011#Dates_Venue_Registration|click here for Dates, Venue, and Registration]] for this event.

== Agenda==

Please [[AHM_2011#Agenda|click here for the agenda for AHM 2011 and Project Week]].

==Background==

From January 10-14, 2011, the twelfth project week for hands-on research and development activity in Image-Guided Therapy and Neuroscience 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==

=== Segmentation ===
* [[2011_Winter_Project_Week:Extension of ABC to detect pathology categories|Extension of ABC (Atlas-Based Classification) to detect pathology categories, with tests on TBI images]] (Bo Wang, Jack Van Horn, Andrei Irimia, Micah Chambers, Marcel Prastawa, Guido Gerig).
* [[2011_Winter_Project_Week:Atrial_Fibrillation|Segmentation of the left atrial wall for atrial fibrillation ablation therapy]] (Behnood Gholami, Yi Gao, and Allen Tannenbaum)
* [[2011_Winter_Project_Week:The_Vascular_Modeling_Toolkit_in_3D_Slicer|The Vascular Modeling Toolkit in 3D Slicer]] (Daniel Haehn, Luca Antiga, Kilian Pohl, Steve Pieper, Ron Kikinis)
* [[2011_Winter_Project_Week:TubeTK_VascularImageSegmentationAndAnalysis|TubeTK for vascular image segmentation and analysis]] (Stephen Aylward, Danielle Pace, Steve Pieper)
* [[2011_Winter_Project_Week:StenosisDetector|A stenosis detector in Slicer4 using VMTK ]](Suares Tamekue, Daniel Haehn, Luca Antiga, Ron Kikinis)
* [[2011_Winter_Project_Week:MeshCurvolver|Surface Region Segmentation for Surgical Planning and Mapping ]] (Peter Karasev, Karol Chudy, Allen Tannenbaum)
* [[2011_Winter_Project_Week:SPECTRE_Integration|Integration of SPECTRE into Slicer]] (Nicole Aucoin, Min Chen)
* [[2011_Winter_Project_Week:NerveSeg|Segmentation of Nerve and Nerve Ganglia in the Spine]] (Adrian Dalca, Giovanna Danagoulian, Ron Kikinis, Ehud Schmidt, Polina Golland)

=== Registration ===
*[[2011_Winter_Project_Week:RegistrationCaseLibrary|The 3DSlicer Registration Case Library]] (Dominik Meier,Ron Kikinis)
*[[2011_Winter_Project_Week:RegistrationAnisotropy|Voxel Anisotropy and Bias Field Effects on Slicer Image Registration]] (Dominik Meier, Andriy Fedorov, William Wells) (tentative)
* [[2011_Winter_Project_Week:DTIRegistrationWizard|DTI registration & resampling wizard]] (Dominik Meier, Hans Johnson, Francois Budin, Mark Scully)
* [[2011_Winter_Project_Week:Efficient co-registration of multiple MR modalities using the ABC|Efficient co-registration of multiple MR modalities using the ABC (atlas-based classification) framework, joint visualization of multiple co-registered modalities]] (Bo Wang, Jack Van Horn, Andrei Irimia, Micah Chambers, Marcel Prastawa, Guido Gerig).
* [[2011_Winter_Project_Week:longitudinal_dti_analysis|Longitudinal DTI Analysis for TBI and HD data for individual patients' follow-up images]] (Anuja Sharma, Guido Gerig)
* [[2011_Winter_Project_Week:Atlas_Registration_in_Slicer3|Atlas Registration in Slicer3]] (Daniel Haehn, Dominik Meier, Kilian Pohl, Ryan Eckbo)
* [[2011_Winter_Project_Week:RegistrationInPresenceOfAnatomicVariation|Registration in the presence of anatomic variation (sliding organ registration)]] (Danielle Pace, Marc Niethammer, Petter Risholm, Tina Kapur, Sandy Wells, Stephen Aylward)
* [[2011_Winter_Project_Week:UncertaintyVisualization|Visualizing registration uncertainty in Slicer3]] (Petter Risholm, William Wells)
* [[2011_Winter_Project_Week:LandmarkRegularization|Landmark-based registration with analytic regularization]] (Nadya Shusharina, Gregory Sharp)
* [[2011_Winter_Project_Week:DTIPipeline|DTI registration/processing pipeline in Slicer3]] (Francois Budin, Clement Vachet)

=== IGT ===
*[[2011_Winter_Project_Week:OpenIGTLink| OpenIGTLink 2.0]] (Junichi Tokuda, Nobuhiko Hata)
*[[2011_Winter_Project_Week:Osteomark|Osteormark, navigation tool for Osteotomy]] (Laurent Chauvin, Nobuhiko Hata)
*[[2011_Winter_Project_Week:Intra-ProceduralProstateMotion|Detection and compensation for prostate motion during MR-guided prostate biopsy]] (A.Fedorov, Andras Lasso)
*[[2011_Winter_Project_Week:ThinClientQtInterfaceForIGT|Thin Client QT Interface for IGT]] (Nicholas Herlambang, Nobuhiko Hata, Steve Pieper, Julien Finet, JC)
*[[2011_Winter_Project_Week:TransformRecorderAndProcedureAnnotation|Transform recorder and (surgical) procedure annotation module]] (Tamas Ungi, Junichi Tokuda)
*[[2011_Winter_Project_Week:SurgicalToolsTracking|Surgical Tools Tracking]] (Martin Rajchl, Feng Li)
*[[2011_Winter_Project_Week:Slicer IGT Looking Forward| Slicer IGT Looking forward]] (Junichi Tokuda, Nobuhiko Hata, Andriy Fedorov, Sandy Wells, Danielle Pace)

=== Radiotherapy ===
* [[2011_Winter_Project_Week:SegEye|Segmentation of the eye structures for Adaptive Radiotherapy]] (Ivan Kolesov, Gregory Sharp, and Allen Tannenbaum)
* [[2011_Winter_Project_Week:DicomRtExport|DICOM-RT export]] (Greg Sharp, Steve Pieper)

=== Analysis ===
* [[2011_Winter_Project_Week:GAMBITCorticalThicknessAnalysis |GAMBIT - Cortical thickness analysis]] - Clement Vachet, Martin Styner
* [[2011_Winter_Project_Week:ParticleShapeAnalysis|Particle shape analysis incorporating surface normals ]] - Beatriz Paniagua, Martin Styner
* [[2011_Winter_Project_Week:NAMICShapeAnalysis |NAMIC shape analysis pipeline in Slicer 3]] - Lucile Bompard, Martin Styner, Clement Vachet, Chris Gloschat
* [[2011_Winter_Project_Week:ParticleShapeEngineering|Particle Systems for Shape Analysis]] - Josh Cates, Manasi Datar, Ross Whitaker
* [[2011_Winter_Project_Week:MRSI_module_and_SIVIC_interface| MRSI module and SIVIC interface]] - Bjoern Menze, Jason Crane, Beck Olson, Polina Golland

=== Informatics ===
* [[2011_Winter_Project_Week:UIowaTHPDTIData|Share all UIowa Traveling Human Phantom DTI data with NAMIC]] - Mark Scully, Hans Johnson, Zack M.
* [[2011_Winter_Project_Week:FetchMIAPI|Recode FetchMI API to work with XNAT 1.5 API]] - Dan Marcus, Misha Milchenko
* [[2011_Winter_Project_Week:XNATSceneSupport|Engineer XNAT infrastructure for handling slicer scene files]] - Dan Marcus, Misha Milchenko

=== Diffusion ===
* [[2011_Winter_Project_Week:DicomToNrrdTestSuite |Test suite for DicomToNrrdConverter]] - Mark Scully, Zach Mullen, Xiaodong Tao, Joy Matsui, Hans Johnson
* [[2011_Winter_Project_Week:DicomToNrrdRefactoring |Requirements gathering for refactoring DicomToNrrdConverter]] - Mark Scully, Xiaodong Tao, Joy Matsui, Hans Johnson
* [[2011_Winter_Project_Week:DTIPrepDocumentation |Documentation and 1st Draft Tutorial for DTIPrep]] - Joy Matsui, Clement Vachet, Mark Scully, Hans Johnson
* [[2011_Winter_Project_Week:VoxelwizeFiberDistributionFromTractography |Voxelwise fiber distribution from tractography]] - Yinpeng Li, Martin Styner
* [[2011_Winter_Project_Week:TwoTensorTracts |Two-tensor full brain tractography pipeline]] - Lauren O'Donnell, Yogesh Rathi, C-F Westin

* [[2011_Winter_Project_Week:FinslerTractography |Finsler tractography in ITK]] - Antonio Tristan-Vega, C-F Westin
* [[Statistical analysis of WM tracts generated by Tractography and Volumetric framework]] - Gopal Veni, Ross Whitaker

=== NA-MIC Kit Internals ===

* [[2011_Winter_Project_Week:Command_line_module_logic_redesign|Command line module logic redesign]] (passing paramenters, tie into workflows) - Jim, Steve
* [[2011_Winter_Project_Week:64bit_Windows_Builds|64bit Windows Builds]] - David Partyka
* [[2011_Winter_Project_Week:Dashboards_Factory_machine_subprojects_and_CDashAtHome|Dashboards: Factory machine, subprojects, and CDash@Home]] - David P, Zack M, Steve, and Stephen
* [[2011_Winter_Project_Week:MIDAS_for_data_hosting|MIDAS for data hosting]] - Zach M and Hans
* [[2011_Winter_Project_Week:VTK_Widgets|vtkWidgets]] JC and Will, Nicole Aucoin
* [[2011_Winter_Project_Week:Annotation_module_in_Slicer4_Display_widget_intersections|Annotation module in Slicer4: Display widget intersections]] (Daniel Haehn, Nicole Aucoin, Steve Pieper)
* [[2011_Winter_Project_Week: Python and Slicer4| Python and Slicer4]]: Workflows, Scripting, and Porting - JC, Jim, Steve, and Danielle
* [[2011_Winter_Project_Week: Slice View Performance| Improve Performance of Slice Rendering in slicer3 and slicer4]] (Steve, Will, Jc, J2, Jim, Luca)
* [[2011_NAMIC_Project_week:_Real-Time_Volume_Rendering_for_Virtual_Colonoscopy| Real-Time Volume Rendering for Virtual Colonoscopy]] (Steve, Alex)
* [[2011_Winter_Project_Week:_Slicer4-ITK4_Continuous_Integration| Slicer4 - ITK4 Integration]] (Bill, Luis)

=== Execution Model ===
* [[2011_Winter_Project_Week::ExtractSEM|Extract SlicerExecutionModel (SEM) into separate entity]]. SEM is the only component needed to build modules compatible with Slicer3D, so it should be easy incorporate into external applications without all of Slicer3D. Jim, Hans
* [[2011_Winter_Project_Week:ExtendSEMXml|Extend SEM xml]] to include sections for explicit grant acknowledgements, pointers to documentation, and pointers to examples. - Hans, Andriy
* [[2011_Winter_Project_Week:SEMXMLSchema|Create a formal schema for the SEM xml so that eternal tools (i.e. nipype) can validate the xml.]] - Hans Johnson, Jim Miller, Tim Olsen
* [[2011_Winter_Project_Week:XMLToMediaWiki|Improve documentation extractor script that converts XML to MediaWiki format so that it can directly push this information into the Slicer3D MediaWiki.]] - (Wiki Systems Admin), Hans Johnson, Steve Pieper, Stephen Aylward
* [[2011_Winter_Project_Week:ExternalToolsMergingStrategies | Improve merging strategies between software that is part of externals tools and part of Slicer.]] - Mark Scully, Hans Johnson

=== Workflows and Integration ===
* [[Winter_project_week_2011_Workflows_SOA|Workflows and Service Oriented Architecture Solutions for Slicer3 Modules]] (Alexander Zaitsev, Wendy Plesniak, Charles Guttmann, Ron Kikinis)

=== 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 28th, 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 28: Engineering Infrastructure Projects
#*November 4: Engineering Infrastructure Projects
#*November 11: DPB Projects: Iowa, Outcomes from Alg Core Retreat
#*November 18: DPB Projects: MGH
#*November 25: DBP Projects, Funded External Collaborations
#*December 2: Funded External Collaborations
#*December 9: Other External Collaborations
#*December 16:Finalize Engineering Projects
#*January 6: Loose Ends
#By December 16, 2010: [[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 16, 2010: 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. the BIRN). 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...