Commontk - User contributions [en]

The Team

2015-02-13T10:01:30Z

Stefan Baumann:

=Founders=
* Hans-Peter Meinzer, German Cancer Research Center, Heidelberg, Germany ''(Catalyst of the CTK effort)''
** Marco Nolden, German Cancer Research Center, Heidelberg, Germany
* Ron Kikinis, Harvard Medical School, Boston, MA, USA ''(Meeting Chair)''
* Ivo Wolf, Mannheim University of Applied Sciences, Institute for Medical Informatics, Mannheim, Germany
* Steve Pieper, Isomics, Cambridge, MA, USA
* Stephen Aylward, Kitware Inc., Carborro, NC, USA
** Julien Finet, Kitware Inc.
** Jean-Christophe Fillion-Robin, Kitware Inc.
** Julien Jomier, Kitware Inc.
** Will Schroeder, Kitware Inc., Clifton Park, NY, USA
* Kevin Cleary, Georgetown University, Washington DC, USA
** Patrick Cheng, Georgetown University, Washington DC, USA
** Ziv Yaniv, Georgetown University, Washington DC, USA
* Lawrence Tarbox, Mallinckrodt Institute of Radiology, St.Louis, MO, USA
* Marco Viceconti, Laboratorio di Tecnologia Medica, Bologna, Italy
** Daniele Giunchi, SCS - B3C , Bologna Italy
** Paolo Quadrani, SCS - B3C , Bologna Italy
* Michael Onken, OFFIS DICOM Team, Oldenburg, Germany
* Nicholas Ayache, Sophia Antipolis, Inria, France
** Olivier Clatz, Sophia Antipolis, Inria, France
** Maxime Sermesant, Sophia Antipolis, Inria, France
** Pierre Fillard, Sophia Antipolis, Inria, France
* Gianluca Paladini, Siemens Corporate Research, Princeton, NJ, USA
* David Clunie, PixelMed Publishing, Bangor, PA, USA

=Supporting institutions=
{| cellspacing="20"
|[[File:Dkfz_logo_en.gif|200px|link=http://www.dkfz.de]]
||Prof. Dr. Hans-Peter Meinzer
|[[File:Kitware_logo_en.png|200px|link=http://www.kitware.com]]
||Stephen Aylward, Ph.D.
|-
|[[File:GeorgetownUniversity_logo_en.svg|200px|link=http://www.georgetown.edu/]]
||Prof. Kevin Cleary, Ph.D.
|[[File:Inria_logo_en.jpg|200px|link=http://www.inria.fr]]
||Nicholas Ayache, Ph.D
|-
|[[File:Isomics_logo_en.png|200px|link=http://www.isomics.com]]
||Steve Pieper, Ph.D.
|[[File:Mannheim_logo_ge.png|200px|link=http://www.uni-mannheim.de]]
||Prof. Dr. Ivo Wolf
|-
|[[File:Offis_logo_en.gif|200px|link=http://dicom.offis.de]]
||Michael Onken
|[[File:PixelMed_logo_en.svg|200px|link=http://www.dclunie.com/]]
||David Clunie
|-
|[[File:Siemens_logo_en.jpg|200px|link=http://www.usa.siemens.com/en/about_us/research/home.htm]]
||Gianluca Paladini
|[[File:SPL_logo.gif|70px]][http://www.spl.harvard.edu Surgical Planning Laboratory]
||Prof. Dr. Ron Kikinis
|-
|[[File:UCL.gif|200px|link=http://www.ucl.ac.uk]]
||Prof. Sebastien Ourselin
|[[File:Upf_logo_it.gif|200px|link=http://www.upf.edu]]
||
|-
||[[File:WashingtonUniversity_logo_en.png|200px|link=http://www.mir.wustl.edu/]]
||Prof. Lawrence Tarbox, Ph.D.
||[[File:Crest-l.png|200px|link=http://www.cistib.org/cistib/index.php]]
||Prof. Alejandro Frangi, Ph.D.<br/>Prof. Marco Viceconti, Ph.D.
|}

=Individual contributors=

The following data is retrieved from [http://www.openhub.net/p/ctk/contributors?query=&sort=commits OpenHub], showing
all active contributors during the last two years (as of 30th October 2014) with at least 10 commits:

* Jean-Christophe Fillion-Robin
* Julien Finet
* Sascha Zelzer
* Steve Pieper
* Marco Nolden
* Matt Clarkson
* Andreas Fetzer
* Ivo Wolf
* Miklos Espak
* Michael Onken
* Alireza Mehrtash
* Nicolas Toussaint
* Stefan Baumann

=Projects contributing to CTK=
<gallery widths="200px" perrow="3">
File:3DSlicer_logo_en.png|[http://www.slicer.org 3D Slicer]
File:Gimias_logo_en.png|[http://www.gimias.org Gimias]
File:MAF3_logo_en.png|[https://www.biomedtown.org/biomed_town/maf3 Maf]
File:MedInria.png|[http://med.inria.fr medInria]
File:Mitk_logo_en.png|[http://www.mitk.org Mitk]
File:ParaView_logo.png|[http://www.paraview.org ParaView]
File:QIICR_logo.png|[http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR)]
</gallery>

=Grants, Fundings and Sponsors=
{|
|[[File:AFRL_logo.png|70px]] || Air Force Research Laboratories under Phases I and II of the SBIR contract "[http://www.vtk.org/Wiki/Maverick Generating Labeled Voxelization for Numerical Simulation]," <br>Topic: AF06-034, Contract #: <code>FA8650-07-C-6756</code>
|-
|[[File:ARRA_logo.png|70px]] || [http://wiki.na-mic.org/Wiki/index.php/Projects:ARRA:SlicerUI ARRA supplement] to [http://nac.spl.harvard.edu NAC]
|-
|[[File:Sfb125.png|120px|link=http://www.cognitionguidedsurgery.de/]] || [http://www.cognitionguidedsurgery.de/ Cognition Guided Surgery, SFB/Transregio 125]
|-
|[[File:NA-MIC_logo.jpg|70px]] || [http://www.na-mic.org National Alliance for Medical Image Computing]
|-
|[[File:NAC_logo.gif|70px]] || [http://nac.spl.harvard.edu Neuroimage Analysis Center]
|-
|[[File:VPH_logo.jpg|70px|link=http://www.vph-noe.eu/]] || [http://www.vph-noe.eu/ Virtual Physiological Human Network of Excellence]
|-
|[[File:QIICR_logo_square.png|70px|link=http://qiicr.org]] || [http://qiicr.org Quantitative Image Informatics for Cancer Research (QIICR), NIH National Cancer Institute, award U24 CA180918]
|}

File:Testmr.txt

2014-11-06T16:51:29Z

Stefan Baumann: uploaded a new version of "File:Testmr.txt"

First file fully anonymized using dcmjs!

CTK-Hackfest-Nov-2014

2014-11-06T16:47:30Z

Stefan Baumann: /* Thursday */

== Event pictures ==

[[File:Ctk.2014,11.png|600px]]

=== Progress ===

== Introduction ==

'''Date:''' November 3-7, 2014

'''Location:'''

German Cancer Research Center, Heidelberg, Germany

More details to follow.

'''Goal:''' A follow on to the [[Commontk:Current_events#Past_events|wildly successful previous hackfests!]]

'''Requirements:''' Attendees must be willing to spend their time during the event writing ctk code that contributes to the main [[CTK-Roadmap | ctk roadmap]]. This means spending the week immersed in C++, Qt, DCMTK, CMake, and related technologies. People who do not feel qualified for this task are politely not invited :)

'''Group size:''' Maximum 20 participants so we can have a manageable working meeting. The organizing committee will invite and select participants based on input from [[TheTeam]].

'''Site Hosts:''' Marco Nolden, Sascha Zelzer, Ivo Wolf

'''Organizing Committee:''' Steve Pieper, Ivo Wolf, Stephen Aylward

'''Future Events:''' Future hackfests will be announced in advance, and we hope lots of people will be interested in participating. The venue and activities at future hackfests will be determined based on the number of active participants in the project. We welcome participation via the CTK email lists, the source code repository, and this website.

== Attendees ==

* So far we have received confirmation for the following people (in no particular order).

Please fill in your intentions in terms of common accommodation.

{|class="wikitable alternance" style="text-align:left; border:1px solid black;"
|+ '''''Participants'''''
|-
! scope=col style="background:#cde6f8;"| Name
! scope=col style="background:#cde6f8;"| Organization
|-
|Marco Nolden
|German Cancer Research Center, Heidelberg, Germany
|-
|Sascha Zelzer
|German Cancer Research Center, Heidelberg, Germany
|-
|Andreas Fetzer
|German Cancer Research Center, Heidelberg, Germany
|-
|Stefan Kislinkiy
|German Cancer Research Center, Heidelberg, Germany
|-
|Ralf Floca
|German Cancer Research Center, Heidelberg, Germany
|-
|Ivo Wolf
|Mannheim University of Applied Sciences, Germany
|-
|Steve Pieper
|Isomics, Inc., USA
|-
|Michael Onken
|Open Connections GmbH / OFFIS
|-
|Jean-Christophe Fillion-Robin
|Kitware, Inc., USA
|-
|Miklos Espak
|University College London, UK
|-
|Nicolas Toussaint
|University College London, UK
|-
|Gergely Zombori
|University College London, UK
|-
|Christian Askeland
|SINTEF Medical Technology, Trondheim, Norway
|-
|Stefan Baumann
|Basel, Switzerland
|-
|Hans Meine
|Fraunhofer MEVIS, Germany
|-
|}

{|class="wikitable alternance" style="text-align:left; border:1px solid black;"
|+ '''''Google Hangout Participants'''''
|-
! scope=col style="background:#cde6f8;"| Name
! scope=col style="background:#cde6f8;"| Organization
! scope=col style="background:#cde6f8;"| Availablity (Central European Time)
|-
|}



{{Note}}There were also other invitations sent to active people on the community, and people who recently showed interest. When their intent will be known they will be added to the list.

== Preparation ==

Developers should bring a laptop with the [http://github.com/commontk/CTK current CTK source code] downloaded and [[Build_Instructions|built]].

Use the [http://public.kitware.com/cgi-bin/mailman/listinfo/ctk-developers CTK developers mailing list] to discuss build issues and topics for ongoing work.

Phone conferences have been scheduled in the weeks leading to the event:

'''https://plus.google.com/hangouts/_/g3vi3lz7sycalj74ys2xpnpr3ya'''

== Topics and Projects ==

Consider reading [http://www.commontk.org/index.php/Contributing_to_CTK#Integrate_your_new_feature Contributing_to_CTK#Integrate_your_new_feature]

Reminder: when integrating branches, remember to use --log --no-ff when merging.

We plan to have concrete hacking topics as well as dedicated discussions in smaller groups. People are encouraged to show their interest in a particular subject by adding their name to the list below.

=== Hacking Topics ===

==== Infrastructure ====

* Qt5 migration (Christian)
** compile and run on Mac
* Packaging / install support (Marco, Jc)
* Fix issue related to [https://github.com/commontk/Artichoke Artichoke] and improve documentation (Jc)
* Dashboard
** General Situation: Continuous/Nightly clients, coverage
** Configurations: Qt4, Qt5, etc.
** Travis CI (Sascha, Steve)
* Incomplete doxygen on the website (Christian)
* Component / target oriented build system (Jc, Sascha)
* Review commontk/* repositories (delete/update/etc.)
* Check support for MacOS 10.10

==== DICOM ====

* dcmtk Features
** Support building with emscripten, pinnacle
** Multi-frame support (Steve, Christian, Michael)
** SEG support
*** Investigate compatibility of DCMTK seg functionality with BrainLab segmentations; [http://slicer.kitware.com/midas3/item/162562 sample dataset] (QIICR community, Steve has access) - RLE compressed
*** Investigate DCMTK RLE compression tools applied to segmentations; trying to apply it to sample objects generates "F: No conversion to transfer syntax RLE Lossless possible!" error; [http://slicer.kitware.com/midas3/item/162428 SPL segmentation dataset example], [http://slicer.kitware.com/midas3/item/161740 PET segmentation example]

* Making CLIs read and write valid DICOM (Steve, Michael)

* Anonymization (Andreas Fetzer, Marco, Steve, Stefan, Ralf)
** Client-side options: gdcmanon, dcmtk (?), dcmjs, DicomCleaner, CTP...
** Testing can use [[File:PieperMRI.tar.gz | this freely sharable identified MR scan]]
** Goal is to de-identify with various tools and compare results with [ftp://medical.nema.org/medical/dicom/Final/sup142_ft.pdf supplement 142 of the DICOM standard].
** There is a separate page, which provides an overview of existing de-identification tools: [[DICOM de-identification tool overview]]

* ctkDICOM improvments (Ralf); discussed ideas:
** Introduce "compact and detailed view mode" to ctkDICOMTableView and ctkDICOMTableManager. Basic idea is that you can give the widgets a list of "high priority" tags -> in compact mode all columns of non priority tags will be filter. You can define the active mode via property / slot (to e.g. easily connect it with a control widget signal).
** Refactoring of one unified "search definition widget" and separated generators for "dicom q/r" and sql statement that use the search definition. This would give the possibility for instance to use the same search widget in different places (e.g. in the ctkDICOMQueryRetrieveWidget or ctkDICOMTableManager)

==== XNAT ====

* Improve and extend the XNAT API (Sascha Zelzer, Miklos Espak, Ralf)
** Python Wrapping (Sascha, Nicolas)
** Data editing (post-poned)
** Uploading (Andreas, Ivo)
** Caching (Miklos, (Ralf))
** C++ VS XNAT data model (Nicolas, Andreas)
** Filtered data query based on data type and/or properties (Miklos)
** Launch pipelines (remote) and follow progress (Miklos)

==== CLI ====

* Make it customisable what options to generate to the final command (Gergely Zombori)
* Finalize integration of CTK CLI frontend into Slicer and investigate how to integrate the backend (Jc)
* Improved entry point / documentation for CLI users & developers

==== Documentation & Presentation ====

* Nice landing page?
* Improve wiki? Something different?

== Agenda ==

==== Monday ====

Start: The meeting room will be open starting at 9am. Official start and kick-off will be early afternoon after everybody arrived.

Opening discussion
* Review topics and projects
* Plans for the week
* Review [https://github.com/commontk/CTK/issues?state=open open issues on github].

Evening:

Dinner 20:15 @ [http://www.heidelberger-kulturbrauerei.de/en/ Kulturbrauerei], [https://www.google.de/maps/dir/Hotel+Holl%C3%A4nder+Hof,+Neckarstaden+66,+69117+Heidelberg/Kulturbrauerei+Heidelberg,+Leyergasse+6,+69117+Heidelberg/@49.413196,8.7102803,18z/data=!3m1!4b1!4m14!4m13!1m5!1m1!1s0x4797c10638e496a5:0xe28b6a91325a2c23!2m2!1d8.709242!2d49.413192!1m5!1m1!1s0x4797c1a81df9996d:0xb0cec22d395e79e1!2m2!1d8.713414!2d49.41318!3e2 directions], Pickup ~20:00 at Holländer Hof

==== Tuesday ====

Morning:

* Steve QIICR
* Michael Onken presentation about upcoming dcmtk modules
* XNAT discussion

Afternoon:

* 13:30 Lab Tour

Evening:

* 16:00 Famous Old City tour guided by Hans-Peter Meinzer

* 20:00 Beer Topics
** Defacing

==== Wednesday ====

Morning

During the day: hack, hack, hack...

==== Thursday ====

Morning:

* IGT & OpenIGTLink discussion

During the day: hack, hack, hack…

Short wrap-up:

Christian:
* Fixed Qt5 DICOM & Plugin Framework issues
* Doxygen fixes
* Started integrating CTK DICOM Widget improvements

JC:
* Using latest version of emscripten
* Website updates for dcmjs
* Re-started Slicer CTK CLI integration

Hans:
* Many discussion topics (Chronicle, CLI)
* CLI documentation overview (CTK Wiki)
* Investigated elasticsearch database for CLI modules
* OpenInventor <-> VTK integration

Stefan:
* Added [[Media:Testmr.txt | mapping/de-identification]] functionality to dcmjs (minimal feature set like CTP)

Steve:
* dcmjs organize tool
** exploring boundaries (extracting data etc.)
** anonymization
* DICOM segmentation object discussions
** How to support CLIs?

Michael:
* Compiled CTK with new dcmtk snapshot (worked)
* Worked on dcmseg module

Marco:
* Discussions about QIICR
* Closed a couple of GitHub issues

Ivo:
* Discussions about QIICR, XNAT
* Compiling MRML outside of Slicer

Andreas:
* XNAT upload (qRestAPI changes)
* DICOM discussions (widget usability, anonymization tools)

Nicolas:
* Wrapped XNAT library into Python (for usage in NiPype)
* Usage outside of a QApplication needs investigation

Gergely:
* Added possibility for optional CLI parameter

Miklos:
* Started XNAT query API
* Hit API limits -> focus on caching objects
* Needs more discussion

Sascha:
* Qt5 fixes
* Travis integration

Evening:

==== Friday ====

During the day: hack, hack, hack...

11:00: Closing discussion

Afternoon: hack or travel

== Travel & Hotel ==

===Local contacts===

* Marco Nolden (m.nolden@dkfz-heidelberg.de)
* Sascha Zelzer (s.zelzer@dkfz-heidelberg.de) [[File:Sascha_phone.png|130px]]
* Andreas Fetzer (a.fetzer@dkfz-heidelberg.de)

===Transportation===

It takes about an hour from Frankfurt Airport (FRA) to Heidelberg Main Station with one change in Mannheim. If you stay in the Old Town you can also look for connections going to "Heidelberg Altstadt". You can look it up at [http://www.bahn.de/p_en/view/index.shtml Deutsche Bahn], but they run quite frequently.

'''Local:''' from the Old Town, "Universitätsplatz", runs [http://www.vrn.de/mam/vrn/einfach-ankommen/dokumente/stadtlinienplaene/heidelberg_schematisch.pdf bus number 32] ([http://www.vrn.de/mam/vrn/einfach-ankommen/dokumente/stadtlinienplaene/heidelberg.pdf geographic map]) via Main Station to DKFZ, exit at "Chirurgische Klinik", bus direction is "Neuenheim". After you exit, DKFZ is on your right.

[[File:Heidelberg_map.png|700px]]

During the day the bus runs every 10 minutes in both directions, timetables are also available at [http://fahrplanauskunft.vrn.de/vrn/XSLT_TRIP_REQUEST2?language=en VRN].

==== To Frankfurt Airport ====

The German Railways is affected by a strike from Thursday to Monday morning. Trains will operate on a limited basis - check the website of [http://www.bahn.de Deutsch Bahn].

You may also use a [http://www.transcontinental-group.com/en/airport-shuttle-buchen Shuttle Bus] departing from the Crown Plaza in Heidelberg. It is recommended to book online as early as possible.

===Lodging===

We recommend to stay in the historic Old Town. There is an easy direct bus ride every 10 minutes from there to DKFZ.

We have reserved a number of rooms at the [http://www.hollaender-hof.de/en/ Holländer Hof] ([http://www.openstreetmap.org/?mlat=49.41317&mlon=8.70925#map=19/49.41317/8.70925 map]) hotel! Please use "CTK 2014" when you do a reservation there. Of course there are plenty of other hotels in that area, e.g. [http://www.hotel-goldener-hecht.de/ Goldener Hecht] or the oldest house in town, [http://www.ritter-heidelberg.de/ Hotel zum Ritter].

===Meeting Room===

The full address for the DKFZ is

Deutsches Krebsforschungszentrum
Im Neuenheimer Feld 280
69120 Heidelberg

We will meet in the main building on the second floor (European counting!). The cryptic room number is D0.02.032. Follow the description below to find it.

When leaving bus 32, you will see something similar to

[[File:DKFZ_Bus.jpg|600px]]

The large building on the right is the DKFZ main bulding

[[File:DKFZ_Hauptgebaeude_neu_600x402.jpg|600px]]

Walk through the main entrance and follow the map

[[File:DKFZ_Hackfest_map.jpg|600px]]

Ask the nice guys at the reception or call us in case of any problems.

===Weather===

November is a rather wet month. [http://www.weather-and-climate.com/average-monthly-Rainfall-Temperature-Sunshine,heidelberg,Germany Average weather in Heidelberg]

===Food===

Plan on having breakfast at your hotel before the meeting. Please email the organizers if you have any allergies or dietary restrictions.

Being a university and hospital campus, there are several lunch possibilities, including cafeterias, a students mensa, and two restaurants.

===Optional Activities in the Area===

File:Testmr.txt

2014-11-06T16:43:39Z

Stefan Baumann: First file fully anonymized using dcmjs!

First file fully anonymized using dcmjs!