https://www.na-mic.org/w/api.php?action=feedcontributions&user=Pinter&feedformat=atomNAMIC Wiki - User contributions [en]2024-03-19T08:37:53ZUser contributionsMediaWiki 1.33.0https://www.na-mic.org/w/index.php?title=Csaba_visit&diff=97982Csaba visit2017-10-24T13:58:26Z<p>Pinter: Logos, emails</p>
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== Introduction == <br />
<br />
Csaba Pinter of PERKLab in Kingston, Ontario, Canada has accepted the invitation to hold an introductory presentation at the [http://www.congress-service.hu/2017/audi/index.html 54th Congress of Audiology of the Hungarian Society of Oto-Rhino-Laryngology, Head & Neck Surgery].<br />
<br />
A section has been organized around his presentation introducing imaging-related work at the Department of Oto-rhino-larnygology and Head-neck surgery and a few related works from other Departments of the University of Szeged.<br />
<br />
Csaba has also held a seminar at the Department of Medical Physics and Medical Informatics. That presentation can also be found below.<br />
<br />
==Faculty==<br />
'''Local organizing contact''':<br />
<br />
'''Attila Nagy PhD''', Department of Oto-Rhino-Laryngology and Head and Neck Surgery and Department of Medical Physics and Medical Informatics, Szeged, Hungary<br />
<br />
''<email>attila@orl.szote.u-szeged.hu</email>''<br />
<br />
<br />
<br />
'''Visiting scientist''':<br />
<br />
'''Csaba Pinter''', Laboratory for Percutaneous Surgery, Queen's University, Kingston, Ontario, Canada<br />
<br />
''<email>csaba.pinter@queensu.ca</email>''<br />
<br />
==Presentation material==<br />
<br />
The presentations can be found below. Note that the slides are in Hungarian!<br />
The files are linked from the server of the Department of Oto-rhino-larnygology and Head-neck surgery.<br />
<br />
<br />
28. 09. 2017, Hotel Forrás<br />
<br />
*'''17:00-17:05''' Opening<br />
<br />
<br />
*'''17:05-17:30''' <br />
''Nyílt forráskódú szoftvercsomagok navigált orvosi beavatkozásokhoz''<br />
<br />
Pintér Csaba, Ungi Tamás, Lassó András, Fichtinger Gábor<br />
<br />
School of Computing, Queen’s University, Canada<br />
<br />
[http://www.orl.szote.u-szeged.hu/~attila/csaba_2017/Pinter_AudiSzeged_OpenSourceNavigation.pptx Slides]<br />
<br />
<br />
*'''17:30-17:40''' <br />
''MRI statisztikai szervatlasz generálása és kiértékelése a fej-nyak régióban''<br />
<br />
Tanács Attila<br />
<br />
Szegedi Tudományegyetem, Informatikai Intézet<br />
<br />
[http://www.orl.szote.u-szeged.hu/~attila/csaba_2017/TanacsA_AUDI2017.pdf Slides]<br />
<br />
<br />
<br />
*'''17:40-17:50''' <br />
''Nyaki érszegmentálás MR vizsgálatokon''<br />
<br />
Nagy Antal<br />
<br />
Szegedi Tudományegyetem, Informatikai Intézet, <br />
<br />
[http://www.orl.szote.u-szeged.hu/~attila/csaba_2017/NagyA_AUDI2017.pdf Slides]<br />
<br />
<br />
*'''17:50-18:00''' <br />
''A sziklacsont elhelyezkedésének változása a koponyán belül a gyermekkor során''<br />
<br />
Nagy Attila<sup>1,2</sup>, Ódor Boglárka<sup>1</sup>, Beöthy Fehér Orsolya<sup>1</sup>, Perényi Ádám<sup>1</sup>, Rovó László<sup>1</sup>, Kiss József Géza<sup>1</sup><br />
<br />
<sup>1</sup>Szegedi Tudományegyetem, Fül-orr-gégészeti és fej- nyaksebészeti klinika, Szeged<br />
<br />
<sup>2</sup>Szegedi Tudományegyetem, Orvosi fizikai és orvosi informatikai intézet, Szeged<br />
<br />
[http://www.orl.szote.u-szeged.hu/~attila/csaba_2017/NagyA_v5.pptx Slides]<br />
<br />
<br />
*'''18:00-18:10''' <br />
''A légúti szűkületek megoldását célzó műtétek hatásosságának vizsgálata számítógépes szimulációval''<br />
<br />
Szakács László<sup>1</sup>, Czirják Attila<sup>2</sup>, Nagy Attila<sup>1,3</sup>, Sztanó Balázs<sup>1</sup>, Kiss József Géza<sup>1</sup>, Rovó László<sup>1</sup><br />
<br />
<sup>1</sup>Szegedi Tudományegyetem, Általános Orvostudományi Kar, Fül-orr-gégészeti és Fej-nyaksebészeti klinika, Szeged<br />
<br />
<sup>2</sup>Szegedi Tudományegyetem, Természettudományi és Informatikai kar, Elméleti Fizikai Tanszék, Szeged<br />
<br />
<sup>3</sup>Szegedi Tudományegyetem, Általános Orvostudományi Kar, Orvosi Fizikai és Orvosi Informatikai Intézet, Szeged<br />
<br />
[http://www.orl.szote.u-szeged.hu/~attila/csaba_2017/ Slides] (to be uploaded)<br />
<br />
<br />
*'''18:10-18:20''' <br />
''Számítógépen készített és tárolt 3 dimenziós objektumok manipulálására alkalmas szoftver fejlesztése''<br />
<br />
Vörös Csaba<sup>1</sup>, Nagy Attila<sup>1,2</sup>, Rovó László<sup>1</sup>, Kiss József Géza<sup>1</sup><br />
<br />
<sup>1</sup>Szegedi Tudományegyetem, Fül-orr-gégészeti és fej- nyaksebészeti klinika, Szeged<br />
<br />
<sup>2</sup>Szegedi Tudományegyetem, Orvosi fizikai és orvosi informatikai intézet, Szeged<br />
<br />
[http://www.orl.szote.u-szeged.hu/~attila/csaba_2017/Conference%20presentation.pptx Slides]<br />
<br />
<br />
*'''18:20-18:30''' <br />
''Több szabadsági fokú beviteli eszköz fejlesztése számítógéppel segített műtéttervezéshez''<br />
<br />
Vecsernyés Endre<sup>1</sup>, Nagy Attila<sup>1,2</sup>, Tóth Ferenc <sup>1</sup>, Rovó László<sup>1</sup>, Kiss József Géza<sup>1</sup><br />
<br />
<sup>1</sup>Fül-orr-gégészeti és fej-nyaksebészeti klinika, Szegedi Tudományegyetem, Szeged<br />
<br />
<sup>2</sup>Orvosi Fizikai és Orvosi Informatikai Intézet, Szegedi Tudományegyetem, Szeged<br />
<br />
[http://www.orl.szote.u-szeged.hu/~attila/csaba_2017/VE_AUDI.pptx Slides]<br />
<br />
<br />
<br />
28. 09. 2017, Department of Medical Physics and Medical Informatics<br />
*'''14:00-14:50''' <br />
Slides of the seminar at the Department of Medical Physics and Medical Informatics<br />
<br />
[http://www.orl.szote.u-szeged.hu/~attila/csaba_2017/Pinter_OrvosiInformatikaSzeged_3DSlicer.pptx Slides]</div>Pinterhttps://www.na-mic.org/w/index.php?title=File:CCO-English-Only_Logo_Black-200x94.png&diff=97981File:CCO-English-Only Logo Black-200x94.png2017-10-24T13:57:00Z<p>Pinter: </p>
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<div></div>Pinterhttps://www.na-mic.org/w/index.php?title=File:NSERC_small.jpg&diff=97980File:NSERC small.jpg2017-10-24T13:52:49Z<p>Pinter: </p>
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<div></div>Pinterhttps://www.na-mic.org/w/index.php?title=File:LogoCco.jpg&diff=97979File:LogoCco.jpg2017-10-24T13:51:56Z<p>Pinter: </p>
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<div></div>Pinterhttps://www.na-mic.org/w/index.php?title=File:CANARIE_v_small.png&diff=97978File:CANARIE v small.png2017-10-24T13:49:52Z<p>Pinter: </p>
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<div></div>Pinterhttps://www.na-mic.org/w/index.php?title=Events&diff=97966Events2017-09-21T18:38:53Z<p>Pinter: /* Upcoming Events */</p>
<hr />
<div>__NOTOC__<br />
== Introduction ==<br />
NA-MIC organizes a variety of events:<br />
* Workshops address specific research focus areas. <br />
* Training events aim at training NA-MIC participants and outsiders in NA-MIC technologies. <br />
* Project weeks are intended for making progress in a variety of projects. <br />
<br />
The majority of NA-MIC events are hands-on and open to collaborators and interested scientists.<br />
<br />
== [[TCON:Main|Telephone Conferences]] ==<br />
== Upcoming Events ==<br />
===2017===<br />
*'''September 18:''' [[HST.583_2017 | Harvard-MIT Division of Science Health and Technology HST.583 Lab- The Life Cycle of Medical Imaging Data]]<br />
*'''September 19:''' [[BWH_Radiology_Residency_Research_Course_Seminar|BWH Radiology Residency Research Course Seminar]]<br />
*'''September 28:''' Csaba Pinter invited presentation [http://www.congress-service.hu/2017/audi/index.html Congress of Audiology], Szeged, Hungary<br />
*'''November 20:''' [[HST.583_2017_Brain_Mapping_for_Neurosurgery | Harvard-MIT Division of Health Science and Technology HST.583 Lab - Brain Mapping for Neurosurgery]]<br />
*'''November 26-December 1:''' [[RSNA_2017| 103rd Scientific Assembly and Annual Meeting of the Radiological Society of North America (RSNA 2017)]], Chicago, IL<br />
<br />
===2018===<br />
*'''January 8-12''': [[Project_Week_27| 27th Project Week, MIT]] <br />
*'''June 25-29''': [[Project_Week_28|28th Project Week, Gran Canaria]]<br />
*'''October 7:''' [http://ncigt.org/igt10 10th NCIGT and NIH Image Guided Therapy Workshop], Boston, MA<br />
<br />
== Standing Events ==<br />
* [[TCON:Main|A list of all upcoming and past teleconferences]]<br />
* [[Engineering:Programming_Events|Hands on Project Events]]<br />
* [https://www.slicer.org/wiki/Slicer:Developer_Meetings Slicer developer meetings]<br />
* [[Event:Journal Club at BWH|Journal Club at BWH]]<br />
<br />
== Past Events ==<br />
===2017===<br />
*September 14: [[MICCAI2017_POCUS_Workshop| POCUS Workshop, MICCAI 2017]], Quebec City, Quebec, Canada<br />
*September 10: [http://qiicr.org QIICR] organized [http://qiicr.org/dicom4miccai DICOM4MICCAI] tutorial at [https://miccai2017.org MICCAI 2017]<br />
*September 8-9: Greg Sharp invited presentation at [http://cbfm2017.com.br/| Brazilian Congress of Medical Physics], Ribeirão Preto, Brazil<br />
----<br />
*July 17-21: [http://wiki.imaging.robarts.ca/ 26th Project Week], Robarts Research Institute, London, ON, Canada<br />
----<br />
*June 26-30: [[2017_Summer_Project_Week|25th Project Week]], Catanzaro Lido, Calabria, Italy<br />
*June 13: [[2017_Non_Profit_Summer_Camp|Healthy Girls Save the World Camp]], UNC-Chapel Hill, NC<br />
*June 6: [[June_2017_BWH_Radiology_Resident_Education| BWH Radiology Resident Research Seminar]], Boston, MA<br />
----<br />
*May 24: [[M-DBS_Workshop2017|M-DBS 2017 Workshop, ICM]], Paris, France <br />
----<br />
*April 22: [[ISMRM_2017| Annual Meeting of the International Society for Magnetic Resonance in Medicine (ISMRM 2017), Honolulu, HI]]<br />
----<br />
*March 25: [[2017_IADR_Workshop|DCBIA Craniofacial Workshop]], 95th General Session & Exhibition of the IADR, San Francisco, CA<br />
*March 14-15: [http://ncigt.org/igt9 9th NCIGT and NIH Image Guided Therapy Workshop], Bethesda, MD<br />
*March 11-12: [[Hiroshima_2017|Seminar for Young Researchers]], Hiroshima, Japan<br />
----<br />
*February 1: [[2017_Universite_Catholique_Lille| 3D Slicer presentation]], Université Catholique de Lille, France<br />
----<br />
*January 12: [[2017_Tutorial_Contest| 2017 Tutorial Contest]], MIT<br />
*January 10: [[BWH_Radiology_Residents_Workshop|BWH Radiology Residents Workshop]], Boston, MA<br />
*January 9-13: [[2017_Winter_Project_Week|Winter Project Week]], MIT<br />
<br />
===2016===<br />
*November 27-December 2: [[RSNA_2016| 102nd Annual Meeting of the Radiological Society of North America, RSNA 2016]], Chicago, IL<br />
*November 17: [[2016_BWH_Radiology_Resident_Education | Radiology Residents 3D Slicer Hands-on workshop]], Boston, MA <br />
----<br />
*October 21: [http://interactivemedical.org/imic2016/ Interactive Medical Image Computing (IMIC) Workshop], Athens, Greece<br />
*October 17-21: [http://miccai.org/ MICCAI 2016], Athens, Greece<br />
*October 7-8: [[media:11thIMRI-Brochure-final.pdf | 11th Interventional MRI Symposium]], Baltimore, MD <br />
**[http://www.hopkinscme.edu/CourseDetail.aspx/80038447 Registration]<br />
**[https://easychair.org/conferences/?conf=imri2016 Abstract Submission] <br />
----<br />
*September 15: [[2016_BWH_Resident_Education | 3D Slicer seminar for BWH Radiology Residents]], Brigham and Women's Hospital, Boston, MA<br />
----<br />
*August 31: [[2016_Beth_Israel_Training_Workshop | 3D Slicer Hands-on Training Workshop]], Beth Israel Deaconess Medical Center, Boston, MA<br />
----<br />
*June 20-25: [[2016_Summer_Project_Week| '''Summer Project Week''']], Heidelberg, Germany<br />
*June 8: [[2016_Beth_Israel_Psychiatry_Seminar | 3D Slicer Seminar, Beth Israel Deaconess Medical Center]], Boston, MA<br />
----<br />
* May 23-27: [https://docs.google.com/document/d/1BIQHLheqYhsfeHhCTVtid5bZMVywlo1UmeK6-ZmHeq8/edit Medical Image Webapp Software Hackfest], Boston, MA<br />
----<br />
*April 27: Andrey Fedorov invited presentation at the [https://cancer.stonybrookmedicine.edu/2016_ResearchSymposium 2016 Gloria and Mark Snyder Symposium for Cancer Medicine], Stony Brook, NY ([https://dx.doi.org/10.6084/m9.figshare.3205939.v1 | slides])<br />
*April 15: [[Mount_Sinai_Hospital_Workshop | 3D Slicer Workshop]], Mount Sinai Hospital, NYC, NY<br />
*April 14: [[StonyBrook_Workshop | 3D Slicer Workshop]], Stony Brook University, Stony Brook, NY<br />
*April 8-9: [[SPL25| SPL 25th Anniversary Celebration]], Harvard Medical School, Boston, MA<br />
*April 5: Greg Sharp lecture ''3D Slicer for Radiotherapy Research'' at [http://dsmf-symposium.dk/program.html Danish Society for Medical Physics Symposium], Copenhagen, Denmark<br />
----<br />
*March 15-16: [http://ncigt.org/8th-ncigt-and-nih-image-guided-therapy-workshop 8th NCIGT and NIH Image Guided Therapy Workshop], Bethesda, MD<br />
*March 13: Ron Kikinis invited presentation at [http://www.ci4cc.org/events/spring2016 Cancer Informatics for Cancer Centers (CI4CC) Spring 2016 Symposium and workshop], Napa, CA (Workshop materials: http://qiicr.org/CI4CC-Spring2016-ASW)<br />
----<br />
*February 11: [[FAID_2016|ICM-MIT-Harvard workshop, French American Innovation Day]], MIT <br />
----<br />
*January 26: [http://iactalks.iac.es/talks/view/865 Ron Kikinis' invited presentation at Instituto de Astrofísica de Canarias - IAC, "Tsunami in the Procedure Room, the Growing Challenge of Managing Data in Image Guided Interventions and Surgery"]<br />
*January 14: [[CHB|3D Slicer Workshop at Children's Hospital]], Boston, MA<br />
*January 7: [[Events:TutorialContestJanuary2016 |2016 Tutorial Contest]], MIT<br />
*January 4-8: [[2016_Winter_Project_Week|'''Winter Project Week''']], MIT<br />
<br />
===2015===<br />
*December 14-18: [[Montevideo_Uruguay_2015| 3D Slicer and SlicerIGT at Universidad de la República]], Montevideo, Uruguay<br />
----<br />
*November 29-December 4: [[RSNA_2015| 101th Annual Meeting of the Radiological Society of North America, RSNA 2015]], Chicago, IL<br />
*November 26-28: [[SlicerCMFWorkshop_Italy2015 | Cranio Maxillo Facial imaging workshop using SlicerCMF]], Italy<br />
*November 23: [[HST.583_2015_Brain_Mapping_for_Neurosurgery | Harvard-MIT Division of Health Science and Technology HST.583 Lab - Brain Mapping for Neurosurgery]]<br />
*November 19: [[Brown_2015| 3D Slicer Workshop at Brown University]], Providence, RI<br />
*November 16: [[MGH_2015 | 3D Slicer Tutorial]], MGH, Boston, MA<br />
----<br />
*October 19-21: [http://www.ci4cc.org/events/fall2015 Fall 2015 CI4CC Symposium and Workshop]: [https://goo.gl/MDq0u8 Quantitative Image Informatics for Cancer Research (QIICR) presentation by Andrey Fedorov], San Diego, CA<br />
*October 9: [http://interactivemedical.org/imic2015/ MICCAI 2015 - Interactive MIC 2nd edition], Munich, Germany<br />
*October 5: [http://projects.iq.harvard.edu/dtichallenge15/home MICCAI 2015 DTI Challenge Workshop - 5th edition], Munich, Germany<br />
----<br />
*September 14: [[HST.583_2015 | Harvard-MIT Division of Science Health and Technology HST.583 Lab- The Life Cycle of Medical Imaging Data]]<br />
*September 1: [[Events:2015_Ron_visit|SPL Introduction and Slicer Workshop]], Szeged, Hungary<br />
----<br />
*August 29: Ron Kikinis Keynote Lecture "[[media:2015-09-06-Tsunami.pptx |Tsunami in the Procedure Room]]: The Growing Challenge of Managing Data in Image-Guided Interventions and Surgery" at the [http://www.iccas.de/symposium/ ICCAS International Symposium on Computer-Assisted Surgery], Leipzig, Germany (the download is about 49MB) <br />
*August 24-25: [[Brno_visit_2015| dMRI Collaboration with CEITEC]], Brno, Czech Republic<br />
*August 17: Ron Kikinis presented the state of 3D Slicer to BISTI, Natcher Building, NIH, Bethesda, MD ([[media:2015-11-11-Slicer-Status.pptx|download here, ~79MB]]).<br />
*August 7-8: Steve Pieper presented 3D Slicer at [http://www.mbl.edu/imaging/escaping-flatland-workshop-2015/| Escaping Flatland: Imaging biological architecture and events in 3 dimensions], Woods Hole Marine Biology Laboratory. [http://videocenter.mbl.edu/videos/video/1123/ Video of the event] is available. Note that two feeds are available and the user can toggle between the live video and the screen.<br />
*August 6: [[Slicer_WS_Morioka_2015| Slicer Workshop]], Morioka, Iwate, Japan<br />
----<br />
*July 15: [http://aapm.org/meetings/2015AM/PRAbs.asp?mid=99&aid=27746 American Association for Medical Physics: Open Libraries for Research], Anaheim, CA<br />
----<br />
*June 21-24: [[2015_Summer_Project_Week|'''Summer Project Week''']], Barcelona, Spain<br />
*June 11: [[UNC_2015 | 3D Slicer Training Workshop for NeuroImaging]], University of North Carolina at Chapel Hill, NC<br />
*June 8: [[BU_2015 | 3D Slicer Training Workshop for Radiologists]], Boston University School of Medicine, Boston, MA<br />
*June 7: [[Autoseg_2015 | Automatic Segmentation Algorithm Workshop]], Toronto, Canada<br />
*June 7: [[IUPESM_2015| Slicer RT Tutorial, World Congress on Medical Physics and Biomedical Engineering]], Toronto, Canada<br />
----<br />
*May 27: [http://qiicr.org QIICR] presentation and 3D Slicer demo at the annual meeting of the NCI [http://itcr.nci.nih.gov/ Informatics Technology for Cancer Research (ITCR)] project, UCSD, San Diego, CA<br />
----<br />
*April 13-14: demonstration of 3D Slicer at the annual face-to-face meeting of the NCI Quantitative Imaging Network, Rockville, MD<br />
----<br />
*March 30-31: 3D Slicer invited demonstrations at [http://www.ci4cc.org/events/spring2015 Cancer Informatics for Cancer Centers (CI4CC) Spring 2015 Symposium & Genomics Workshop], Bethesda, MD<br />
*March 26: [[Shiga_2015_Workshop | 3D Slicer Workshop]], Shiga, Japan<br />
*March 25-26: [[Shanghai_2015 | 3D Slicer Invited Workshop]], Shanghai, China<br />
*March 24: [[Hangzhou_2015 | 3D Slicer Invited Workshop]], Hangzhou, China<br />
*March 11: [[Construction and Superimposition of 3D Surface Models IADR 2015]], Boston, MA<br />
----<br />
*February 27-28: [[2015_TWMU_Seminar| Medical Device Seminar]], Tokyo Women's Medical University, Tokyo, Japan<br />
*February 19: [[Stanford 2015|3D Slicer invited tutorial]], Stanford University<br />
----<br />
*January 22: [http://acoustic.univ-rennes1.fr/doku.php/mdbs2015 Deep Brain Stimulation Workshop], Rennes, France<br />
*January 5-9: [[2015_Winter_Project_Week| '''Winter Project Week''']], Salt Lake City, UT<br />
<br />
===2014===<br />
*December 16-17: [[Moffitt_2014|3D Slicer Invited workshop]], Moffitt Cancer Center, Tampa, FL<br />
----<br />
*November 30-December 5: [[RSNA_2014| 100th Annual Meeting of the Radiological Society of North America, RSNA 2014]], Chicago, IL<br />
*November 18-19: [[Iowa2014| 3D Slicer Workshop]], Iowa City, IA<br />
*November 20: [[CMF_Workshop_Cleveland_2014| 3D Cranio Maxillo Facial workshop]], CWRU, Cleveland, OH<br />
----<br />
*October 27: [[Prof_Sugiyama_and_Dr_Oyama_visit | Prof. Sugiyama and Dr. Oyama visit at BWH]]<br />
*October 18-22: [http://w3.cns.org/meetings/2014/ Annual Meeting of the Congress of Neurological Surgeons], Boston, MA<br />
*October 10-11: [http://radiologie.uniklinikum-leipzig.de/radiologie.site,postext,imri,a_id,700.html 10th Interventional MRI Symposium], Leipzig, Germany<br />
*October 4: [[Pretoria2014| 3D Slicer Workshop]] at the [http://www.pah.org.za/ Steve Biko Academic Hosptial] in Pretoria, South Africa<br />
----<br />
*September 18-19: 7th NCIGT and NIH Image Guided Therapy Workshop, Cambridge, MA<br />
*September 18: [http://www.slicerigt.org/wp/miccai-2014-tutorial/ Building image-guidance systems from open-source components] tutorial at MICCAI'14, Cambridge, MA<br />
*September 15: [[DBS_Meeting_2014 | Deep Brain Stimulation Meeting, MICCAI 2014]], Boston, MA<br />
*September 14: [[DTI_Challenge_2014| DTI Tractography Challenge, MICCAI 2014]], Boston, MA<br />
*September 14: [http://interactivemedical.org/imic2014/index.html IMIC 2014 at MICCAI 2014], Boston, MA<br />
----<br />
*August 26-30: [http://www.slicerigt.org/wp/embc-2014-tutorial/ EMBC'14 Tutorial: Building image-guidance systems from open-source components], Chicago, IL<br />
*August 5: [[AAPM 2014 | 3D Slicer User Group at AAPM 2014]], Austin, TX<br />
----<br />
*July 1: [[2014_Neurotrauma_Symposium| 32nd Annual Neurotrauma Symposium: S08 Breakout Session on Advances in Multimodal Imaging of TBI]] organized by John van Horn with scientific presentations by Guido Gerig and Andrei Irimia (all NA-MIC), San Francisco, CA<br />
----<br />
*June 26: [http://www.na-mic.org/Wiki/index.php/2014_Tutorial_Contest Slicer Tutorial Contest, MIT, Cambridge, MA ]<br />
*June 23-27: [[2014_Summer_Project_Week| '''Summer Project Week at MIT''']]<br />
----<br />
*April 15:[[Brown_University_Workshop | 3D Slicer workshop]], Brown University, Providence, RI<br />
----<br />
*March 28: [http://slicer.kitware.com/midas3/download/item/133719/2014-QIN_F2F-Fedorov-QIICR_Slicer.pdf Slicer/QIICR presentation] Annual Face to face meeting of the Quantitative Imaging Network, NCI, Rockville, MD<br />
*March 19: [[CEA_2014| Follow-up meeting on the use of Slicer]] Prof. Dhenain's team, CEA Paris, France<br />
*March 10-14: [[Pichl_2014| Winter School for Medical Physics]], Pichl-Schladming, Austria<br />
*March 6-10: [[ECR_2014| European Congress of Radiology]], Vienna, Austria<br />
----<br />
*February 18-20: [[Second_Medical_Image_Registration_Retreat,_Puerto_Rico| Second Medical Image Registration Retreat]], San Juan, Puerto Rico<br />
*February 16: [[SPIE_2014 | Grand Challenges Panel]], SPIE 2014, San Diego, CA<br />
*February 14: [http://www.na-mic.org/Wiki/index.php/USC_2014 Slicer Training Workshop], Los Angeles, CA<br />
----<br />
*January 27-29: [http://www.na-mic.org/Wiki/index.php/TWMU_Visit_2014 Visit by Tokyo Women's Medical University and Japan National Cancer Center], SNR Lab, BWH, Boston, MA<br />
*January 7: [http://wiki.na-mic.org/Wiki/index.php/2014_SLC_Training_Workshop 3D Slicer Training Workshop], Salt Lake City, UT<br />
*January 6-10: [[AHM_2014| '''AHM, EAB''']], [[2014_Winter_Project_Week|'''Winter Project Week''']], Salt Lake City, UT<br />
*January 4: [http://www.sci.utah.edu/cibcwksp2014.html Software Tools for Image Based Modeling, Simulation, and Visualization], Workshop, Salt Lake City, UT<br />
<br />
===2013===<br />
*December 17: [http://wiki.na-mic.org/Wiki/index.php/CEA_2013 MIRCEN/CEA Slicer event], Paris, France<br />
*December 1-6: [[RSNA_2013| RSNA 2013]], Chicago, IL<br />
----<br />
*November 20: [[CMF_Workshop_Cleveland_2013| 3D Cranio Maxillo Facial Workshop, CWRU]] Cleveland, OH<br />
----<br />
*October 27-30:[[TWMU_Visit_2013| Visit by Tokyo Women's Medical University Visit]], SNR Lab, BWH<br />
*October 22-23:[[QIICR_2013| QIICR brainstorming and kickoff meeting]], 1249 Boylston St., Boston<br />
*October 17: [[Brno_2013| 3D Slicer Workshop]], Brno, Czech Republic<br />
----<br />
*September 30: [[Changchun_2013| 3D Slicer invited seminar]], Changchun, China<br />
*September 29: [[Beijing_2013| 3D Slicer Invited Workshop, PLA Hospital]], Beijing, China<br />
*September 26: [http://www.dkfz.de/en/mbi/ctk-miccai2013/index.html MICCAI 2013 CTK Tutorial], Nagoya, Japan<br />
*September 22: [[MICCAI2013| MICCAI 2013 DTI Tractography Challenge on Peritumoral White Matter Anatomy for Neurosurgical Decision-Making]], Nagoya, Japan<br />
*September 11: [[WFNS2013| Sonia Pujol's invited lectures, 15th WFNS World Congress of Neurosurgery]], Seoul, Korea<br />
----<br />
*August 5: [[AAPM 2013 | 3D Slicer User Group, AAPM 2013]], Indanapolis, IN<br />
*August 1-2: [[BRAINS_CAMP| BRAINSCamp Workshop]], Iowa City, IA<br />
----<br />
*July 19: [[Dr.Dhenain's visit to the SPL, Boston, MA |Dr. Dhenain's visit to the SPL]], Boston, MA<br />
----<br />
*June 26-29: [[CARS2013| 3D Slicer hands-on workshop on Image-Guided Therapy and joint Slicer/CTK/MITK Workshop]], CARS 2013, Heidelberg, Germany<br />
*June 26: [http://tbi.ci.uchicago.edu/diffusion-mri-tbi-workshop Diffusion MRI in Traumatic Brain Injury 2013; Workshop on Diffusion MRI in Traumatic Brain Injury: Software Tools and International Shared Data Repository], Heidelberg, Germany<br />
*June 17-21: [[2013_Summer_Project_Week|'''Summer Project Week at MIT]]''', [[2013_Tutorial_Contest|Summer 2013 Tutorial Contest]]<br />
*June 14: [[UAEM_Visit|Prof. Avila-Vilchis and Prof. Vilchis-Gonzales visiting the SPL]], Boston, MA<br />
*June 14: [[BWH_2013| 3D Slicer Hands-on Workshop]], Surgical Planning Lab, 1249 Boylston St., Boston, MA<br />
----<br />
*May 31: [[AAPM_New_England_Chapter_Summer_Meeting| Invited Lecture, AAPM Chapter New England Summer Meeting]], Portsmouth, NH<br />
*May 24: [[Kitware_Course| 3D Slicer: Visualize and Analyze your datasets, Kitware Training Course,]] Lyon, France<br />
*May 20-24: [http://www.commontk.org/index.php/CTK-Hackfest-May-2013 CTK Hackfest], Kingston, Ontario, Canada<br />
*May 11: [http://www.youtube.com/watch?v=9t1V-Ro0Cak SlicerIGT hands-on demo], Science Rendezvous, Kingston, Ontario, Canada<br />
----<br />
*April 22: [[2013_ISMRM_CardiacStudyGroup_CARMA|ISMRM 2013 Cardiac Study Group Tutorial]]: Slicer for segmentation and enhancement quantification in cardiac LGE-MRI. Salt Lake City, UT<br />
*April 15: [[2013_Juntendo_University| DTI Challenge Presentation, Jutendo University, Tokyo, Japan]]<br />
*April 10-11: [http://www.na-mic.org/Wiki/index.php/Iwate_2013_Training Slicer Ultrasound Workshop], Iwate, Japan<br />
*April 9: [http://www.na-mic.org/Wiki/index.php/Tokyo_2013_Training Slicer Workshop], Tokyo, Japan<br />
*April 8: [[Imaging_in_Neuroscience| Imaging in Neuroscience Course]], Boston<br />
----<br />
*March 21-23: [http://ncigt.org/igt6 6th NCIGT and NIH Image Guided Therapy Workshop] in Crystal City, VA<br />
*March 11: [[CIR_visit_Vienna_Medical_Center | Slicer Lecture]], Computational Image Analysis and Radiology Laboratory, Medical University, Vienna, Austria<br />
*March 11: [[SlicerRT_workshop | SlicerRT Workshop]], Medical University, Vienna, Austria<br />
*March 8: [http://www.na-mic.org/Wiki/index.php/Autoseg_2013 Automatic Segmentation Algorithm Workshop], Boston, MA<br />
*March 7-11: [http://www.na-mic.org/Wiki/index.php/ECR_2013 European Congress of Radiology], Vienna, Austria<br />
*March 4-5: 3D Slicer is presented at the annual face-to-face meeting of the [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin NCI Quantitative Imaging Network ] ([[Media:3DSlicer-NCI-QIN-F2F-March2013_poster_Fedorov.ppt|poster]] and [[Media:3DSlicer-NCI-QIN-F2F-March2013_tool_sharing_slides_Fedorov.ppt|slides]])<br />
*March 4: [[2013-03-4- TWMU_Visit| Delegates from Research Administration Office, Tokyo Women's Medical University visits SNR Lab/NCIGT and AMIGO]]<br />
----<br />
*February 28-March 5: [[2013_Dr_Chen_Visit | Visit of Dr. Xiaolei Chen, PLA General Hospital, Beijing]], SPL<br />
*February 22: [[2013-02-22 Dr. Takahashi's Visit to SNR Lab/NCIGT and AMIGO|Dr. Takahashi's Visit to SNR Lab/NCIGT and AMIGO]]<br />
*February 14: [[2013-02-14-Slicer_Demo_at_Memorial_Sloan_Kettering_Cancer_Center | Demo of the Slicer segmentation and registration tools]], Memorial Sloan Kettering Cancer Center<br />
*February 14: [[2013-02-14-Korean_Surgical_Robot_Research_Team_Visit | Surgical Navigation and Robotics Laboratory hosts a robotic surgery research group from Korea]]<br />
*February 9-14: [http://www.na-mic.org/Wiki/index.php/SPIE_2013_DTI_Workshop SPIE 2013 Diffusion Tensor Imaging Course], Orlando, FL<br />
*February 7: [[2013-02-07-MGH_Slicer_user_meeting | Slicer user/developer meeting with the MGH user group]]<br />
----<br />
*January 31: [[GolbyLabMeeting_DTIChallenge | MICCAI DTI Challenge Presentation]], Golby Lab Meeting, Brigham and Women's Hospital, Boston, MA<br />
*January 28: [http://www.assembla.com/wiki/show/slicerrt/20130128_slicer_matlab_personal_cloud_meeting Slicer Matlab personal cloud meeting]<br />
*January 7-11: [[AHM_2013|'''AHM, EAB, Winter Project Week in Salt Lake City]]'''<br />
<br />
===2012===<br />
*December 10: [[ PNL_2012 | PNL Slicer4 Training Workshop]]<br />
*December 3: [[HST_2012 | Harvard-MIT Division of Health Science and Technology - Diffusion Tensor Imaging Course]]<br />
----<br />
*November 25-30: [[RSNA_2012 | 98th Annual Meeting of the Radiological Society of North America (RSNA 2012)]], Chicago, IL<br />
*November 14: [[CMF_Workshop_Cleveland_2012| 3D Cranio Maxillo Facial Workshop, CWRU]] Cleveland, OH<br />
*November 8-9: [http://meetings.nigms.nih.gov/index.cfm?event=general&ID=15208 NCBC showcase event in Washington DC]: [[media:NA-MIC-Overview-2012-11.pdf|PDF of the overview slides]]<br />
----<br />
* October 8: [[Niguarda_Ospedale_Visit| Invited visit to the Epilepsy and Parkinson Surgery Centre "Claudio Munari" Ospedale Niguarda "Ca' Granda"]], Milan, Italy<br />
* October 1: [[DTI_Tractography_Challenge_MICCAI_2012| DTI Tractography Challenge, MICCAI 2012, Nice, France]]<br />
* October 1: [http://www.sci.utah.edu/stia2012-home.html 2nd International MICCAI Workshop on Spatiotemporal Image Analysis for Longitudinal and Time-Series Image Data (STIA'12]), MICCAI 2012, Nice, France<br />
----<br />
* September 25-26: [[Pieper-MeVis-2012-09| Steve Pieper visited MeVis]]<br />
* September 21: [http://www.ncigt.org/pages/IGT_Workshop_2012 5th NCIGT and NIH Image Guided Therapy Workshop], Boston, MA<br />
* September 20: [[DrShekhar_Visit_Sep_2012|Dr. Raj Shekhar's visit to NCIGT]]<br />
* September 12: [[Universidad Autonoma del Estado de Mexico Symposium | 3DSlicer invited lecture]], First Symposium on Medical Bioengineering, Universidad Autónoma del Estado de México, Mexico City, Mexico<br />
* September 10:''' [[HST_583_2012| Harvard-MIT Division of Science Health and Technology HST.583 - Neuroimage Analysis Lab]]<br />
----<br />
* August 29: [[BU_Slicer4_Training_Session| BU Slicer4 Training session]]<br />
* August 20-21: [[Core 1 Retreat 2012|Core 1 Retreat 2012]] Park City, UT<br />
* August 20: [[Slicer4.2Planning|Slicer 4.2 Planning meeting]]<br />
----<br />
* July 30: [[AAPM_2012 | 3D Slicer User Group]] AAPM, Charlotte, NC<br />
* July 9-13: [http://www.commontk.org/index.php/CTK-Hackfest-Jul-2012 CTK Hackfest], Boston, MA<br />
----<br />
* June 30: [[CARS_2012 | NA-MIC IGT Workshop, CARS 2012]] <br />
* June 18-22: [[2012_Summer_Project_Week|'''Summer Project Week at MIT''']]; [[2012_Tutorial_Contest| Summer 2012 Tutorial Contest]]<br />
----<br />
* May 21-22: [[Madrid-May-21-2012-Slicer-Workshop| Slicer workshop]] Madrid, Spain<br />
* May 16: [http://www.ias.uwa.edu.au/lectures/kikinis| Public lecture, UWA], Perth, Australia <br />
* May 14: [http://www.ias.uwa.edu.au/masterclass/kikinis Masterclass, UWA], Perth, Australia<br />
* May 2: [http://www.hisa.org.au/events/event_details.asp?id=224112 Slicer Workshop], St. Vincent's Hospital, Fitzroy, Melbourne, Australia <br />
----<br />
* April 30-May 1: [http://www.cs.ucl.ac.uk/opensource_mia_ws_2012/ Slicer presentation], International Symposium on Biomedical Imaging (ISBI 2012)], Barcelona, Spain<br />
* April 26: [http://www.hisa.org.au/events/event_details.asp?id=224111 Slicer Workshop], St. Vincent's Hospital, Sydney, Australia<br />
* April 5: [[NEU-Medical-Physics-Seminar| Northeastern University Medical Physics Seminar, Gregory Sharp, Nobuhiko Hata]]<br />
----<br />
* March 20-21: [[Iowa-March-20-2012-Slicer-Workshop| Slicer Workshop in Iowa]] <br />
* March 16: [[Particle_UNC_Utah| Particle training seminar, UNC]] Chapel Hill, NC<br />
* March 5-6: Slicer booth presentation at the annual [https://wiki.nci.nih.gov/display/CIP/QIN Quantitative Imaging Network] face-to-face meeting; NCI, Washington DC<br />
----<br />
* February 29: [[Chapel-Hill-February-29-2012-Slicer-Talk| Slicer talk]], UNC<br />
* February 27: [[Slicer-4.1| Plans for Slicer 4.1]]<br />
* February 14: [[TWMU_Medtronics_OpenIGTLink| TWMU Open IGT Link - Stealth station Project, Kick-off]], Tokyo, Japan<br />
* February 5: [[SPIE_2012_DTI_Workshop| SPIE 2012 DTI Course]], San Diego, CA<br />
----<br />
* January 9-13: [[AHM_2012|'''AHM, EAB'']], [[2012_Winter_Project_Week|'''Winter Project Week in Salt Lake City''']]<br />
<br />
=== 2011 ===<br />
*November 27-December 2: [[RSNA_2011 | 97th Annual Meeting of the Radiological Society of North America (RSNA 2011)]], Chicago, IL<br />
*November 14-18: [http://www.commontk.org/index.php/CTK-Hackfest-Nov-2011 CTK Hackfest], Sophia Antipolis, France<br />
*November 11: [[SFN2011 Diffusion_Tensor_Imaging_Analysis Workshop |White Matter Exploration with Diffusion Tensor Imaging: Fundamentals and Perspectives - SFN 2011 Workshop]], Washington DC<br />
*November 9: [[CMF_Workshop_Cleveland| 3D Cranio Maxillo Facial Workshop, CWRU]] Cleveland, OH<br />
*November 3: [[2011_Slicer4-PreRSNAHackFest|Slicer4 PreRSNA Hackfest, Google hangouts]]<br />
*November 2: [[BWH_Resident_Fair| 3DSlicer exhibit]], BWH Resident Fair, Boston, MA<br />
----<br />
*October 20: [[2011_Slicer4-Documentation-Sprint|Slicer4 Documentation Sprint]]<br />
*October 14-15: [[2011_Algorithms_Retreat|Algorithm Core Retreat in New England]]<br />
*October 12-13: [http://www.ncigt.org/pages/IGT_Workshop_2011 NCIGT Workshop], Washington DC<br />
----<br />
*September 28: [http://wiki.na-mic.org/Wiki/index.php/Event:Journal_Club_at_BWH Journal Club talk: Seyed-Ahmad Ahmadi]<br />
*September 26-28: [[Events:2011_Hungary_Slicer_Training|Programming and End-User Training]] Szeged, Hungary<br />
*September 18: [http://www.na-mic.org/Wiki/index.php/Events:_DTI_Tractography_Challenge_MICCAI_2011 DTI Tractography for Neurosurgical Planning: A Grand Challenge - MICCAI 2011 Workshop], Toronto, Canada'''<br />
----<br />
*August 4: [[Events:UBC_3D_Slicer_workshop_August_2011|UBC 3D Slicer Workshop]]<br />
*August 2: [[Events:2011-08-02-AAPM-Slicer-Users-Group-Meeting|3D Slicer users group meeting]], AAPM annual meeting, Vancouver, BC, Canada]]<br />
----<br />
*July 19-21: [[Events:Slicer4-Review-07-2011 | Slicer 4 Review and Programming Sprint]], 1249 Boylston St., Boston, MA<br />
----<br />
*June 26-30: [[Events:3DSlicer_Booth_OHBM_2011 | 3DSlicer Booth, OHBM 2011]], Quebec City, Canada<br />
*June 20-24: [[2011_Summer_Project_Week|'''Summer Project Week at MIT''']]<br />
*June 15: [[Events:2011-06-15-Robarts-Slicer-Workshop|Slicer Workshop]], Biomedical Imaging Research Centre, University of Western Ontario, Canada<br />
*June 13: [http://www.na-mic.org/Wiki/index.php/Summer_2011_Tutorial_Contest Summer 2011 Tutorial Contest] Submission dead-line.<br />
*June 7: [[Events:2011-06-07-UCSF-Diffusion-Imaging-Workshop|UCSF Diffusion Imaging Workshop]], San Francisco<br />
----<br />
*May 5: [[Events:Computational_Methods_for_Radiation_Oncology|Computational Methods for Radiation Oncology]], Boston, MA<br />
----<br />
*April 27: [[Events:Slicer-Hands-On-Hiroshima-2011|Slicer and OpenIGTLink Hands-on Training]], Hiroshima, Japan<br />
*April 22: [[Event:2011-04-UtahDBP-Training|Slicer Hands-on Training For The Utah Afib Team]]<br />
*April 12: [[Event:2011-04-DiMaioTalk|Talk by Simon DiMaio "da Vinci and Beyond"]]<br />
*April 5: [http://www.na-mic.org/Wiki/index.php/Events:_Johns_Hopkins_University_Seminar_April_2011 Training Workshop], Johns Hopkins University, Baltimore, MD<br />
----<br />
*March 16-18: [http://vizbi.org VIZBI 2011] in Cambridge, MA includes NAMIC-affiliated speakers and VTK tutorials.<br />
*March 15-16: [http://catalyst.harvard.edu/services/ittm/module1.html Harvard Catalyst Biomarkers and Imaging in Drug Development course] includes [[media:Pieper-Image Processing Strategies.pptx|a presentation on image processing approaches]] including NA-MIC and 3D Slicer.<br />
*March 11: [[CTSC:Slicer_handson.021810| 3D Slicer Quantitative Medical Image Data Visualization Hands-On Workshop, Countway Room 403, (12-1pm)]] <br />
*March 4: New [https://www.slicer.org/wiki/Slicer3:3.6_Final_Issues#DONE:_Issues_fixed_for_inclusion_in_Slicer_3.6.3_--_included_in_release_builds_of_March_4.2C_2011 Slicer3.6.3 Patch Release]<br />
----<br />
*February 19-23: [[Event:2011_Registration_Retreat|Registration Retreat]]<br />
*February 18: [[CTSC:Slicer_handson.021810| 3D Slicer Quantitative Medical Image Data Visualization Hands-On Workshop]], Harvard Countway Library room 403, (12-1pm)<br />
*February 7-11: [http://www.commontk.org/index.php/CTK-Hackfest-Feb-2011 CTK Hackfest], Chapel Hill, NC<br />
*February 4: [[Media:Fedorov-MGH-4Feb2011.pdf|Presentation of 3D Slicer for the MGH tumor measurement group]]<br />
----<br />
*January 10-14: '''[[AHM_2011|AHM, EAB]]''', [[2011_Winter_Project_Week|Winter Project Week in Salt Lake City]]'''<br />
<br />
=== 2010 ===<br />
*December 8: [[Events:Manchester-Dec-2010|Slicer Workshop]], Manchester, UK<br />
*December 6-7: [[Events:Dundee-Dec-2010|Slicer Workshop]], Dundee, UK<br />
----<br />
*November 28-December 3: RSNA 2010, The 96th Annual Meeting of the Radiological Society of North America, Chicago IL<br />
**November 29: 2:30 pm-4:00 pm: [[Events:RSNA_2010| 3D Interactive Visualization of DICOM images with Slicer]], Chicago IL<br />
**November 30: 10:30 am-12:00 pm: [[Events:RSNA_2010_CTSA| Quantitative Medical Imaging for Clinical Research and Practice]], Chicago IL<br />
**December 2: 10:30 am-12:00 pm: [[Events:RSNA_2010_didactic| Lifecycle of an imaging biomarker: from validation to dissemination]], Chicago IL<br />
* November 17-18: [[EngineeringRetreat2010|Engineering Core retreat]]<br />
* November 12: [[MGH-NA-MIC-2010-Kickoff|MGH Kick-off meeting with Algorithms and Engineering]]<br />
* November 8-9: [[2010-WestCoastMaster|West Coast Events]]<br />
* November 5-6: [[AlgorithmRetreat2010|Algorithm Core retreat]]<br />
* November 4-6: [[WidgetDesign2010|Widget Design Fiesta]], Kitware, South Carborro, NC<br />
* November 4-5: [[media:HataJJTalkNov2010.pdf |Robotics Presentation by Noby Hata]], Advances in Surgical Technologies Symposium, Celebration, FL<br />
----<br />
* October 25-26: [[Iowa-NA-MIC-2010-Kickoff| Iowa NA-MIC Kickoff meeting (UNC Core 1 visit)]]<br />
* October 18:[[HST_583_2010_DTI_Course| Harvard MIT Division of Health Sciences and Technology - Diffusion Tensor Imaging Lab]] <br />
----<br />
* September 24: [http://lcib.rutgers.edu/miccai2010/ Prostate Cancer Imaging Workshop] MICCAI 2010, Beijing, China<br />
* September 23: [http://www.grand-challenge.org/index.php/MICCAI_2010_Workshop Workshop on Medical Image Analysis for the Clinic - A Grand Challenge] <br />
* September 23: [[Beijing_2010_NA-MIC_Workshop|Slicer Tutorial]], Chinese PLA General Hospital in Beijing, China<br />
* September 20: [[MICCAI_2010| NA-MIC Tutorial]], MICCAI 2010, Beijing, China<br />
* September 13: [[HST_583_2010| Harvard MIT Division of Health Sciences and Technology - Neuroimage Analysis Lab]]<br />
----<br />
* August 12-13: [[QtAugust2010| Review of Qt port]]<br />
* August 11: [[2010-Slicer-UNCDuke|Slicer training event]], UNC and Duke<br />
* August 10: [[2010-Sato-talk|Research retreat of SNR Laboratory, followed by Dr. Yoshinobu Sato's talk]]<br />
* August 5: [http://www.termine-meduniwien.at/mediafiles/38/Vortragsankuendigung_Prof_Ron_KIKINIS_05082010.pdf?sid=4f2a2b592fc7004cea39a34993b1d72d Presentation], AKH, Vienna, Austria<br />
----<br />
* July 1: [[2010-Slicer-StLouis|Slicer training event in St. Louis]]<br />
----<br />
* June 26: [[2010_CARS| NA-MIC Tutorial]], Computer Assisted Radiology and Surgery Conference in Geneva, Switzerland<br />
* June 22" [http://www.na-mic.org/Wiki/index.php/Summer_2010_Tutorial_Contest Slicer Tutorial Contest, MIT, Cambridge, MA]<br />
* June 21-25: '''[[2010_Summer_Project_Week|Summer Project Week at MIT]]'''<br />
* June 18: [[2010_CCA_Retreat|Clinical Computational Anatomy one day retreat]], Boston, MA<br />
----<br />
* May 20-23:[[cscbce_2010 | 5th Canadian Student Conference <br />
on Biomedical Computing and Engineering]]<br />
* May 17-21: [http://www.commontk.org/index.php/CTK-Hackfest-May-2010 CTK Hackfest], Georgetown University<br />
* May 12: [http://catalyst.harvard.edu/services/imagingcourses.html 3D Slicer Medical Image Data Registration Hands-On Workshop], Countway Library, Harvard Medical School, Boston, MA<br />
----<br />
* April 29: [[2010_Slicer36_Module_Cull|Review of modules to keep and cull for the 3.6 release]]<br />
* April 28: [http://catalyst.harvard.edu/services/imagingcourses.html 3D Slicer Medical Image Data Visualization Hands-On Workshop]], Countway Library, Harvard Medical School, Boston, MA<br />
* April 9-10: [[2010_University.of.Iowa| NA-MIC Training Workshop]], University of Iowa<br />
* April 7: [http://catalyst.harvard.edu/services/imagingcourses.html 3D Slicer Medical Image Data Registration Hands-On Workshop], Countway Library, Harvard Medical School, Boston, MA<br />
----<br />
* March 24: [http://catalyst.harvard.edu/services/imagingcourses.html 3D Slicer Medical Image Data Visualization Hands-On Workshop], Countway Library, Harvard Medical School, Boston, MA<br />
* March 19: [[U-Tokyo-visit-03192010| NCIGT Workshop with delegates from University of Tokyo]], Brigham and Women's Hospital, Boston, MA<br />
* March 16: [[Events:Slicer-Hands-On-Tokyo-2010| Image Guided Therapy research using 3D Slicer - Hands-On Workshop]], Tokyo Women's Medical University, Tokyo, Japan (page in Japanese)<br />
* March 10: [http://summit2010.amia.org/session-details NA-MIC Presentation], AMIA 2010<br />
* March 9: Registration Clinic at [http://www.ncigt.org/pages/IGT_Workshop_2010 IGT Workshop], Arlington, VA<br />
* March 7-10: Several NA-MIC personnel are participating in [[Events:CTK-Pre-Hackfest-2010|The CTK Pre-Hackfest]], Heidelberg, Germany. This meeting is a kick off that is expected to lead to active working meetings similar to the NA-MIC Project Week activities. The meeting is organized by the [http://commontk.org CTK] group.<br />
* March 3: Steve Pieper presents on "Visualizing Anatomy and Function from MRI Data", [http://vizbi.org/2010/ the 2010 EMBO Workshop on Visualizing Biological Data]. NA-MIC Wiki page with [[VIZBI2010|Supplemental information from the VIZBI Conference]]. [http://www.nature.com/nmeth/journal/v7/n3s/index.html A special edition of Nature Methods] contains papers by the presenters.<br />
----<br />
* February 24: [[CTSC:Slicer_handson.022410| 3D Slicer Medical Image Data Visualization Hands-On Workshop]], Countway Library, Harvard Medical School, Boston, MA<br />
* February 14: [[Events:CTK-Workshop-SanDiego-2010| 4th CTK Workshop]], SPIE, San Diego, CA<br />
* February 9: [[Hata_BBN_visit|Hata BBN lecture]]<br />
----<br />
* January 4-8: '''[[AHM_2010|AHM, EAB'''], [[2010_Winter_Project_Week|Winter Project Week in Salt Lake City]]'''<br />
<br />
===2009===<br />
* December 16-17: [[Dec-2009-SlicerAIMBrainstorming|Slicer Annotation and Markup Brainstorming]]<br />
* December 15: [[Dec-2009-SlicerXND-DesignAndEngineering | Slicer/XND Preliminary Design & Engineering Planning Session]], WUSTL]]<br />
* December 1: [[Events:RSNA_CTSA_2009| CTSA]], RSNA, Chicago, IL<br />
----<br />
* November 30: [[Events:RSNA_2009| 3-D Interactive Visualization of DICOM images with Slicer - RSNA 2009]], 95th Annual Meeting of the Radiological Society of North America, Chicago, IL<br />
* November 29: [[Events:CTK-Workshop-Chicago-2009| 3rd CTK Workshop]], RSNA, Chicago, IL<br />
* November 23: [[CTSC:Slicer_handson.112309| 3D Slicer Medical Image Data Visualization Hands-On Workshop]], , Countway Library, Harvard Medical School, Boston, MA<br />
----<br />
* October 16: [[SFN2009 Slicer DTI Workshop | Mapping the Brain with Diffusion Tensor Imaging - A Hands-On Workshop]] [http://www.sfn.org/am2009/ Annual Meeting of the Society of Neuroscience], Chicago, IL<br />
* October 9: [[Events:VT-NAMIC-NCBC-Collaboration-meeting-2009| VirginiaTech-NA-MIC collaboration progress update and planning meeting]], Surgical Planning Laboratory, 1249 Boylston Street, Boston, MA<br />
----<br />
* September 30: [[CTSC:ACRIN 09/30/09| Quantitative Imaging Workshop]] ACRIN fall meeting, Arlington, VA. Workshop in collaboration with Duke University and Johns Hopkins.<br />
* September 25: [[Events:CTK-Workshop-September-2009| 2nd CTK Workshop]], Oxford UK<br />
* September 24: [http://campwww.informatik.tu-muenchen.de/AMIARCS09/doku.php Augmented Environments for Medical Imaging including Augmented Reality in Computer-Aided Surgery (AMI ARCS)] MICCAI 2009 Workshop, London, UK. Demonstration of the [[DBP2:JHU:PerkStation | Perk Station]]. One-on-one tutorial available [mailto:lasso@cs.queensu.ca] on request.<br />
* September 24: [http://smarts.lcsr.jhu.edu/CAI-Workshop-2009 Systems and Architectures for CAI] MICCAI 2009 Workshop, London, UK. Presentation of the [[DBP2:JHU:Roadmap | computer assisted intervention plug-in module for 3D Slicer]].<br />
* September 24: [http://www.cs.ucl.ac.uk/miccai/dmfc Diffusion Modelling and the Fibre Cup] MICCAI 2009 Workshop, London, UK. Presentation of the DTI tractography validation pilot study.<br />
* September 20-24: [http://wiki.na-mic.org/Wiki/index.php/2009_prostate_segmentation_challenge_MICCAI Prostate MRI Segmentation Challenge"], [http://grand-challenge2009.bigr.nl/index.php MICCAI 3D Segmentation in the clinic: a grand challenge].<br />
* September 20: [http://lmi.bwh.harvard.edu/DMRI09 MICCAI 2009 Tutorial in London: Trends in High Angular Resolution Diffusion Imaging and Brain Tissue Modelling]<br />
* September 20: [http://people.csail.mit.edu/pohl/pmmia09.html MICCAI 2009 Workshop: Probabilistic Models for Medical Image Analysis]<br />
* September 20: MICCAI Workshop on Information theoretic similarity measures for image registration and segmentation<br />
* September 16-17: [[Sept-2009-SlicerWidgetsBrainstorm|Brainstorming Session on next generation widgets for Slicer]]<br />
----<br />
* August 25: [[Events:Slicer_Workshop_August_2009|Slicer Workshop]] at [http://www.ibmisps-worldcongress.org/precongress.asp IBMISPS], Surgical Planning Laboratory, 1249 Boylston Street, Boston, MA<br />
* August 21: [[Events:Registration_Summit_August_2009|Registration Meeting]], Surgical Planning Laboratory, 1249 Boylston Street, Boston, MA<br />
----<br />
* June 29: [[Events:CTK-Workshop-June-2009|Common Toolkit Workshop]], [http://www.dkfz.de/index.html DKFZ, Heidelberg, Germany, hosted by the [http://www.dkfz-heidelberg.de/en/mbi/index.html MBI].<br />
* June 28: [http://www.biomedicalimaging.org/2009/Tutorial_04.asp Tutorial on Statistical Shape Analysis: Theory, Software, and Applications] at [http://www.biomedicalimaging.org/2009/default.asp ISBI 2009], Boston, MA.<br />
* June 25: [[Events:TutorialContestJune2009 | Summer 2009 Tutorial Contest]]<br />
* June 22-26: '''[[2009_Summer_Project_Week|The FIRST JOINT Summer Project Week at MIT]]'''<br />
* June 17: [[CAOS2009_Slicer Workshop| Hands-On Workshop for Slicer IGT for Computer Aided Orthopeadic Surgery]]<br />
* June 17: [[SlicerKyusyuJune2009Lecture| Lecture and demonstration, Image Guided Therapy of abdominal organs]], Noby Hata, Kysyu University Medical School, Kyusyu, Japan<br />
* June 16: [[SlicerNagoyaJune2009Workshop| Workshop: How to make your custom IGT software using 3D Slicer]], Noby Hata, Nagoya Institute of Technology, Nagoya, Japan<br />
----<br />
* May 11-12: Core 1 PI meeting, Georgia Tech.<br />
* May 8: [http://www.na-mic.org/Wiki/index.php/IMFAR2009 IMFAR 2009] - [http://www.autism-insar.org/index.php?option=com_content&task=view&id=36&Itemid=105 Presentation], 8th Annual International Meeting for Autism Research (IMFAR) in Chicago, IL] entitled Use of the Slicer3 Toolkit to Produce Regional Cortical Thickness Measurement of Pediatric MRI Data".<br />
* May 8: Focus session on [[Volume Rendering and Loadable Modules: (Engineering & Usability Notes)]].<br />
* May 4-5: Core 1 / Core 2 visit at Georgia Tech ([[May 4, 2009 Notes]], [[May 5, 2009 Notes]]).<br />
----<br />
* March 19: [[NCI Slicer Tutorial 03-19-2009|NCI Slicer tutorial, ]] We had to reschedule! New date TBD!<br />
* March 4: [[2009-03-04-Editor-Usability|Interactive Editor usability]] session in Ron's office<br />
----<br />
* February 24: 1249 Boylston: [https://www.slicer.org/wiki/Slicer3:Using3.4 Afternoon session to walk through common Slicer3.4 usage scenarios]<br />
* February 24: BWH (location: Mellins Library) [[BWH_RadiologyResident_Training2009.1| NA-MIC 3D Slicer 3.2 Hands-On Workshop]] <br />
* February 17-20: [[GWE_MiniRetreat|GWE Mini Retreat]], Boston, MA<br />
----<br />
* January 28-30: [https://www.slicer.org/wiki/Slicer3:MiniRetreat_January_28-30,2009 Slicer3 MiniRetreat]<br />
* January 7: [[Events:TutorialContestJan2009| Winter 2009 Tutorial Contest]] <br />
* January 5-9: '''[[AHM_2009| AHM,]] [[2009_EAB|EAB,]] [[2009_Winter_Project_Week|Winter Project Week in Salt Lake City]]'''<br />
<br />
=== 2008 ===<br />
* December 15-16: [[2008_Engineering_review_at_UNC|2008 Engineering review]], UNC, Chapel Hill<br />
* Fall Semester 2008 Ibanez and Schroeder teach [http://public.kitware.com/OpenSourceSoftwarePractice/index.php/Main_Page Open Source Software Course], Rensselaer Polytechnic Institute<br />
* December 8-12: [[2008_IGT_Project_Week|IGT Hands-on Project Week]], Boston<br />
* December 1: [[Events:RSNA2008| Tutorial]], RSNA]], [http://rsna2008.rsna.org/ RSNA conference website]<br />
----<br />
* November 15-19: [[NA-MIC_Lupus_DBP_Worskhop_SFN2008|NA-MIC Lupus DBP White Matter Lesion Tutorial Release at 2008 Society for Neuroscience Annual Meeting]], Washington, DC<br />
* November 18: [[Slicer3_Q&A_2008-11-18|Slicer Q&A Session]], BWH<br />
* November 4: [[NA-MIC_3D_Visualization_Workshop_Massachussetts_General_Hospital|NA-MIC 3D Visualization Workshop]], Massachusetts General Hospital, Boston, MA<br />
----<br />
* October 30 : [[NA-MIC_3D_Visualization_Workshop_Brigham_and_Women's_Hospital| NA-MIC 3D Visualization Workshop]], Brigham and Women's Hospital, Boston, MA<br />
* October 28: [[Harvard_Medical_Education_Day | Harvard Medical Education Day]], Boston, MA<br />
* October 21: Nobuhiko Hata talk, entitled "Role of Image Processing, Navigation and Robots in MRI-guided Intervention", Bioimaging Sciences Division, Department of Radiology, Yale University School of Medicine, New Heaven, CT<br />
* October 17: Nobuhiko Hata talk, entitled "Role of Image Processing, Navigation and Robots in MRI-guided Intervention", Robarts Institute, University of Western Ontario, Ontario, Canada <br />
* October 15-16: [[Robarts_Training_Session | NA-MIC kit training event at The University of Western Ontario]], London, Ontario, Canada<br />
* October 7: [[Stefan_Baumann_visit | Stefan Baumann, Novartis]], 1249 Boylston St., Boston, MA<br />
* October 7: [[Slicer_Day_October_2008|Slicer in the Fall]], 1249 Boylston St., Boston, MA<br />
----<br />
* September 10: [[Miccai_2008_Tutorial| Interfacing third-party software with the NA-MIC Kit]]: Tutorial at MICCAI 2008, New York City<br />
* September 10: [[Miccai_2008_Prostate_Workshop| Prostate image analysis and computer-assisted intervention]]: Workshop at MICCAI 2008, New York City<br />
* September 6: [[Miccai_2008_Systems_and_Architecture_Workshop| Systems & architecture for computer]] Workshop, MICCAI 2008, New York City<br />
* September 6: [[Miccai_2008_Segmentation_Workshop| Segmentation in the Clinic Challenge]]: Workshop at MICCAI 2008, New York City<br />
* September 3: [[Stanford_2008_Slicer_Workshop| Slicer Training]], Stanford University, CA<br />
----<br />
* August 21-22: [[Events:August2008XNATDesktop|Visit by WashU Developers to Boston for Discussions of XND]]<br />
* August 15: [[Events:NCI_Workshop_August_2008|August 15 2008, NA-MIC Workshop]], NCI<br />
* August 13-14: [[Events:August_2008_NCBC_AHM|NCBC all hands meeting]]<br />
* August 1: [[Events:August2008XNATDesktop| Planning TCon for XNAT Desktop Slicer interface]]<br />
----<br />
* July 30-August 1: [[2008_July_RFA_Experiment_Georgetown | RFA Interventional Experiment]], Georgetown University<br />
* July 17: Steve Pieper presented NA-MIC and Slicer Module development at the [http://www.ipam.ucla.edu/programs/mbi2008/ IPAM MBI] Summer School [[Media:Pieper-UCLA-MBI-2008-07-17.ppt|(Slides)]]<br />
* July 10 or 11: [[2008 July Slicer Introduction to Princess Margaret Hospital|Slicer Introduction]], Princess Margaret Hospital<br />
----<br />
* June 30: Steve Pieper presented at the [http://www.nitrc.org NITRC] all hands meeting.<br />
* June 26: [[2008_June_IGT_Tumor_Growth_Model_Demo_SPL|Tumor Growth Model Software Demo]], SPL<br />
* June 23-27: [[2008_Summer_Project_Week|'''Summer Project Week at MIT''']]<br />
* June 23: [[2008_July_Slicer_IGT_VV_Link_Session_II|Slicer IGT Integration with Brainlab via VVLink]]<br />
* June 16-17: [[2008 June Workshop Germany |Training Event]], Germany<br />
* March - June: [[3D_Ultrasound_Module_in_Slicer_3|Slicer IGT training for graduate students at SJTU, Shanghai, China (every Thursday 10 am - noon)]]<br />
----<br />
* May 22-23: [[2008_Core_1_Core_3_mtg|Cores 1-3 Technical Meeting]], Utah<br />
* May 21: [[2008_Core_1_UNC_Utah_DTI| Core 1 UNC & Utah Technical Meeting about DTI tool development]], Utah<br />
* May 21: Kilian Pohl presented on segmentation tools in 3D Slicer at the [http://www.dkfz.de/en/mbi/index.html Division of Medical and Biological Informatics, DKFZ, Germany] ([[media:Pohl_dkfz_08.pdf | Slides]]) <br />
* May 12: [[Events:May12_2008_FirstMondaySeminar | First Monday Seminar Talk given by Drs. Ichiro Sakuma and Nassir Navab]], Brigham and Women's Hospital, <br />
* May 8: [[Events:2008_05_08_Collaboration_UWA_Perth|Conference Call to Explore Collaboration with Adam Wittek]], UWA, Perth, Australia<br />
* May 2: [[2008_5_2_Hata_Talk_U_Michigan | Nobuhiko Hata's talk]], Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI<br />
----<br />
* April 14: [https://www.slicer.org/wiki/Slicer3:Slicer3_Workshop_UNC_Chapel_Hill_2008#Preparation_for_the_Workshop Full day Slicer 3 Users and Plug-in Workshop] hosted by UNC-Chapel Hill faculty<br />
* April 7: [[2008_David_Hawkes|2008 Dr. David Hawkes of UCL's visit to SPL]]<br />
----<br />
* March 31-April 11: [[2008_Platel_visit_from_TUE|2008 Dr. Platel's, IGT grp leader from Technical University Eindhoven, to SPL]]<br />
* March 24-27: [[2008_Engineering_review_at_Utah|2008 Engineering review]], Utah<br />
* March 19: [[Events:HST-563-March2008|Harvard-MIT Division of Health Sciences and Technology (HST), Lecture on Interventional MRI by Hata, Kikinis, HST 563]]<br />
* March 12: Steve Pieper presented on the NA-MIC Kit and 3D Slicer at the [http://www.cisst.org/wiki/Seminar_2008_03_12_3D_Slicer Johns Hopkins CISST] ([[media:Pieper-JHU-seminar-2008-03-12.ppt | Slides]])<br />
* March 10-11: [[IGT:March_2008_IGT_Workshop|IGT Workshop, Rockville, MD]]<br />
* Discussion of NA-MIC Kit for Cardiac EP with [http://www.bidmc.harvard.edu/cmr BIDMC].<br />
----<br />
* February 20: [https://www.slicer.org/wiki/Slicer3:Spring-2008-User-Training#Preparation_for_the_Workshop Spring 2008 Slicer3 User Training Workshop ] at the SPL 1249 Boylston St, Boston<br />
* February 5-7: [https://www.slicer.org/wiki/Slicer3:MiniRetreat Slicer3 Mini-Retreat, Boston]<br />
----<br />
* January 7-11: '''[[AHM_2008| AHM,]] [[2008_EAB|EAB,]] [[2008_Winter_Project_Week|Winter Project Week in Salt Lake City]]'''<br />
<br />
=== 2007 ===<br />
* December 12-14: [[2007_December_Slicer_IGT_Programming|Slicer IGT Programming Event]]<br />
----<br />
* November 2: [http://www.insightsoftwareconsortium.org/wiki/index.php/2007_MICCAI_Open_Workshop Third Annual Open Source Workshop at MICCAI]<br />
----<br />
* October 16-17: [http://nbirn.net/about/current/ahm2007.shtm BIRN AHM] Query Atlas and Qdec interfaces in Slicer 3 presented at the BIRN AHM.<br />
* October 14-20: [[2007_October_Collaboration_Visit_Robert_Israel|Robert Israel Collaboration Visit to the Surgical Planning Laboratory]]<br />
** [http://wiki.na-mic.org/Wiki/index.php/Slicer3:Module:QueryAtlas See this page] for links to QueryAtlas slides, movies and example datasets.<br />
** [http://wiki.na-mic.org/Wiki/index.php/Image:Slicer3QDEC_AHM2007.ppt See this page] for links to Qdec slides.<br />
* October 1-2: [[SanteFe.Tractography.Conference | Contrasting Tractography Methods Conference, Santa Fe]]<br />
----<br />
* September 12: [[Engineering:September 12, 2007 | Engineering End of Summer Meeting]]<br />
* September 11: [[GPU.Enabled.Tools.Meeting | GPU-enabling of NA-MIC Algorithms, Boston]]<br />
----<br />
* August 21: [[DBP2:UNC:Cortical Thickness Roadmap | UNC DBP Roadmap Tcon]]<br />
----<br />
* June 25-29: '''[[2007_Programming/Project_Week_MIT|Summer Project Week at MIT]]'''<br />
* June 9: [[Training:OHBM2007_Training_Workshop|OHBM DTI Training Workshop, Chicago]]<br />
* June 1: [[2007_Pohl_at_CCB|Pohl Talk]], CCB: A Hierarchical Segmentation Algorithm for MR Brain Images<br />
----<br />
* May 29-31: [[2007_Core_1_Meeting|Annual Core 1 Workshop]], Boston<br />
----<br />
* April 24: Steve Pieper presented Slicer3 and the NA-MIC Kit to the [http://gray.mgh.harvard.edu/content/index.php Medical Physics group at MGH] [http://wiki.na-mic.org/Wiki/images/9/9c/Pieper-MGH-medical-physics-2007-04-24.ppt (slides)]<br />
----<br />
* March 29-30: [https://www.slicer.org/wiki/Slicer3:MiniRetreat_March_29%2C_30%2C_2007 Slicer3 Mini-Retreat], Boston<br />
----<br />
* February 21-22: Vince Calhoun from MIND is visiting at MIT and MGH [http://www.csail.mit.edu/events/eventcalendar/calendar.php?show=event&id=1349 Talk announecement]<br />
* February 3 and 10: [http://mri.radiology.uiowa.edu/mediawiki/index.php/ITK_Programming_Short_Course_-_Feb_2007 Iowa ITK Programming Short Course]<br />
* February 7-8: [https://www.slicer.org/wiki/Slicer3:MiniRetreat Slicer3 Mini-Retreat], Boston<br />
----<br />
* January 29: [[P41-2007-Joint-Retreat | CFIT NAC P41 2007 Joint Retreat]]<br />
* January 16: [[2007-01-16 Core 5, Core 6 Summit]]<br />
* January 10-12: '''[[AHM_2007|AHM, EAB, Winter Project Half Week in Salt Lake City]]'''<br />
<br />
=== 2006 ===<br />
* December 12: [https://www.slicer.org/wiki/Slicer3:Alpha-release Slicer3 retreat], Kitware, Inc.<br />
----<br />
* November 15: [https://www.slicer.org/wiki/Slicer3:Usability Usability session with PNL], BWH]<br />
* November 7-8: [[2006_November_Meshing_Project_Visit| Meshing Collaborator Project Visit to BWH]]<br />
* November 1: [[Training:User_Workshop_Fall_HCNR_2006| NA-MIC Training Workshop at the Harvard Center for Neurodegeneration and Repair]], Boston<br />
----<br />
* October 26: [[Oct-26-2006-MIND-visit_Visiting_the_MIND_institute|New DBP MIND Institute Visit]]<br />
* October 23-26: [http://www.nbirn.net/press/current/ahm2006.shtm <nowiki>| BIRN All Hands Meeting</nowiki>]<br />
* October 19-20: [[IGT:October_2006_IGT_Workshop| NCIGT Workshop on Open System Architectures for Image-Guided Therapy]]<br />
* October 17: [[Core1-3-meeting-2006|Coordination meeting]] between Core 1 and Core 3 to plan the specifics for the third and last year of the current DBP's<br />
* October 1: [http://www.insightsoftwareconsortium.org/wiki/index.php/2006_MICCAI_Open_Workshop MICCAI_2006 Open Source Workshop], MICCAI 2006, Copenhagen, Denmark<br />
----<br />
* September 19-20: [[2006_September_Slicer3_Update| Slicer 3 Update Meeting]], Boston, MA<br />
* September 14-15: We have been invited to participate in [http://usms.nist.gov/workshops/bioimaging.htm NIH Workshop on Standards in Change Measurement]. This workshop will potentially set the stage for additional workshops that focus on Image Guided Interventions and Open Source standards.<br />
* September 6: [http://www.ibmisps.org/pdf/InformationparticipantsANGLAIS.pdf 2006 IBMISPS conference:] [[Media:Kikinis-IBMISPS-09-06-2006.ppt|talk]] by [[media:Kikinis-FOSS.ppt|R. Kikinis on FOSS]] ([[2006 FOSS Abstract Kikinis]])<br />
----<br />
* July 19: [[Training:NLM_Workshop_2006| NA-MIC Training Workshop]], NLM<br />
* July 17-19: [[NIH:_2006_All_NCBC_Meeting| All NCBC All Hands Meeting, NLM<br />
* July 13-14: [http://bsp.csie.nctu.edu.tw/lssa06/ 2nd IEEE-NLM International Life Science Systems and Applications Workshop, Lister Hill Auditorium, NIH, chaired by Stephen Wong, co-sponsored by IEEE, NLM, and NAMIC]<br />
* July 2: Ron Kikinis [[Media:NA-MIC-Kit-07-01-2006.ppt| presentation]] (28MB ppt file) at the [http://www.future-cad.org/fcad/Docs/CFP_for_2nd_Int_Sympo_2006_ver3.2.pdf The 2nd International Symposium on Intelligent Assistance in Diagnosis of Multi-Dimensional Medical Images ]<br />
----<br />
* June 26-30: '''[[2006_Programming/Project_Week_MIT|Summer Project Week at MIT]]'''<br />
* June 8-9: [[Georgia_Tech_visit_to_UNC%2C_June_8-9|Georgia Tech visit to UNC: Shape Analysis Discussion]]<br />
* June 5: [https://www.slicer.org/wiki/Slicer:Slicer3-June-5-2006-Retreat Slicer 3 Retreat]<br />
----<br />
* May 30: [http://www.cimit.org/forum/forum.html CIMIT Forum] with Steve Pieper and Luis Ibanez ([[Media:CIMIT-BIRN-update-2006-05-30.ppt| Steve's Slides]])([[Media:CIMIT-2006-IGSTK-InsightJournal.ppt| Luis' Slides]])<br />
* May 26: [[Training:DTI_Workshop|UNC-Chapel Hill NA-MIC DTI Analysis Training Workshop]]<br />
* May 23-24: [[Algorithms:Core1Visit_May06| NA-MIC Core 1 meeting]], UNC]]<br />
* May 19: [[Slicer:StevePieper_RonKikinis_VisitToDartmouth_051906|Steve Pieper and Ron Kikinis Visit to Dartmouth]]<br />
* May 15: [[DBP:Harvard:Collaboration:GTech#Progress|Delphine Nain]], PNL<br />
----<br />
* April 27: [[Training:NIH_Workshop_2006|NA-MIC Training Workshop]], NIH<br />
* April 24: [http://www.nimh.nih.gov/neuroinformatics/springagenda2006.cfm The Human Brain Project: Linking Within and Beyond] Natcher Conference Center, NIH Campus, Bethesda, Maryland: National Alliance for Medical Image Computing: Science & Technology of One National Center for Biomedical Computing [[Media:NA-MIC_Kit_revised.ppt| (this is a slightly modified version of the presentation)]]<br />
* April 12-13: [[DBP:Harvard:Collaboration:Toronto|James Kennedy and Aristotle Voineskos at the PNL]]<br />
* April 10-11: [[Training:MIND_Institute_Workshop_Spring_2006| NA-MIC Training Workshop]], MIND Institute, NM<br />
* April 10-11: Steve Pieper presented the NA-MIC Kit at [http://www.biomedicalimaging.org ISBI] 2006 on April 7, 2006 ([[Media:NA-MIC-2006-04-07-ISBI.ppt| Slides]], [[Media:Pieper-ISBI-2006-revised.pdf| Paper]]).<br />
* April 3-4: [https://www.slicer.org/wiki/Slicer3:_Alpha1_Meeting Design Review and Work meeting on Slicer3 (alpha1 release)]<br />
----<br />
* February 22-24: [[Engineering:Slicer3_and_GPU| Meeting at Kitware to discuss Slicer3 (Thursday) and GPU programming (Friday)]]<br />
* February 22: [[DBP:Sylvain_Doug_visit_Dartmouth_Feb_22_2006|Sylvain Bouix to visit Dartmouth]]<br />
* February 20-23: [[IGT:Workshop_Feb_2006|IGT and FUS Workshops]]<br />
----<br />
* January 24: [[Training:User_Workshop_SPL_Winter_HCNR_2005| HCNR User Training Workshop]], Surgical Planning Laboratory, Boston, MA<br />
* January 8-13: '''[[AHM_2006:AHM_2006| AHM, EAB, Winter Project Week in Salt Lake City]]'''<br />
<br />
=== 2005 ===<br />
* December 20: [[DBP:Marek_Kubicki_visit_Dartmouth_December_20_2005| Marek Kubicki visit to Dartmouth]]<br />
* December 17: [[Collaboration:GT-UCI| Jim Fallon from UC Irvine visit to Georgia Tech for work on Rule-Based Segmentation]]<br />
* December 14: [[DBP:Andy_Saykin_visit_BWH_December_14_2005|Andy Saykin and Group visit to Brigham and Women's Hospital]]<br />
* December 1: [[DBP:Dartmouth_Harvard_Slicer_Training_12_01_2005| Dartmouth Group Slicer Training Followup at Harvard]], 1249 Boylston St., Boston, MA<br />
----<br />
* November 27-December 2: [http://rsna2005.rsna.org/rsna2005/V2005/index.cvn RSNA 2005, Chicago: Slicer session], Open Source Imaging Tools Workshop<br />
* November 18: [[DBP:Harvard:Collaboration:GTech#Progress|Ramsey Al-Hakim at the PNL]]<br />
* November 17-18: [[Collaboration:GT-Kitware|John Melonakos at Kitware -- Bayesian Classification Filter addition to ITK]]<br />
* November 16: [[IGT:2005_Nov_16_IGT_Consortium_Kickoff| IGT Consortium Kickoff]]<br />
* November 16: [[Collaboration:UNC-UCI|Jim Fallon and Martina from UC Irvine visit to UNC on DTI tools and clinical projects]]<br />
* November 15: [[Engineering:Slicer3.0_November_15_2005| Slicer 3.0 Meeting]], Surgical Planning Laboratory, Boston, MA<br />
----<br />
* October 29: [[Dissemination:MICCAI_Workshop_2005|ISC and NA-MIC Workshop on Open Source Toolkits, Applications, and their uses in Medical Image Analysis]], MICCAI 2005, Palm Springs, CA<br />
* October 29: Informal NA-MIC Lunch, MICCAI 2005, Palm Springs, CA<br />
* October 20: [[2005_AHM:_3D_Slicer/Freesurfer_Workshop|Slicer Training Workshop, AHM BIRN]], San Diego, CA<br />
* October 7: [[Collaboration:UNC-PNL|UNC visit at the Psychiatry NeuroImaging Laboratory]]<br />
* October 5-7: [[Dissemination:EPFL_Workshop_2005| Advanced ITK and Slicer Workshop]], Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland<br />
----<br />
* September 30: [[Training:User_Workshop_SPL_Fall_2005|User Training Workshop]], Surgical Planning Laboratory, Boylston St, Boston, MA<br />
* September 26-28: [[Engineering:Core_3_Programming_Week#1_Feedback|DBP and Engineering Session on Feedback from Programming Week Projects, and Planning the next 6-months]]<br />
* September 16: [[Training:User_Workshop_MGH_Summer_2005| User Training Workshop]], MGH<br />
----<br />
* August 11: [[Dissemination:CSB2005|Invited Lecture about NA-MIC]]<br />
----<br />
* July 20: [[Collaboration:Workshop_July_20_2005|UNC visit of Georgia Tech for collaborative work on shape and DTI algorithms]]<br />
----<br />
* June 27-July 1: [[Engineering:Programmers_Week_Summer_2005| '''Summer Project Week at MIT''']]<br />
* June 22-23: [[Dissemination:NCRR_NIBIB_PI_Meeting_June_22-23_2005|NCRR/NIBIB PI Meeting]]<br />
* June 16-19: [[Collaboration:Workshop_June_16-19_2005|Georgia Tech visit of UC-Irvine for collaborative work on anatomically accurate algorithms.]]<br />
----<br />
* May 26-27: [[Dissemination:Workshop_May_26-27_2005|User Training and Dissemination Workshop]], at Dartmouth<br />
----<br />
* April 21-22: [[DBP:Andy_Saykin_visit_BWH_April_21_2005| Andy Saykin visit to Brigham and Women's Hospital and MIT]]<br />
----<br />
* March 25: University of Utah visit of Harvard VA for collaborative work on DTMRI.<br />
* March 21-23: [[FBIRN:retreat2005|fBIRN Retreat in Irvine with User Tutorials for Slicer, Brains2 Wednesday on March 23]]<br />
----<br />
* February 20-22: [[AHM_2005:Main|'''The First All-Hands-Meeting and Programming Event in Salt Lake City, Utah''']]<br />
* February 17-18: [[Dissemination:Workshop_Feb17-18_2005| Dissemination Workshop]], UCSD]]<br />
----<br />
* January 26: Slicer User Workshop at BWH: [https://www.slicer.org/wiki/Slicer:User_Workshop_Jan26 Information for Atendees]<br />
* January 24-25: Dissemination Workshop at [[Dissemination:Workshop_Jan24-25_Boston|Agenda]], [[Dissemination:Workshop_Jan2005_Interested_Attendee_List|List of Participants]], [[Talk:Dissemination:Workshop_Jan24-25_Boston_Feedback|Attendee Feedback]]<br />
* January 17-18: [http://www.imaginggenetics.uci.edu First International Imaging Genetics Conference] at the Beckman Center of the National Academy of Sciences in Irvine, CA.<br />
<br />
=== 2004 ===<br />
<br />
* December 9-10: Dissemination Workshop in the Surgical Planning Laboratory, BWH: [[Dissemination:Workshop_Dec9-10_Boston|Agenda]], [[Dissemination:Workshop_Dec9-10_Boston_Presentations|Presentations]], [[Dissemination:Workshop_Dec9:10_Attendees_List|List of Participants]], [[Dissemination:Workshop_Dec9:10_Summary|Summary]], [[Talk:Dissemination:Workshop_Dec9-10_Boston_Feedback|Attendee Feedback]]<br />
----<br />
* November 16: Dissemination Meeting: [[Dissemination:Kickoff_Agenda|Agenda]], [[Dissemination:Kickoff_Summary|Summary]]<br />
----<br />
* October 15: [[Kickoff:Main| NA-MIC Kickoff Meeting]]</div>Pinterhttps://www.na-mic.org/w/index.php?title=File:20170629_RemoteUsParameterChange_Small.gif&diff=96837File:20170629 RemoteUsParameterChange Small.gif2017-06-30T09:21:40Z<p>Pinter: Pinter uploaded a new version of File:20170629 RemoteUsParameterChange Small.gif</p>
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<div></div>Pinterhttps://www.na-mic.org/w/index.php?title=File:20170629_RemoteUsParameterChange_Small.gif&diff=96834File:20170629 RemoteUsParameterChange Small.gif2017-06-30T09:19:29Z<p>Pinter: Pinter uploaded a new version of File:20170629 RemoteUsParameterChange Small.gif</p>
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<div></div>Pinterhttps://www.na-mic.org/w/index.php?title=Project_Week_25/Tracked-Ultrasound-Standardization-IV&diff=96816Project Week 25/Tracked-Ultrasound-Standardization-IV2017-06-30T08:53:59Z<p>Pinter: </p>
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<div>__NOTOC__<br />
Back to [[Project_Week_25#Projects|Projects List]]<br />
<br />
==Key Investigators==<br />
* [http://nist.mni.mcgill.ca/?page_id=369 Simon Drouin] (Montreal Neurological Institute, Canada)<br />
* [http://perk.cs.queensu.ca/users/lasso Andras Lasso] (Queen's University, Canada)<br />
* [http://perk.cs.queensu.ca/users/pinter Csaba Pinter] (Queen's University, Canada)<br />
* [http://www.sintef.no/en/all-employees/employee/?empId=541 Ole Vegard Solberg] (SINTEF, Norway)<br />
* [http://www.ap-lab.ca/people/ Etienne Leger] (Applied Perception Lab, Concordia University, Canada )<br />
* Longquan Chen (electronically) (Brigham and Women's Hospital, Harvard Medical School, USA)<br />
* [http://www.imaging.robarts.ca/petergrp/node/113 Adam Rankin] (electronically) (Robarts Research Institute, Canada)<br />
<br />
==Project Description==<br />
{| class="wikitable"<br />
! style="text-align: left; width:27%" | Objective<br />
! style="text-align: left; width:27%" | Approach and Plan<br />
! style="text-align: left; width:27%" | Progress and Next Steps<br />
|- style="vertical-align:top;"<br />
|<br />
<!-- Objective bullet points --><br />
* [http://www.plustoolkit.org Plus toolkit] provides access to numerous hardware devices (imaging devices, tracking devices, navigations systems, sensors, etc.) and makes it available through [http://www.openigtlink.org OpenIGTLink] protocol<br />
* Create a common library, [http://igsio.github.io OpenIGTLinkIO] that makes communication with Plus (and OpenIGTLink-compatible devices or software) very simple:<br />
** Ensure software interoperability<br />
** Share software maintenance workload<br />
** Make it easy to share new features<br />
* Add specific features for tracked ultrasound and and augmented reality in surgical navigation<br />
|<br />
<!-- Approach and Plan bullet points --><br />
* Improve message header sent by Plus Toolkit for US machines(Ole Vegar, Simon)<br />
* Build a complete US session simulation (OpenIGTLinkIO motifs, Plus config, Automated tests) (Ole Vega, Simon)<br />
* Add missing functionality in OpenIGTLinkIO to complete reintegration in OpenIGTLinkIF (Simon, Longquan )<br />
* Improve support to launch Plus server remotely (Csaba + Andras)<br />
* Adapt OpenIGTLinkIO to handle video compression functionality added to OpenIGTLink (Etienne + Longquan + Adam)<br />
|<br />
<!-- Progress and Next steps (fill out at the end of project week) --><br />
<br />
* Progress in OpenIGTLinkIO (changes in [https://github.com/SINTEFMedtek/OpenIGTLinkIO/tree/feature/CX-114-support-for-openigtlink3 branch on SINTEF's fork] of OpenIGTLinkIO )<br />
** Simplified handling of command messages in OpenIGTLinkIO.<br />
** US parameters are now in the header of each image header.<br />
<br />
* Created a US simulation session where 2 parameters (depth and frequency) of the US machine can be remotely controlled. (TODO: put file here)<br />
<br />
* Added support for video streaming (including compression) in OpenIGTLinkIO (Lonquan, remotely). Changes are in Longquan's fork [https://github.com/leochan2009/OpenIGTLinkIO master branch].<br />
<br />
* Remote change of ultrasound parameters. Topic branch: https://github.com/cpinter/PlusLib/tree/set-us-parameters-command<br />
** New command to Plus called vtkPlusSetUsParameterCommand<br />
** Received command is propagated to the ultrasound device and parameter change is requested<br />
** Example command syntax: <Command Name="SetFrequencyMhz" ParameterDoubleValue="4" /> (Parameter argument not final)<br />
<br />
* Next step<br />
** Polish code and merge SINTEF's and Longquan's master branch for OpenIGTLinkIO and Csaba's topic branch in Plus.<br />
** Add support (both in Plus and OpenIGTLinkIO) for automatic probing of US machine capabilities and settable parameters.<br />
** Finish the work on remote Plus server launch.<br />
** Build an auto-populated GUI to control US machine in OpenIGTLinkIO. GUI is populated according to parameters recovered from probing US machine remotely<br />
<br />
|}<br />
<br />
==Illustrations==<br />
Remote change of ultrasound imaging parameters:<br />
<br />
{| class="wikitable"<br />
! style="text-align: left; width:50%" | [[image:20170629_RemoteUsParameterChange1.png|400px]]<br />
! style="text-align: left; width:50%" | [[image:20170629_RemoteUsParameterChange6.png|400px]]<br />
! style="text-align: left; width:50%" | [[image:20170629_RemoteUsParameterChange_Small.gif|400px]] Click image to see animation<br />
|- style="vertical-align:top;"<br />
|}<br />
<br />
Progress of the project during past project weeks:<br />
<br />
{| class="wikitable"<br />
! style="text-align: left; width:50%" | [[image:1-before-winter-2016.jpeg|400px]]<br />
! style="text-align: left; width:50%" | [[image:2-winter-2016.jpeg|400px]]<br />
|- style="vertical-align:top;"<br />
|<br />
[[image:3-summer-2016.jpeg|400px]] <br />
| <br />
[[image:4-winter-2017.jpeg|400px]]<br />
|}<br />
<br />
==Background and References==<br />
*Winter 2017 [[2017_Winter_Project_Week/Tracked_Ultrasound_Standardization | project page ]]<br />
*Winter 2016 [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | project page]]<br />
*Summer 2016 [[ 2016 Summer Project Week/Tracked Ultrasound Standardization | project page]]<br />
<!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --></div>Pinterhttps://www.na-mic.org/w/index.php?title=File:20170629_RemoteUsParameterChange_Small.gif&diff=96812File:20170629 RemoteUsParameterChange Small.gif2017-06-30T08:51:39Z<p>Pinter: </p>
<hr />
<div></div>Pinterhttps://www.na-mic.org/w/index.php?title=Project_Week_25/Tracked-Ultrasound-Standardization-IV&diff=96773Project Week 25/Tracked-Ultrasound-Standardization-IV2017-06-29T09:32:04Z<p>Pinter: /* Illustrations */</p>
<hr />
<div>__NOTOC__<br />
Back to [[Project_Week_25#Projects|Projects List]]<br />
<br />
==Key Investigators==<br />
* [http://nist.mni.mcgill.ca/?page_id=369 Simon Drouin] (Montreal Neurological Institute, Canada)<br />
* [http://perk.cs.queensu.ca/users/lasso Andras Lasso] (Queen's University, Canada)<br />
* [http://perk.cs.queensu.ca/users/pinter Csaba Pinter] (Queen's University, Canada)<br />
* [http://www.sintef.no/en/all-employees/employee/?empId=541 Ole Vegard Solberg] (SINTEF, Norway)<br />
* [http://www.ap-lab.ca/people/ Etienne Leger] (Applied Perception Lab, Concordia University, Canada )<br />
* Longquan Chen (electronically) (Brigham and Women's Hospital, Harvard Medical School, USA)<br />
* [http://www.imaging.robarts.ca/petergrp/node/113 Adam Rankin] (electronically) (Robarts Research Institute, Canada)<br />
<br />
==Project Description==<br />
{| class="wikitable"<br />
! style="text-align: left; width:27%" | Objective<br />
! style="text-align: left; width:27%" | Approach and Plan<br />
! style="text-align: left; width:27%" | Progress and Next Steps<br />
|- style="vertical-align:top;"<br />
|<br />
<!-- Objective bullet points --><br />
* [http://www.plustoolkit.org Plus toolkit] provides access to numerous hardware devices (imaging devices, tracking devices, navigations systems, sensors, etc.) and makes it available through [http://www.openigtlink.org OpenIGTLink] protocol<br />
* Create a common library, [http://igsio.github.io OpenIGTLinkIO] that makes communication with Plus (and OpenIGTLink-compatible devices or software) very simple:<br />
** Ensure software interoperability<br />
** Share software maintenance workload<br />
** Make it easy to share new features<br />
* Add specific features for tracked ultrasound and and augmented reality in surgical navigation<br />
|<br />
<!-- Approach and Plan bullet points --><br />
* Improve message header sent by Plus Toolkit for US machines(Ole Vegar, Simon)<br />
* Build a complete US session simulation (OpenIGTLinkIO motifs, Plus config, Automated tests) (Ole Vega, Simon)<br />
* Add missing functionality in OpenIGTLinkIO to complete reintegration in OpenIGTLinkIF (Simon, Longquan )<br />
* Improve support to launch Plus server remotely (Csaba + Andras)<br />
* Adapt OpenIGTLinkIO to handle video compression functionality added to OpenIGTLink (Etienne + Longquan + Adam)<br />
|<br />
<!-- Progress and Next steps (fill out at the end of project week) --><br />
[Please start each sentence in a new line]<br />
<br />
* Remote change of ultrasound parameters. Topic branch: https://github.com/cpinter/PlusLib/tree/set-us-parameters-command<br />
** New command to Plus called vtkPlusSetUsParameterCommand<br />
** Received command is propagated to the ultrasound device and parameter change is requested<br />
** Example command syntax: <Command Name="SetFrequencyMhz" ParameterDoubleValue="4" /> (Parameter argument not final)<br />
|}<br />
<br />
==Illustrations==<br />
Remote change of ultrasound imaging parameters:<br />
<br />
{| class="wikitable"<br />
! style="text-align: left; width:50%" | [[image:20170629_RemoteUsParameterChange1.png|400px]]<br />
! style="text-align: left; width:50%" | [[image:20170629_RemoteUsParameterChange6.png|400px]]<br />
|- style="vertical-align:top;"<br />
|}<br />
<br />
Progress of the project during past project weeks:<br />
<br />
{| class="wikitable"<br />
! style="text-align: left; width:50%" | [[image:1-before-winter-2016.jpeg|400px]]<br />
! style="text-align: left; width:50%" | [[image:2-winter-2016.jpeg|400px]]<br />
|- style="vertical-align:top;"<br />
|<br />
[[image:3-summer-2016.jpeg|400px]] <br />
| <br />
[[image:4-winter-2017.jpeg|400px]]<br />
|}<br />
<br />
==Background and References==<br />
*Winter 2017 [[2017_Winter_Project_Week/Tracked_Ultrasound_Standardization | project page ]]<br />
*Winter 2016 [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | project page]]<br />
*Summer 2016 [[ 2016 Summer Project Week/Tracked Ultrasound Standardization | project page]]<br />
<!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --></div>Pinterhttps://www.na-mic.org/w/index.php?title=File:20170629_RemoteUsParameterChange6.png&diff=96772File:20170629 RemoteUsParameterChange6.png2017-06-29T09:30:22Z<p>Pinter: </p>
<hr />
<div></div>Pinterhttps://www.na-mic.org/w/index.php?title=File:20170629_RemoteUsParameterChange1.png&diff=96771File:20170629 RemoteUsParameterChange1.png2017-06-29T09:30:09Z<p>Pinter: </p>
<hr />
<div></div>Pinterhttps://www.na-mic.org/w/index.php?title=Project_Week_25/Tracked-Ultrasound-Standardization-IV&diff=96770Project Week 25/Tracked-Ultrasound-Standardization-IV2017-06-29T09:28:02Z<p>Pinter: </p>
<hr />
<div>__NOTOC__<br />
Back to [[Project_Week_25#Projects|Projects List]]<br />
<br />
==Key Investigators==<br />
* [http://nist.mni.mcgill.ca/?page_id=369 Simon Drouin] (Montreal Neurological Institute, Canada)<br />
* [http://perk.cs.queensu.ca/users/lasso Andras Lasso] (Queen's University, Canada)<br />
* [http://perk.cs.queensu.ca/users/pinter Csaba Pinter] (Queen's University, Canada)<br />
* [http://www.sintef.no/en/all-employees/employee/?empId=541 Ole Vegard Solberg] (SINTEF, Norway)<br />
* [http://www.ap-lab.ca/people/ Etienne Leger] (Applied Perception Lab, Concordia University, Canada )<br />
* Longquan Chen (electronically) (Brigham and Women's Hospital, Harvard Medical School, USA)<br />
* [http://www.imaging.robarts.ca/petergrp/node/113 Adam Rankin] (electronically) (Robarts Research Institute, Canada)<br />
<br />
==Project Description==<br />
{| class="wikitable"<br />
! style="text-align: left; width:27%" | Objective<br />
! style="text-align: left; width:27%" | Approach and Plan<br />
! style="text-align: left; width:27%" | Progress and Next Steps<br />
|- style="vertical-align:top;"<br />
|<br />
<!-- Objective bullet points --><br />
* [http://www.plustoolkit.org Plus toolkit] provides access to numerous hardware devices (imaging devices, tracking devices, navigations systems, sensors, etc.) and makes it available through [http://www.openigtlink.org OpenIGTLink] protocol<br />
* Create a common library, [http://igsio.github.io OpenIGTLinkIO] that makes communication with Plus (and OpenIGTLink-compatible devices or software) very simple:<br />
** Ensure software interoperability<br />
** Share software maintenance workload<br />
** Make it easy to share new features<br />
* Add specific features for tracked ultrasound and and augmented reality in surgical navigation<br />
|<br />
<!-- Approach and Plan bullet points --><br />
* Improve message header sent by Plus Toolkit for US machines(Ole Vegar, Simon)<br />
* Build a complete US session simulation (OpenIGTLinkIO motifs, Plus config, Automated tests) (Ole Vega, Simon)<br />
* Add missing functionality in OpenIGTLinkIO to complete reintegration in OpenIGTLinkIF (Simon, Longquan )<br />
* Improve support to launch Plus server remotely (Csaba + Andras)<br />
* Adapt OpenIGTLinkIO to handle video compression functionality added to OpenIGTLink (Etienne + Longquan + Adam)<br />
|<br />
<!-- Progress and Next steps (fill out at the end of project week) --><br />
[Please start each sentence in a new line]<br />
<br />
* Remote change of ultrasound parameters. Topic branch: https://github.com/cpinter/PlusLib/tree/set-us-parameters-command<br />
** New command to Plus called vtkPlusSetUsParameterCommand<br />
** Received command is propagated to the ultrasound device and parameter change is requested<br />
** Example command syntax: <Command Name="SetFrequencyMhz" ParameterDoubleValue="4" /> (Parameter argument not final)<br />
|}<br />
<br />
==Illustrations==<br />
Progress of the project during past project weeks:<br />
<br />
{| class="wikitable"<br />
! style="text-align: left; width:50%" | [[image:1-before-winter-2016.jpeg|400px]]<br />
! style="text-align: left; width:50%" | [[image:2-winter-2016.jpeg|400px]]<br />
|- style="vertical-align:top;"<br />
|<br />
[[image:3-summer-2016.jpeg|400px]] <br />
| <br />
[[image:4-winter-2017.jpeg|400px]]<br />
|}<br />
<br />
==Background and References==<br />
*Winter 2017 [[2017_Winter_Project_Week/Tracked_Ultrasound_Standardization | project page ]]<br />
*Winter 2016 [[2016_Winter_Project_Week/Projects/TrackedUltrasoundStandardization | project page]]<br />
*Summer 2016 [[ 2016 Summer Project Week/Tracked Ultrasound Standardization | project page]]<br />
<!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --></div>Pinterhttps://www.na-mic.org/w/index.php?title=Project_Week_25/Segment_editor_breakout_session&diff=96741Project Week 25/Segment editor breakout session2017-06-27T08:17:11Z<p>Pinter: </p>
<hr />
<div>Tuesday, 11AM-1PM<br />
<br />
== Preparation ==<br />
To follow along with the demo, please<br />
* Download the latest nightly ([http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.7.0-2017-06-25-win-amd64.exe&checksum=bd1c36264179b4be443557bdcf60f841 Windows], [http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.7.0-2017-06-25-macosx-amd64.dmg&checksum=89d6c6066c4f799ade03aed8ef5d168a Mac], [http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.7.0-2017-06-25-linux-amd64.tar.gz&checksum=d050b331d4c3a9efc49ebee8e7b88ddc Linux])<br />
* Install the SegmentEditorExtraEffects extension from the Extension Manager within Slicer<br />
* Download<br />
** [https://www.slicer.org/w/images/a/a6/BasePiece.zip Phantom base STL file] for the 3D printing section<br />
** [https://www.slicer.org/w/images/b/bb/WhiteMatterExplorationData.zip Neurosurgery tutorial dataset] (which is also available in the DataStore module in Slicer)<br />
** CTChest dataset in the Sample Data module<br />
<br />
== Agenda ==<br />
<br />
* Demo (Csaba Pinter, Andras Lasso)<br />
** 3D Printing<br />
** Neurosurgery<br />
** Tips & Tricks<br />
* Discussion</div>Pinterhttps://www.na-mic.org/w/index.php?title=Project_Week_25/Segment_editor_breakout_session&diff=96740Project Week 25/Segment editor breakout session2017-06-26T16:17:59Z<p>Pinter: </p>
<hr />
<div>Tuesday, 11AM-1PM<br />
<br />
== Preparation ==<br />
To follow along with the demo, please<br />
* Download the latest nightly ([http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.7.0-2017-06-25-win-amd64.exe&checksum=bd1c36264179b4be443557bdcf60f841 Windows], [http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.7.0-2017-06-25-macosx-amd64.dmg&checksum=89d6c6066c4f799ade03aed8ef5d168a Mac], [http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.7.0-2017-06-25-linux-amd64.tar.gz&checksum=d050b331d4c3a9efc49ebee8e7b88ddc Linux])<br />
* Install the SegmentEditorExtraEffects extension from the Extension Manager within Slicer<br />
* Download [https://www.slicer.org/w/images/a/a6/BasePiece.zip the phantom base STL file] for the 3D printing section, and the [https://www.slicer.org/w/images/b/bb/WhiteMatterExplorationData.zip neurosurgery tutorial dataset] (which is also available in the DataStore module in Slicer)<br />
<br />
== Agenda ==<br />
<br />
* Demo (Csaba Pinter, Andras Lasso)<br />
** 3D Printing<br />
** Neurosurgery<br />
** Tips & Tricks<br />
* Discussion</div>Pinterhttps://www.na-mic.org/w/index.php?title=Project_Week_25/Segment_editor_breakout_session&diff=96739Project Week 25/Segment editor breakout session2017-06-26T16:04:55Z<p>Pinter: </p>
<hr />
<div>Tuesday, 11AM-1PM<br />
<br />
== Preparation ==<br />
To follow along with the demo, please<br />
* Download the latest nightly ([http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.7.0-2017-06-25-win-amd64.exe&checksum=bd1c36264179b4be443557bdcf60f841 Windows], [http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.7.0-2017-06-25-macosx-amd64.dmg&checksum=89d6c6066c4f799ade03aed8ef5d168a Mac], [http://slicer.kitware.com/midas3/api/rest?method=midas.bitstream.download&name=Slicer-4.7.0-2017-06-25-linux-amd64.tar.gz&checksum=d050b331d4c3a9efc49ebee8e7b88ddc Linux])<br />
* Install the SegmentEditorExtraEffects extension from the Extension Manager within Slicer<br />
* Download [http://www.na-mic.org/Wiki/images/1/1e/BasePiece.stl the phantom base STL file] for the 3D printing section, and the [https://www.slicer.org/w/images/b/bb/WhiteMatterExplorationData.zip neurosurgery tutorial dataset] (which is also available in the DataStore module in Slicer)<br />
<br />
== Agenda ==<br />
<br />
* Demo (Csaba Pinter, Andras Lasso)<br />
** 3D Printing<br />
** Neurosurgery<br />
** Tips & Tricks<br />
* Discussion</div>Pinterhttps://www.na-mic.org/w/index.php?title=Project_Week_25/Segment_editor_breakout_session&diff=96738Project Week 25/Segment editor breakout session2017-06-26T15:56:39Z<p>Pinter: </p>
<hr />
<div>Tuesday, 11AM-1PM<br />
<br />
== Agenda ==<br />
<br />
*Demo (Csaba Pinter, Andras Lasso)<br />
**To follow along, please download the latest nightly ([http://slicer.cdash.org/viewFiles.php?buildid=1050466 Windows], [http://slicer.cdash.org/viewFiles.php?buildid=1050465 Mac], [http://slicer.cdash.org/viewFiles.php?buildid=1050464 Linux]), and the SegmentEditorExtraEffects extension from the Extension Manager within Slicer<br />
**Sections: 3D Printing, Neurosurgery, Tips & Tricks<br />
*Discussion</div>Pinterhttps://www.na-mic.org/w/index.php?title=Project_Week_25/Segment_editor_breakout_session&diff=96737Project Week 25/Segment editor breakout session2017-06-26T15:55:51Z<p>Pinter: </p>
<hr />
<div>Agenda<br />
<br />
*Demo (Csaba Pinter, Andras Lasso)<br />
**To follow along, please download the latest nightly ([http://slicer.cdash.org/viewFiles.php?buildid=1050466 Windows], [http://slicer.cdash.org/viewFiles.php?buildid=1050465 Mac], [http://slicer.cdash.org/viewFiles.php?buildid=1050464 Linux]), and the SegmentEditorExtraEffects extension from the Extension Manager within Slicer<br />
**Sections: 3D Printing, Neurosurgery, Tips & Tricks<br />
*Discussion</div>Pinterhttps://www.na-mic.org/w/index.php?title=Project_Week_25&diff=95697Project Week 252017-05-31T15:44:29Z<p>Pinter: /* Projects */</p>
<hr />
<div>__NOTOC__<br />
Back to [[Events]]<br />
<br />
A summary of all past [[Project_Events#Past_Project_Weeks|Project Events]].<br />
<br />
[[image:PW25.png|300px]] [[image:IEL_logo.png|225px]]<br />
<br><br />
<br />
=Welcome to the web page for the 25th Project Week!=<br />
<br />
It is a pleasure to announce that the 25th Project week will be held in [https://goo.gl/maps/b9CpkFxNyWN2 Catanzaro Lido] (Calabria, Italy) on June 26-30, 2017. This is the first time in Italy for the Slicer Community, and the event is organized in cooperation with [http://www.imagenglab.com ImagEngLab]. Catanzaro Lido is a city on the Ionian Sea, in the middle of Squillace Gulf where, according to the ancient legend, Odysseus started his journey back to Ithaca. Of course bring your swimsuit...the conference room and the hotel are 20 meters far away from the beach!<br />
<br />
This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.<br />
<br />
Please make sure that you are on the NA-MIC Project Week [http://public.kitware.com/mailman/listinfo/na-mic-project-week mailing list].<br />
<br />
===Local Organizing Committee===<br />
*[http://www.imagenglab.com/newsite/mf_spadea/ Maria Francesca Spadea, PhD]<br />
*[http://www.imagenglab.com/newsite/paolo_zaffino/ Paolo Zaffino, PhD].<br />
<br />
==Hangouts for preparation==<br />
#(Tina Kapur) Hangout #1: April 5th, 2017 - 9.00 AM Boston time: [https://plus.google.com/events/cjh9ag37hm1e7peplatphl7kh2g?authkey=COWc5cKc77jymgE event page] ([[PW25 Hangouts Notes|Notes]])<br />
#(Steve Pieper) Hangout #2: Wednesday April 12, 2017, 9am EDT (GMT-4): Web browser based computing: Dockerized Slicer with remote computing and GPU computing; Cornerstone/LesionTracker OHIF; XTK->AMI (threejs); ePad; vtk.js; QWebEngine; [https://plus.google.com/hangouts/_/kitware.com/pw-25?hceid=a2l0d2FyZS5jb21fc2IwN2kxNzFvbGFjOWFhdmg0NmlyNDk1YzRAZ3JvdXAuY2FsZW5kYXIuZ29vZ2xlLmNvbQ.fffs75fitbu0mvpl3vvmrcqf3s&authuser=0 hangout page]<br />
#(Andras Lasso) Hangout #3: Wednesday April 19, 2017, 9am EDT (GMT-4) Connecting devices such as surgical navigation, ultrasound, 3D Slicer, PLUS, OpenIGTLink, Augmented reality; [https://hangouts.google.com/hangouts/_/kitware.com/pw-25?authuser=0 hangout page]<br />
#(Tina Kapur) Hangout #4: Wednesday April 26, 2017, 9am EDT (GMT-4) Deep Learning for Detection of Cancer and Instruments; [https://hangouts.google.com/hangouts/_/kitware.com/pw-25?authuser=0 hangout page];<br />
#(Simon Drouin) Hangout #5: Wednesday May 3, 2017, 9am EDT (GMT-4)Volume Rendering, Augmented Reality, and Virtual Reality. [https://docs.google.com/document/d/1UwdSzjnDm1yEeQ44OEhXWbH6V83Uo1Cd4KngxoyrRdI/edit Notes];[https://plus.google.com/hangouts/_/kitware.com/pw-25?hceid=a2l0d2FyZS5jb21fc2IwN2kxNzFvbGFjOWFhdmg0NmlyNDk1YzRAZ3JvdXAuY2FsZW5kYXIuZ29vZ2xlLmNvbQ.fffs75fitbu0mvpl3vvmrcqf3s&authuser=0 hangout page]<br />
#(Tina Kapur) Hangout #6: Wednesday May 10, 2017, 9am EDT (GMT-4) For new participants: What is project week and how to get the most out of participating in it? [https://hangouts.google.com/hangouts/_/kitware.com/pw-25?authuser=0 hangout page]<br />
#(Andrey Fedorov) Hangout #7: Wednesday May 17, 2017, 9am EDT (GMT-4) DICOM for Quantitative Imaging and integration with processing applications. [https://hangouts.google.com/hangouts/_/kitware.com/pw-25?authuser=0 hangout page] ([http://bit.ly/2017NSPW-DICOM notes])<br />
#(Tina Kapur) Hangout #8: Wednesday May 24, 2017, 9am EDT (GMT-4) Review of Projects and teams that have been provided on the wiki page by participants, internationalization strategy for Slicer. [https://hangouts.google.com/hangouts/_/kitware.com/pw-25?authuser=0 hangout page]<br />
#(Francesca Spadea) Hangout #9: Wednesday May 31, 2017, 9am EDT (GMT-4) Review of local logistics -- all registered attendees should join [https://zoom.us/j/879371330 zoom "hangout" page]<br />
#(TBD) Hangout #10: Wednesday June 7, 2017, 9am EDT (GMT-4) TBD [https://zoom.us/j/879371330 zoom "hangout" page]<br />
#(TBD) Hangout #11: Wednesday June 14, 2017, 9am EDT (GMT-4) TBD [https://zoom.us/j/879371330 zoom "hangout" page]<br />
#(Francesca Spadea) Hangout #12: Wednesday June 21, 2017, 9am EDT (GMT-4) Review of local logistics -- all registered attendees with questions should join [https://zoom.us/j/879371330 zoom "hangout" page]<br />
<br />
==Logistics==<br />
<br />
*'''Dates:''' June 26-30, 2017. Consider staying for one more day (leaving Sunday morning), as a day off in a gorgeous sea place is planned on July 1st. More details in the calendar below.<br />
*'''Location:''' [http://www.hotelperladelporto.it/en/home-page.aspx Perla del Porto Hotel]<br />
**[mailto:prenotazioni@hotelperladelporto.it Booking]. Subject line: "Slicer Summer Project Week 2017". <br />
***Special rates are:<br />
****Single room, full bed, 79 € per night (1 person)<br />
****Single room, queen bed 89 € per night (1 person)<br />
****Double room, queen bed 99 € per night (2 people)<br />
****Triple room, 110 € (3 people)<br />
*'''REGISTRATION:''' To register please visit this [http://www.imagenglab.com/newsite/project-week page]<br />
*'''Registration Fee:''' 320€ and it includes lunches, coffee breaks and airport connections<br />
*'''Hotel:''' [http://www.hotelperladelporto.it/en/home-page.aspx Perla del Porto Hotel]. The closest airport is [http://www.lameziaairport.it/english/ Lamezia Terme Airport (IATA: SUF)].<br />
*'''Transportation from Airport to Hotel''' Your registration fee includes ground transportation [https://www.google.com/maps/dir/Lamezia+Terme+International+Airport,+Via+Aeroporto,+88046+Lamezia+Terme+CZ,+Italy/BEST+WESTERN+PLUS+Hotel+Perla+Del+Porto,+Via+Martiri+di+Cefalonia,+64,+88100+Catanzaro,+Italy/@38.868758,16.1564814,10z/data=!3m1!4b1!4m14!4m13!1m5!1m1!1s0x133fe15a3cbed47f:0x544ab120c3de78a6!2m2!1d16.2434017!2d38.9065845!1m5!1m1!1s0x134003d668252a13:0x2989caf676f45a72!2m2!1d16.6312407!2d38.827712!3e0 to/from the hotel and airport].<br />
** Please fill out this form to request transportation https://goo.gl/forms/7vmhxZSHy8Z1A62z2<br />
*'''Local points of interest (pubs, restaurants, bar):''' [https://www.google.com/maps/d/viewer?mid=1FU63ik9Do3zzP6K2kvLVTtM2at8&ll=38.86221979925013%2C16.44292274999998&z=12 map (constantly updated)]<br />
<br />
==Calendar==<br />
<br />
<br />
{{#widget:Google Calendar<br />
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com<br />
|timezone=America/New_York&dates=20170108%2F20170114<br />
|title=NA-MIC Project Week (Timezone is Italy / GMT+02.)<br />
|view=WEEK<br />
|dates=20170626/20170701<br />
}}<br />
<br />
iCal (.ics) link: https://calendar.google.com/calendar/ical/kitware.com_sb07i171olac9aavh46ir495c4%40group.calendar.google.com/public/basic.ics<br />
<br />
=Projects=<br />
<br />
Please put a brief preliminary title for your project here with some names in parenthesis for potential team members<br />
<br />
#Needle segmentation Project 1 (Guillaume Pernelle, Tina Kapur, Paolo Zaffino, Salvatore Scaramuzzino, Francesca Spadea)<br />
#Needle segmentation Project 2 (Paolo Zaffino, Salvatore Scaramuzzino, Francesca Spadea, Guillaume Pernelle, Tina Kapur)<br />
#DICOM Segmentation support for Cornerstone / OHIF Viewer (Erik Ziegler, Steve Pieper, Marco Nolden, Tina Kapur)<br />
#Conversion of DICOM single frame MR to Enhanced Multiframe (Michael Onken, Steve Pieper, Andras Lasso, Csaba Pinter)<br />
#Human-Computer Interaction under sterile conditions (Christian Hansen, Julian Hettig, Benjamin Hatscher, David Black, Marco Nolden, Juan Ruiz)<br />
#Development and evaluation of new AR visualization techniques to support radiological interventions (Christian Hansen, Florian Heinrich, Andrè Mewes, Juan Ruiz, Marco Nolden)<br />
#Interactive manipulation of plots and graphs: i) panning; ii) click and drag; iii) data selection (Davide Punzo, Steve Pieper, Jean-Christophe Fillion-Robin)<br />
#Next generation of volume rendering in VTK (Simon Drouin, Steve Pieper, Ole Vegard Solberg, Andras Lasso)<br />
#Tracked Ultrasound Standardization IV: Controlling US acquisition (Simon Drouin, Ole Vegard Solberg, Csaba Pinter, Andras Lasso [electronically: Longquan Chen, Adam Rankin])<br />
#Steerable catheters path planner extension for brain surgery applications (Alberto Favaro, Marlene Pinzi)<br />
#Improving depth perception in interventional Augmented Reality visualization/(+sonification?) (Simon Drouin, Christian Hansen, David Black)<br />
#DICOM for Quantitative Imaging and integration with processing applications (Jasmin Metzger, Marco Nolden, Steve Pieper)<br />
#Intra-operative deformable registration based on dense point cloud reconstruction (Sara Moccia, Andre Mewes, Gino Gulamhussene, Florian Heinrich)<br />
#Segmentation for improving image registration of preoperative MRI/intraoperative ultrasound images for neuro-navigation (Jennifer Nitsch, Scheherazade Kraß)<br />
#CNN for pseudoCT generation from T1/T2 MRI (Giampaolo Pileggi, Paolo Zaffino, Salvatore Scaramuzzino, Maria Francesca Spadea, Gino Gulamhussene, Anneke Meyer)<br />
#Internationalizing Slicer modules (Juan Ruiz Alzola, )<br />
#Interfacing Slicer to mobile phone-controlled sensors (Juan Ruiz Alzola, )<br />
#Slicer and 3D Printing (Juan Ruiz Alzola, Mike Halle, Christian Hansen)<br />
#Slicer export to VR (Juan Ruiz Alzola, Mike Halle,)<br />
#Deep Learning: Data augmentation for prostate segmentation (Anneke Meyer, Christian Hansen, Andrey Federov)<br />
#2D Slice to 3D volume registration to support radiologic interventions (Gino Gulamhussene,)<br />
<br />
=Registrants=<br />
<br />
Do not add your name to this list - it is maintained by the organizers based on your paid registration. To register, visit this [http://www.imagenglab.com/newsite/project-week/ registration site].<br />
<br />
# Kikinis, Ron :: Brigham and Women's Hospital, Harvard Medical School, USA<br />
# Pieper, Steve :: Isomics, Inc., USA<br />
# Kapur, Tina :: Brigham and Women's Hospital, Harvard Medical School, USA<br />
# Spadea, Maria Francesca :: Magna Graecia University, Italy<br />
# Zaffino, Paolo :: Magna Graecia University, Italy<br />
# Scaramuzzino, Salvatore :: Magna Graecia University/ASL Vercelli, Italy<br />
# Pileggi, Giampaolo :: Magna Graecia University, Italy/DKFZ, Germany<br />
# Rackerseder, Julia :: Technische Universität München, Germany<br />
# Pinter, Csaba :: Queen's University, Canada<br />
# Kraß, Scheherazade :: University of Bremen, Germany<br />
# Gerig, Guido :: NYU Tandon School of Engineering, USA<br />
# Punzo, Davide :: Kapteyn Astronomical Institute, Netherlands<br />
# Drouin, Simon :: NeuroImaging and Surgical Technologies (NIST) Lab, Canada<br />
# Lasso, Andras :: School of Computing, Queen's University, Canada<br />
# Favaro, Alberto :: Politecnico di Milano, Italy<br />
# Leger, Etienne :: Concordia University, Canada<br />
# Ziegler, Erik :: Ziegler Consult SAS<br />
# Onken, Michael :: Open Connections GmbH, Germany<br />
# Pinzi, Marlene :: Imperial College, UK<br />
# Nitsch, Jennifer :: University Of Bremen, Germany<br />
# Moccia, Sara :: Politecnico di Milano, Italy<br />
# Black, David :: Fraunhofer Institute for Medical Image Computing MEVIS, Bremen, Germany<br />
# Penzkofer, Tobias :: Charité Universitätsmedizin, Berlin, Germany<br />
# Hansen, Christian :: Universität Magdeburg, Germany<br />
# Vegard Solberg, Ole :: Norway<br />
# Heinrich, Florian :: Universität Magdeburg, Germany<br />
# Mewes, André :: Universität Magdeburg, Germany<br />
# Hatscher, Benjamin :: Universität Magdeburg, Germany<br />
# Hettig, Julian :: Universität Magdeburg, Germany<br />
# Meyer, Anneke :: Universität Magdeburg, Germany<br />
# Gulamhussene, Gino :: Universität Magdeburg, Germany<br />
# Cassetta, Roberto :: Politecnico di Milano, Italy<br />
# Fillion-Robin, Jean-Christophe :: Kitware, USA</div>Pinterhttps://www.na-mic.org/w/index.php?title=File:SegmentationFor3DPrinting_TutorialContestWinter2017.pptx&diff=95209File:SegmentationFor3DPrinting TutorialContestWinter2017.pptx2017-01-17T16:01:45Z<p>Pinter: Pinter uploaded a new version of File:SegmentationFor3DPrinting TutorialContestWinter2017.pptx</p>
<hr />
<div></div>Pinterhttps://www.na-mic.org/w/index.php?title=File:SegmentationFor3DPrinting_TutorialContestWinter2017.pdf&diff=95208File:SegmentationFor3DPrinting TutorialContestWinter2017.pdf2017-01-17T16:01:32Z<p>Pinter: Pinter uploaded a new version of File:SegmentationFor3DPrinting TutorialContestWinter2017.pdf</p>
<hr />
<div></div>Pinterhttps://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/SubjectHierarchyRefactoring&diff=950152017 Winter Project Week/SubjectHierarchyRefactoring2017-01-13T14:54:07Z<p>Pinter: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]<br />
Image:20170109_SubjectHierarchy.png|Subject hierarchy tree<br />
<!-- Use the "Upload file" link on the left and then add a line to this list like "File:MyAlgorithmScreenshot.png" --><br />
</gallery><br />
<br />
==Key Investigators==<br />
* Csaba Pinter (Queen's)<br />
* ? (JC, Steve, Andras)<br />
* Jorge Onieva<br />
<br />
==Project Description==<br />
{| class="wikitable"<br />
! style="text-align: left; width:27%" | Objective<br />
! style="text-align: left; width:27%" | Approach and Plan<br />
! style="text-align: left; width:27%" | Progress and Next Steps<br />
|- style="vertical-align:top;"<br />
|<br />
<!-- Objective bullet points --><br />
Although the subject hierarchy mechanism is in place and is already used, there are several issues and limitations that cannot be addressed in its current form:<br />
* Subject hierarchy needs to be disabled by default, because<br />
** A second node is created for each data node and the scene can grow very large in case of many data nodes<br />
** Model hierarchies and subject hierarchies are not fully compatible, so problems may arise in case of complex model hierarchies (such as atlases)<br />
** Because of this, a popup is shown to the user, which is confusing for users. It prevents some from using SH, and is annoying for the others<br />
* Expanded state is reset to all extended when switching to another module and back. This can be very frustrating when there are many subjects or folders, because the user sees it very differently after returning to SH<br />
* Manual re-ordering of nodes is not possible<br />
* Node selector based on subject hierarchy (e.g. where it's possible to start selecting by patient in some way) cannot be implemented without major changes<br />
These issues are due to<br />
* The overly complex Qt MRML scene model infrastructure, which is rigid in some ways, and bloated in others<br />
** Can only show nodes, so if an item is needed to be shown, a new node needs to be created (thus the lot of SH nodes and the virtual branches, see below). Also pointer tracking of nodes complicates things.<br />
** Index calculation is very complex and gets even more complex in the sub classes.<br />
** The features that are needed for specific models but are implemented in the base model overcomplicate the implementation (e.g. pre- and post items)<br />
* Unstable workarounds implemented in the current subject hierarchy infrastructure to accommodate certain use cases<br />
** Nested associations that use the MRML hierarchy associations in a nested way so that the same nodes can be added both to model and subject hierarchies<br />
** Virtual branches to accommodate data that do not correspond to MRML nodes one-on-one (segments contained by segmentations, fiducials contained by markups)<br />
** Postfixes of the SH nodes to differentiate them from the associated data nodes<br />
This necessitates a re-design of the subject hierarchy mechanism. The proposed solution is to store the whole subject hierarchy tree in one node, the internals of which are synchronized with the data nodes of the scene. A new Qt item model needs to be implemented for this node that supplies the information to the tree view and the future node selectors.<br />
|<br />
<!-- Approach and Plan bullet points --><br />
* Store the whole tree in one vtkMRMLSubjectHierarchy node<br />
** Items have unique identifier numbers that is strictly incremental<br />
** Item information can be accessed using accessors, the item class itself is private<br />
* Automatically populate from added nodes (as before), observe modified and removed events<br />
* Implement new Qt item model that is synchronized with the subject hierarchy node instead of the scene<br />
* Import model hierarchies to SH node on entering SH module if new detected (thus model hierarchies can be fully used from <br />
* Subject hierarchy logic makes sure there is only one SH node and it is valid (at import, deletion, potential undo, etc.)<br />
|<br />
<!-- Progress and Next steps bullet points (fill out at the end of project week) --><br />
* Rewrote all subject hierarchy classes (node, logic, model, tree view, plugin handler, plugin logic, abstract plugin) and updating classes using subject hierarchy<br />
* It compiles, but need to work on making it really work<br />
* Need to make sure all components, all plugins work well. Also need to check all extensions and update them if they use subject hierarchy directly<br />
|}<br />
<br />
==Background and References==<br />
<!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --></div>Pinterhttps://www.na-mic.org/w/index.php?title=File:SegmentationFor3DPrinting_TutorialContestWinter2017.pptx&diff=94853File:SegmentationFor3DPrinting TutorialContestWinter2017.pptx2017-01-12T17:34:25Z<p>Pinter: Pinter uploaded a new version of File:SegmentationFor3DPrinting TutorialContestWinter2017.pptx</p>
<hr />
<div></div>Pinterhttps://www.na-mic.org/w/index.php?title=File:SegmentationFor3DPrinting_TutorialContestWinter2017.pdf&diff=94852File:SegmentationFor3DPrinting TutorialContestWinter2017.pdf2017-01-12T17:33:50Z<p>Pinter: Pinter uploaded a new version of File:SegmentationFor3DPrinting TutorialContestWinter2017.pdf</p>
<hr />
<div></div>Pinterhttps://www.na-mic.org/w/index.php?title=2017_Tutorial_Contest&diff=948482017 Tutorial Contest2017-01-12T17:25:07Z<p>Pinter: </p>
<hr />
<div>[[2017_Winter_Project_Week#Agenda|Back to Winter project week Agenda]]<br />
==Introduction==<br />
[http://www.slicer.org Slicer4.6] is used to perform meaningful research tasks. As part of the 3D Slicer Training activities we are building a curated portfolio of tutorials for the basic functions and specialized functionality available in Slicer. <br />
<br />
The primary purpose of the Winter 2017 tutorial contest is to enrich the training materials that are available to end-users and developers using 3D Slicer. The contest provides members of the medical image computing and radiology research community a methodology and a framework for developing step-by-step tutorials on advanced image analysis methods. We believe participants will be motivated to join this event to enhance the dissemination of their own algorithms that they have incorporated into the Slicer4 platform, and to enhance training of Slicer4 functionality for their own laboratory groups.<br />
<br />
==Organizer==<br />
Sonia Pujol, Ph.D., Director of Training, Neuroimage Analysis Center, Brigham and Women's Hospital, Harvard Medical School<br />
<br />
==Categories==<br />
*Category 1 (*new*): '''DEMONSTRATION'''. This category allows new comers to the Slicer community to provide short demos based on slides and/or videos of their application. <br />
*Category 2: '''ALGORITHM TUTORIAL'''. In this category the tutorial will teach a user how to make an algorithm work on their data.<br />
*Category 3: '''EXTENSION TUTORIAL'''. In this category, the tutorial will teach a user how to use an Extension of Slicer.<br />
*Category 4: '''END TO END SOLUTION TUTORIAL'''. In this category, the tutorial will teach a user how to solve a particular clinical problem using a workflow implemented in Slicer.<br />
*Category 5: '''TUTORIAL UPGRADE/UPDATE"'. This category allows teams who participated in the past tutorial contest editions to submit an update/upgrade of their previous submission.<br />
<br />
Entries in each category require the following material: <br />
* scientific background and application motivation<br />
* step-by-step instructions<br />
* anonymized sample dataset<br />
<br />
=Rules=<br />
The evaluation criteria for the 2017 tutorial contest are below:<br />
*Tutorial must be based on the Slicer 4.6 release version of the software. <br />
*To enter the contest, you must provide 'a version of the tutorial that works on all supported platforms (Mac,Windows,Linux)<br />
*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]<br />
*Tutorial data must be anonymized<br />
*Tutorial must include contact information of the primary author (e-mail and phone number) <br />
*Tutorial must follow the guidelines specified above and use the [[Media:TutorialContest_Template_2016.ppt | Winter 2017 contest tutorial template]].<br />
*If applicable, the tutorial must provide clear directions for downloading and installing additional modules <br><br />
<br />
=Submission Process=<br />
'''<span style="background-color: pink"> Submission dead-line: Wednesday January 11, 2017'''</span><br />
* To enter the contest, please follow the 5 steps below:<br />
**1. Create a wiki page for your tutorial on the NA-MIC wiki.<br />
**2. Upload your slides/demos and tutorial dataset. Your tutorial and data must be named as 'TutorialName_TutorialContestWinter2017.pdf' and 'TutorialData_TutorialContestWinter2017.zip'<br />
**3. Add a link to the uploaded tutorial and datasets on your tutorial page. <br />
**4. Copy the template of the [http://wiki.na-mic.org/Wiki/index.php/Training:Winter_2017_Contest_Table Winter 2017 test table ] on your tutorial page, and document the status of your cross-platform testing (Mac, Windows, Linux).<br />
**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) to receive a confirmation of your submission.<br />
<br />
=Tutorials=<br />
*Simple Python Tool for Quality Control of DWI data (Laurent Chauvin)<br />
*[https://www.nitrc.org/docman/view.php/308/1982/SPHARM-PDM_Tutorial_July2015.pdf SPHARM-PDM (Beatriz Paniagua)]<br />
*[http://www.na-mic.org/Wiki/images/a/a6/SegmentationFor3DPrinting_TutorialContestWinter2017.pdf Segmentation for 3D printing] (Csaba Pinter)<br />
*[[Media:ROSIGTLTutorial_Tokuda_Jan2017.pptx| Integration of Robot Operating System (ROS) and 3D Slicer using OpenIGTLink (Junichi Tokuda)]]<br />
*Slicer Pathology (Erich Bremer)<br />
*[[Media:Fiber_Bundle_Volume_Measurement.pptx|Fiber Bundle Volume Measurement]], [[Media:FiberVolume_data.zip| tutorial data]] (Shun Gong)<br />
<br />
= Review Session=<br />
The review session of the 2017 Tutorial Contest will take place on Thursday January 12 at the Massachusetts Institute of Technology, Cambrigde, MA as part of the Winter 2017 Slicer Project Week.<br />
All contestants will be invited to present brief highlights of their tutorials. Each presentation should be 5-minute summary of the submission.<br />
*Judges:<br />
**Rebekka Lauer, Humboldt-University, Berlin <br />
**Parvin Mousavi, Brigham and Women's Hospital<br />
**Peter Anderson<br />
<br />
=Results=<br />
The winner of the 2017 tutorial contest will be announced on Friday January 13 during the closing session of the Slicer Project Week.</div>Pinterhttps://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/2017TutorialContest&diff=948472017 Winter Project Week/2017TutorialContest2017-01-12T17:24:17Z<p>Pinter: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]<br />
<!-- Use the "Upload file" link on the left and then add a line to this list like "File:MyAlgorithmScreenshot.png" --><br />
</gallery><br />
<br />
==Key Investigators==<br />
Sonia Pujol, Ph.D., Director of Training, Neuroimage Analysis Center<br />
<br />
==Project Description==<br />
{| class="wikitable"<br />
! style="text-align: left; width:27%" | <br />
Objective: <br />
! style="text-align: left; width:27%" | <br />
Approach and Plan: <br />
! style="text-align: left; width:27%" | Progress and Next Steps<br />
|- style="vertical-align:top;"<br />
|<br />
<!-- Objective bullet points --><br />
* The primary purpose of the Winter 2017 tutorial contest is to enrich the training materials that are available to end-users and developers using 3D Slicer. <br />
|<br />
<!-- Approach and Plan bullet points --><br />
* The contest provides members of the medical image computing and radiology research community a methodology and a framework for developing step-by-step tutorials on advanced image analysis methods. <br />
|<br />
<!-- Progress and Next steps bullet points (fill out at the end of project week) --><br />
*<br />
|}<br />
<br />
==Tutorials==<br />
Tutorials are available on the [[2017_Tutorial_Contest|Tutorial contest]] event page<br />
# '''Segmentation for 3D printing'''<br />
#* [http://www.na-mic.org/Wiki/images/3/3f/SegmentationFor3DPrinting_TutorialContestWinter2017.pptx This tutorial] ([http://www.na-mic.org/Wiki/images/a/a6/SegmentationFor3DPrinting_TutorialContestWinter2017.pdf PDF]) creates a printable STL model from a section of the spinal column segmented from a CT image, attached to a base designed in CAD software.<br />
#* Author: Csaba Pinter (Queen's University, Canada)<br />
#* Dataset: The CT image is the CTChest dataset accessible from the Sample Data module in Slicer. The phantom base can be downloaded [http://www.na-mic.org/Wiki/images/1/1e/BasePiece.stl here]</div>Pinterhttps://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/2017TutorialContest&diff=948412017 Winter Project Week/2017TutorialContest2017-01-12T16:53:25Z<p>Pinter: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]<br />
<!-- Use the "Upload file" link on the left and then add a line to this list like "File:MyAlgorithmScreenshot.png" --><br />
</gallery><br />
<br />
==Key Investigators==<br />
Sonia Pujol, Ph.D., Director of Training, Neuroimage Analysis Center<br />
<br />
==Project Description==<br />
{| class="wikitable"<br />
! style="text-align: left; width:27%" | <br />
Objective: <br />
! style="text-align: left; width:27%" | <br />
Approach and Plan: <br />
! style="text-align: left; width:27%" | Progress and Next Steps<br />
|- style="vertical-align:top;"<br />
|<br />
<!-- Objective bullet points --><br />
* The primary purpose of the Winter 2017 tutorial contest is to enrich the training materials that are available to end-users and developers using 3D Slicer. <br />
|<br />
<!-- Approach and Plan bullet points --><br />
* The contest provides members of the medical image computing and radiology research community a methodology and a framework for developing step-by-step tutorials on advanced image analysis methods. <br />
|<br />
<!-- Progress and Next steps bullet points (fill out at the end of project week) --><br />
*<br />
|}<br />
<br />
==Tutorials==<br />
# '''Segmentation for 3D printing'''<br />
#* [http://www.na-mic.org/Wiki/images/3/3f/SegmentationFor3DPrinting_TutorialContestWinter2017.pptx This tutorial] ([http://www.na-mic.org/Wiki/images/a/a6/SegmentationFor3DPrinting_TutorialContestWinter2017.pdf PDF]) creates a printable STL model from a section of the spinal column segmented from a CT image, attached to a base designed in CAD software.<br />
#* Author: Csaba Pinter (Queen's University, Canada)<br />
#* Dataset: The CT image is the CTChest dataset accessible from the Sample Data module in Slicer. The phantom base can be downloaded [http://www.na-mic.org/Wiki/images/1/1e/BasePiece.stl here]</div>Pinterhttps://www.na-mic.org/w/index.php?title=File:SegmentationFor3DPrinting_TutorialContestWinter2017.pdf&diff=94840File:SegmentationFor3DPrinting TutorialContestWinter2017.pdf2017-01-12T16:53:14Z<p>Pinter: </p>
<hr />
<div></div>Pinterhttps://www.na-mic.org/w/index.php?title=File:SegmentationFor3DPrinting_TutorialContestWinter2017.pptx&diff=94839File:SegmentationFor3DPrinting TutorialContestWinter2017.pptx2017-01-12T16:51:25Z<p>Pinter: </p>
<hr />
<div></div>Pinterhttps://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/2017TutorialContest&diff=948182017 Winter Project Week/2017TutorialContest2017-01-12T05:22:03Z<p>Pinter: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]<br />
<!-- Use the "Upload file" link on the left and then add a line to this list like "File:MyAlgorithmScreenshot.png" --><br />
</gallery><br />
<br />
==Key Investigators==<br />
Sonia Pujol, Ph.D., Director of Training, Neuroimage Analysis Center<br />
<br />
==Project Description==<br />
{| class="wikitable"<br />
! style="text-align: left; width:27%" | <br />
Objective: <br />
! style="text-align: left; width:27%" | <br />
Approach and Plan: <br />
! style="text-align: left; width:27%" | Progress and Next Steps<br />
|- style="vertical-align:top;"<br />
|<br />
<!-- Objective bullet points --><br />
* The primary purpose of the Winter 2017 tutorial contest is to enrich the training materials that are available to end-users and developers using 3D Slicer. <br />
|<br />
<!-- Approach and Plan bullet points --><br />
* The contest provides members of the medical image computing and radiology research community a methodology and a framework for developing step-by-step tutorials on advanced image analysis methods. <br />
|<br />
<!-- Progress and Next steps bullet points (fill out at the end of project week) --><br />
*<br />
|}<br />
<br />
==Tutorials==<br />
# '''Segmentation for 3D printing'''<br />
#* This tutorial (TODO slides link) creates a printable STL model from a section of the spinal column segmented from a CT image, attached to a base designed in CAD software.<br />
#* Author: Csaba Pinter (Queen's University, Canada)<br />
#* Dataset: The CT image is the CTChest dataset accessible from the Sample Data module in Slicer. The phantom base can be downloaded [http://www.na-mic.org/Wiki/images/1/1e/BasePiece.stl here]</div>Pinterhttps://www.na-mic.org/w/index.php?title=File:BasePiece.stl&diff=94817File:BasePiece.stl2017-01-12T05:15:14Z<p>Pinter: </p>
<hr />
<div></div>Pinterhttps://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/ImprovementsToSegmentEditor&diff=948162017 Winter Project Week/ImprovementsToSegmentEditor2017-01-12T02:09:37Z<p>Pinter: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]<br />
Image:SegmentationHighlights01s.png|Highlights of segmentations 1<br />
Image:SegmentationHighlights02s.png|Highlights of segmentations 2<br />
Image:20160526_SegmentationObject.PNG|Segmentation object<br />
<!-- Use the "Upload file" link on the left and then add a line to this list like "File:MyAlgorithmScreenshot.png" --><br />
</gallery><br />
<br />
==Key Investigators==<br />
* Csaba Pinter (Queen's)<br />
* Andras Lasso (Queen's)<br />
<br />
==Project Description==<br />
{| class="wikitable"<br />
! style="text-align: left; width:27%" | Objective<br />
! style="text-align: left; width:27%" | Approach and Plan<br />
! style="text-align: left; width:27%" | Progress and Next Steps<br />
|- style="vertical-align:top;"<br />
|<br />
<!-- Objective bullet points --><br />
* Segment Editor is the new version of the Editor module used for segmentating structures from anatomical images<br />
* The module is quite new, so we'd love to<br />
** help people adopt the new module<br />
** hear any feedback about the module<br />
|<br />
<!-- Approach and Plan bullet points --><br />
* Breakout session in Kiva room at 12PM on Wednesday<br />
|<br />
<!-- Progress and Next steps bullet points (fill out at the end of project week) --><br />
* About 30 participants. Presentation + demo + discussion<br />
* Basics of the underlying Segmentations infrastructure presented (Csaba): [https://www.slicer.org/w/images/6/64/20160526_Segmentations.pptx these slides] ([https://www.slicer.org/w/images/a/ae/20160526_Segmentations.pdf PDF]) (This is a longer version of the slides presented. More information on the [https://www.slicer.org/wiki/Documentation/Nightly/Modules/Segmentations Segmentations module wiki page])<br />
* Segment Editor features presented (Andras)<br />
** CTACardio<br />
*** Thresholding<br />
**** Apply<br />
**** Crop right arm with scissors in slice view, circle ROI<br />
**** Create model<br />
**** Undo<br />
**** Use for paint<br />
*** Paint:<br />
**** Segment vessel in right arm<br />
**** Create model<br />
**** Change spacing<br />
**** Sphere paint<br />
*** Hollow model:<br />
**** Copy segment<br />
**** Grow segment<br />
**** Subtract segment<br />
**** Cut ends<br />
*** Masking:<br />
**** Editable area: inside all segments<br />
**** Paint<br />
**** Grow<br />
**** New segment, Outside all segments<br />
**** Grow<br />
**** New segment, Overwrite other segments (default)<br />
**** Paint<br />
**** Overwrite other segments: None<br />
** Auto-complete:<br />
*** Geometric:<br />
**** CTACardio<br />
**** Abdominal muscles<br />
*** Growcut<br />
**** MRBrainTumor1<br />
**** Growcut<br />
**** Fix leakage<br />
**** Smoothing<br />
**** Segment stats<br />
** Scissors:<br />
*** CTChest, bone threshold<br />
*** Island / Keep largest<br />
*** Create surface<br />
*** Create new segment (for ribs)<br />
*** Editable: inside all<br />
*** Scissors - fill outside<br />
*** Split islands to segments<br />
*** Separate lowest vertebra with 3d scissors<br />
** Slice thickness is used by paint tool 2D size<br />
** Segmentation on oblique slices<br />
** Segmentation on vesselness filtering result<br />
* '''Video coming soon'''<br />
* Discussion meeting minutes<br />
** Rename Apply for paint to Use as mask in all effects (in Threshold)<br />
** Logical/Copy -> Copy from<br />
** Threshold is easy to leave on, and then the result will be surprising (e.g. when expanding)<br />
** Clipping circle, adding margin (Adam)<br />
** First master volume resolution remains the segment resolution -> make it clearer?<br />
*** Explain master volume in a tooltip or similar<br />
** Auto-complete/Fill/Initialize -> rename to make it clear what it does (Preview?)<br />
** Alexis' comments<br />
*** Create surface button name and icon (suggests that it creates a model node) -> Show surface? (may be confusing due to the wait)<br />
*** Confusion about Segmentations and Segment Editor (Add/Remove is possible in two places)<br />
*** Auto-complete contains very different operations -> make it two buttons?<br />
** Effect button size and layout issues -> Make it more similar to Quantitative Reporting? (Undo/redo under effects, remove the empty area in the effects box)<br />
** Jump to center of the segment in the slice views (Greg) -> Actions in the table or similarly to markups?<br />
** 3D cursor in the 3D view -> moves in slices if you are not super careful not to move the mouse before clicking<br />
** Template effect extension<br />
** Volume clip features in segment editor (Christian) -> User interactions might be problematic<br />
|}<br />
<br />
==Background and References==<br />
<!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --></div>Pinterhttps://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/ImprovementsToSegmentEditor&diff=948062017 Winter Project Week/ImprovementsToSegmentEditor2017-01-11T19:33:47Z<p>Pinter: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]<br />
Image:SegmentationHighlights01s.png|Highlights of segmentations 1<br />
Image:SegmentationHighlights02s.png|Highlights of segmentations 2<br />
Image:20160526_SegmentationObject.PNG|Segmentation object<br />
<!-- Use the "Upload file" link on the left and then add a line to this list like "File:MyAlgorithmScreenshot.png" --><br />
</gallery><br />
<br />
==Key Investigators==<br />
* Csaba Pinter (Queen's)<br />
* Andras Lasso (Queen's)<br />
<br />
==Project Description==<br />
{| class="wikitable"<br />
! style="text-align: left; width:27%" | Objective<br />
! style="text-align: left; width:27%" | Approach and Plan<br />
! style="text-align: left; width:27%" | Progress and Next Steps<br />
|- style="vertical-align:top;"<br />
|<br />
<!-- Objective bullet points --><br />
* Segment Editor is the new version of the Editor module used for segmentating structures from anatomical images<br />
* The module is quite new, so we'd love to<br />
** help people adopt the new module<br />
** hear any feedback about the module<br />
|<br />
<!-- Approach and Plan bullet points --><br />
* Breakout session in Kiva room at 12PM on Wednesday<br />
|<br />
<!-- Progress and Next steps bullet points (fill out at the end of project week) --><br />
* About 30 participants. Presentation + demo + discussion<br />
* Basics of the underlying Segmentations infrastructure presented (Csaba): [https://www.slicer.org/w/images/6/64/20160526_Segmentations.pptx these slides] ([https://www.slicer.org/w/images/a/ae/20160526_Segmentations.pdf PDF]) (This is a longer version of the slides presented. More information on the [https://www.slicer.org/wiki/Documentation/Nightly/Modules/Segmentations Segmentations module wiki page])<br />
* Segment Editor features presented (Andras)<br />
** CTACardio<br />
*** Thresholding<br />
**** Apply<br />
**** Crop right arm with scissors in slice view, circle ROI<br />
**** Create model<br />
**** Undo<br />
**** Use for paint<br />
*** Paint:<br />
**** Segment vessel in right arm<br />
**** Create model<br />
**** Change spacing<br />
**** Sphere paint<br />
*** Hollow model:<br />
**** Copy segment<br />
**** Grow segment<br />
**** Subtract segment<br />
**** Cut ends<br />
*** Masking:<br />
**** Editable area: inside all segments<br />
**** Paint<br />
**** Grow<br />
**** New segment, Outside all segments<br />
**** Grow<br />
**** New segment, Overwrite other segments (default)<br />
**** Paint<br />
**** Overwrite other segments: None<br />
** Auto-complete:<br />
*** Geometric:<br />
**** CTACardio<br />
**** Abdominal muscles<br />
*** Growcut<br />
**** MRBrainTumor1<br />
**** Growcut<br />
**** Fix leakage<br />
**** Smoothing<br />
**** Segment stats<br />
** Scissors:<br />
*** CTChest, bone threshold<br />
*** Island / Keep largest<br />
*** Create surface<br />
*** Create new segment (for ribs)<br />
*** Editable: inside all<br />
*** Scissors - fill outside<br />
*** Split islands to segments<br />
*** Separate lowest vertebra with 3d scissors<br />
** Slice thickness is used by paint tool 2D size<br />
** Segmentation on oblique slices<br />
** Segmentation on vesselness filtering result<br />
* '''Video coming soon'''<br />
* Discussion meeting minutes<br />
** Rename Apply for paint to Use as mask in all effects (in Threshold)<br />
** Logical/Copy -> Copy from<br />
** Threshold is easy to leave on, and then the result will be surprising (e.g. when expanding)<br />
** Clipping circle, adding margin (ask details from Adam)<br />
** First master volume resolution remains the segment resolution -> make it clearer?<br />
*** Explain master volume in a tooltip or similar<br />
** Auto-complete/Fill/Initialize -> rename to make it clear what it does (Preview?)<br />
** Alexis' comments<br />
*** Create surface button name and icon (suggests that it creates a model node) -> Show surface? (may be confusing due to the wait)<br />
*** Confusion about Segmentations and Segment Editor (Add/Remove is possible in two places)<br />
*** Auto-complete contains very different operations -> make it two buttons?<br />
** Effect button size and layout issues -> Make it more similar to Quantitative Reporting? (Undo/redo under effects, remove the empty area in the effects box)<br />
** Jump to center of the segment in the slice views (Greg) -> Actions in the table or similarly to markups?<br />
** 3D cursor in the 3D view -> moves in slices if you are not super careful not to move the mouse before clicking<br />
** Template effect extension<br />
** Volume clip features in segment editor (Christian) -> User interactions might be problematic<br />
|}<br />
<br />
==Background and References==<br />
<!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --></div>Pinterhttps://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/ImprovementsToSegmentEditor&diff=947712017 Winter Project Week/ImprovementsToSegmentEditor2017-01-10T19:07:18Z<p>Pinter: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]<br />
Image:SegmentationHighlights01s.png|Highlights of segmentations 1<br />
Image:SegmentationHighlights02s.png|Highlights of segmentations 2<br />
Image:20160526_SegmentationObject.PNG|Segmentation object<br />
<!-- Use the "Upload file" link on the left and then add a line to this list like "File:MyAlgorithmScreenshot.png" --><br />
</gallery><br />
<br />
==Key Investigators==<br />
* Csaba Pinter (Queen's)<br />
* Andras Lasso (Queen's)<br />
<br />
==Project Description==<br />
{| class="wikitable"<br />
! style="text-align: left; width:27%" | Objective<br />
! style="text-align: left; width:27%" | Approach and Plan<br />
! style="text-align: left; width:27%" | Progress and Next Steps<br />
|- style="vertical-align:top;"<br />
|<br />
<!-- Objective bullet points --><br />
* Segment Editor is the new version of the Editor module used for segmentating structures from anatomical images<br />
* The module is quite new, so we'd love to<br />
** help people adopt the new module<br />
** hear any feedback about the module<br />
|<br />
<!-- Approach and Plan bullet points --><br />
* Breakout session in Kiva room at 12PM on Wednesday<br />
|<br />
<!-- Progress and Next steps bullet points (fill out at the end of project week) --><br />
*<br />
|}<br />
<br />
==Background and References==<br />
<!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --></div>Pinterhttps://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/SubjectHierarchyRefactoring&diff=947032017 Winter Project Week/SubjectHierarchyRefactoring2017-01-09T19:12:43Z<p>Pinter: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]<br />
Image:20170109_SubjectHierarchy.png|Subject hierarchy tree<br />
<!-- Use the "Upload file" link on the left and then add a line to this list like "File:MyAlgorithmScreenshot.png" --><br />
</gallery><br />
<br />
==Key Investigators==<br />
* Csaba Pinter (Queen's)<br />
* ? (JC, Steve, Andras)<br />
* Jorge Onieva<br />
<br />
==Project Description==<br />
{| class="wikitable"<br />
! style="text-align: left; width:27%" | Objective<br />
! style="text-align: left; width:27%" | Approach and Plan<br />
! style="text-align: left; width:27%" | Progress and Next Steps<br />
|- style="vertical-align:top;"<br />
|<br />
<!-- Objective bullet points --><br />
Although the subject hierarchy mechanism is in place and is already used, there are several issues and limitations that cannot be addressed in its current form:<br />
* Subject hierarchy needs to be disabled by default, because<br />
** A second node is created for each data node and the scene can grow very large in case of many data nodes<br />
** Model hierarchies and subject hierarchies are not fully compatible, so problems may arise in case of complex model hierarchies (such as atlases)<br />
** Because of this, a popup is shown to the user, which is confusing for users. It prevents some from using SH, and is annoying for the others<br />
* Expanded state is reset to all extended when switching to another module and back. This can be very frustrating when there are many subjects or folders, because the user sees it very differently after returning to SH<br />
* Manual re-ordering of nodes is not possible<br />
* Node selector based on subject hierarchy (e.g. where it's possible to start selecting by patient in some way) cannot be implemented without major changes<br />
These issues are due to<br />
* The overly complex Qt MRML scene model infrastructure, which is rigid in some ways, and bloated in others<br />
** Can only show nodes, so if an item is needed to be shown, a new node needs to be created (thus the lot of SH nodes and the virtual branches, see below). Also pointer tracking of nodes complicates things.<br />
** Index calculation is very complex and gets even more complex in the sub classes.<br />
** The features that are needed for specific models but are implemented in the base model overcomplicate the implementation (e.g. pre- and post items)<br />
* Unstable workarounds implemented in the current subject hierarchy infrastructure to accommodate certain use cases<br />
** Nested associations that use the MRML hierarchy associations in a nested way so that the same nodes can be added both to model and subject hierarchies<br />
** Virtual branches to accommodate data that do not correspond to MRML nodes one-on-one (segments contained by segmentations, fiducials contained by markups)<br />
** Postfixes of the SH nodes to differentiate them from the associated data nodes<br />
This necessitates a re-design of the subject hierarchy mechanism. The proposed solution is to store the whole subject hierarchy tree in one node, the internals of which are synchronized with the data nodes of the scene. A new Qt item model needs to be implemented for this node that supplies the information to the tree view and the future node selectors.<br />
|<br />
<!-- Approach and Plan bullet points --><br />
* Store the whole tree in one vtkMRMLSubjectHierarchy node<br />
** Items have unique identifier numbers that is strictly incremental<br />
** Item information can be accessed using accessors, the item class itself is private<br />
* Automatically populate from added nodes (as before), observe modified and removed events<br />
* Implement new Qt item model that is synchronized with the subject hierarchy node instead of the scene<br />
* Import model hierarchies to SH node on entering SH module if new detected (thus model hierarchies can be fully used from <br />
* Subject hierarchy logic makes sure there is only one SH node and it is valid (at import, deletion, potential undo, etc.)<br />
|<br />
<!-- Progress and Next steps bullet points (fill out at the end of project week) --><br />
*<br />
|}<br />
<br />
==Background and References==<br />
<!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --></div>Pinterhttps://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/SubjectHierarchyRefactoring&diff=947022017 Winter Project Week/SubjectHierarchyRefactoring2017-01-09T19:12:03Z<p>Pinter: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]<br />
Image:20170109_SubjectHierarchy.png|Subject hierarchy tree<br />
<!-- Use the "Upload file" link on the left and then add a line to this list like "File:MyAlgorithmScreenshot.png" --><br />
</gallery><br />
<br />
==Key Investigators==<br />
* Csaba Pinter (Queen's)<br />
* ? (JC, Steve, Andras)<br />
<br />
==Project Description==<br />
{| class="wikitable"<br />
! style="text-align: left; width:27%" | Objective<br />
! style="text-align: left; width:27%" | Approach and Plan<br />
! style="text-align: left; width:27%" | Progress and Next Steps<br />
|- style="vertical-align:top;"<br />
|<br />
<!-- Objective bullet points --><br />
Although the subject hierarchy mechanism is in place and is already used, there are several issues and limitations that cannot be addressed in its current form:<br />
* Subject hierarchy needs to be disabled by default, because<br />
** A second node is created for each data node and the scene can grow very large in case of many data nodes<br />
** Model hierarchies and subject hierarchies are not fully compatible, so problems may arise in case of complex model hierarchies (such as atlases)<br />
** Because of this, a popup is shown to the user, which is confusing for users. It prevents some from using SH, and is annoying for the others<br />
* Expanded state is reset to all extended when switching to another module and back. This can be very frustrating when there are many subjects or folders, because the user sees it very differently after returning to SH<br />
* Manual re-ordering of nodes is not possible<br />
* Node selector based on subject hierarchy (e.g. where it's possible to start selecting by patient in some way) cannot be implemented without major changes<br />
These issues are due to<br />
* The overly complex Qt MRML scene model infrastructure, which is rigid in some ways, and bloated in others<br />
** Can only show nodes, so if an item is needed to be shown, a new node needs to be created (thus the lot of SH nodes and the virtual branches, see below). Also pointer tracking of nodes complicates things.<br />
** Index calculation is very complex and gets even more complex in the sub classes.<br />
** The features that are needed for specific models but are implemented in the base model overcomplicate the implementation (e.g. pre- and post items)<br />
* Unstable workarounds implemented in the current subject hierarchy infrastructure to accommodate certain use cases<br />
** Nested associations that use the MRML hierarchy associations in a nested way so that the same nodes can be added both to model and subject hierarchies<br />
** Virtual branches to accommodate data that do not correspond to MRML nodes one-on-one (segments contained by segmentations, fiducials contained by markups)<br />
** Postfixes of the SH nodes to differentiate them from the associated data nodes<br />
This necessitates a re-design of the subject hierarchy mechanism. The proposed solution is to store the whole subject hierarchy tree in one node, the internals of which are synchronized with the data nodes of the scene. A new Qt item model needs to be implemented for this node that supplies the information to the tree view and the future node selectors.<br />
|<br />
<!-- Approach and Plan bullet points --><br />
* Store the whole tree in one vtkMRMLSubjectHierarchy node<br />
** Items have unique identifier numbers that is strictly incremental<br />
** Item information can be accessed using accessors, the item class itself is private<br />
* Automatically populate from added nodes (as before), observe modified and removed events<br />
* Implement new Qt item model that is synchronized with the subject hierarchy node instead of the scene<br />
* Import model hierarchies to SH node on entering SH module if new detected (thus model hierarchies can be fully used from <br />
* Subject hierarchy logic makes sure there is only one SH node and it is valid (at import, deletion, potential undo, etc.)<br />
|<br />
<!-- Progress and Next steps bullet points (fill out at the end of project week) --><br />
*<br />
|}<br />
<br />
==Background and References==<br />
<!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --></div>Pinterhttps://www.na-mic.org/w/index.php?title=File:20170109_SubjectHierarchy.png&diff=94701File:20170109 SubjectHierarchy.png2017-01-09T19:11:21Z<p>Pinter: </p>
<hr />
<div></div>Pinterhttps://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/ImprovementsToSegmentEditor&diff=946742017 Winter Project Week/ImprovementsToSegmentEditor2017-01-09T18:36:14Z<p>Pinter: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]<br />
Image:SegmentationHighlights01s.png|Highlights of segmentations 1<br />
Image:SegmentationHighlights02s.png|Highlights of segmentations 2<br />
Image:20160526_SegmentationObject.PNG|Segmentation object<br />
<!-- Use the "Upload file" link on the left and then add a line to this list like "File:MyAlgorithmScreenshot.png" --><br />
</gallery><br />
<br />
==Key Investigators==<br />
* Csaba Pinter (Queen's)<br />
* Andras Lasso (Queen's)<br />
<br />
==Project Description==<br />
{| class="wikitable"<br />
! style="text-align: left; width:27%" | Objective<br />
! style="text-align: left; width:27%" | Approach and Plan<br />
! style="text-align: left; width:27%" | Progress and Next Steps<br />
|- style="vertical-align:top;"<br />
|<br />
<!-- Objective bullet points --><br />
* Segment Editor is the new version of the Editor module used for segmentating structures from anatomical images<br />
* The module is quite new, so we'd love to<br />
** help people adopt the new module<br />
** hear any feedback about the module<br />
|<br />
<!-- Approach and Plan bullet points --><br />
* TBD<br />
|<br />
<!-- Progress and Next steps bullet points (fill out at the end of project week) --><br />
*<br />
|}<br />
<br />
==Background and References==<br />
<!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --></div>Pinterhttps://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/ImprovementsToSegmentEditor&diff=946672017 Winter Project Week/ImprovementsToSegmentEditor2017-01-09T18:32:50Z<p>Pinter: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]<br />
<!-- Use the "Upload file" link on the left and then add a line to this list like "File:MyAlgorithmScreenshot.png" --><br />
</gallery><br />
<br />
==Key Investigators==<br />
* Csaba Pinter (Queen's)<br />
* Andras Lasso (Queen's)<br />
<br />
==Project Description==<br />
{| class="wikitable"<br />
! style="text-align: left; width:27%" | Objective<br />
! style="text-align: left; width:27%" | Approach and Plan<br />
! style="text-align: left; width:27%" | Progress and Next Steps<br />
|- style="vertical-align:top;"<br />
|<br />
<!-- Objective bullet points --><br />
* Segment Editor is the new version of the Editor module used for segmentating structures from anatomical images<br />
* The module is quite new, so we'd love to<br />
** help people adopt the new module<br />
** hear any feedback about the module<br />
|<br />
<!-- Approach and Plan bullet points --><br />
* TBD<br />
|<br />
<!-- Progress and Next steps bullet points (fill out at the end of project week) --><br />
*<br />
|}<br />
<br />
==Background and References==<br />
<!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --></div>Pinterhttps://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/ImprovementsToSegmentEditor&diff=946642017 Winter Project Week/ImprovementsToSegmentEditor2017-01-09T18:32:30Z<p>Pinter: Created page with "__NOTOC__ <gallery> Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|Projects List <!-- Use the "Upload file" link on the l..."</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]<br />
<!-- Use the "Upload file" link on the left and then add a line to this list like "File:MyAlgorithmScreenshot.png" --><br />
</gallery><br />
<br />
==Key Investigators==<br />
* Csaba Pinter (Queen's)<br />
* Andras (Queen's)<br />
<br />
==Project Description==<br />
{| class="wikitable"<br />
! style="text-align: left; width:27%" | Objective<br />
! style="text-align: left; width:27%" | Approach and Plan<br />
! style="text-align: left; width:27%" | Progress and Next Steps<br />
|- style="vertical-align:top;"<br />
|<br />
<!-- Objective bullet points --><br />
* Segment Editor is the new version of the Editor module used for segmentating structures from anatomical images<br />
* The module is quite new, so we'd love to<br />
** help people adopt the new module<br />
** hear any feedback about the module<br />
|<br />
<!-- Approach and Plan bullet points --><br />
* TBD<br />
|<br />
<!-- Progress and Next steps bullet points (fill out at the end of project week) --><br />
*<br />
|}<br />
<br />
==Background and References==<br />
<!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --></div>Pinterhttps://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week&diff=946582017 Winter Project Week2017-01-09T18:30:13Z<p>Pinter: </p>
<hr />
<div>__NOTOC__<br />
[[image:PW-Winter2017.png|300px]]<br />
<br />
=Welcome to the web page for the 24th Project Week!=<br />
<br />
The 24th NA-MIC Project Week open source hackathon is being held during the week of January 9-13, 2017 at MIT. Please go through this page for information, and if you have questions, please contact [https://www.spl.harvard.edu/pages/People/tkapur Tina Kapur, PhD].<br />
<br />
==Logistics==<br />
<br />
*'''Dates:''' January 9-13, 2017.<br />
*'''Location:''' [https://www.google.com/maps/place/MIT:+Computer+Science+and+Artificial+Intelligence+Laboratory/@42.361864,-71.090563,16z/data=!4m2!3m1!1s0x0:0x303ada1e9664dfed?hl=en MIT CSAIL], Cambridge, MA. (Rooms: [[MIT_Project_Week_Rooms#Kiva|Kiva]], R&D)<br />
*'''Transportation:''' Public transportation is highly encouraged, as no parking permits will be issued by MIT. For a list of local garages, please see [http://web.mit.edu/facilities/transportation/parking/visitors/public_parking.html here]<br />
*'''REGISTRATION:''' Register [https://www.regonline.com/2017projectweek here]. Registration Fee: $330.<br />
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.<br />
*'''Next Project Week:'''' [http://wiki.na-mic.org/Wiki/index.php/2017_Summer_Project_Week June 26-30, 2017, Catanzaro, Italy]<br />
<br />
== Introduction ==<br />
The National Alliance for Medical Image Computing (NAMIC), was founded in 2005 and chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], enhancements to the underlying building blocks [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an open source hackathon event called Project Week.<br />
<br />
[[Engineering:Programming_Events|Project Week]] is a semi-annual open source hackathon which draws 60-120 researchers. As of August 2014, it is a [http://www.miccai.org/organization MICCAI] endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event. <br />
<br />
Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.<br />
<br />
Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO]. <br />
<br />
A summary of all previous Project Events is available [[Project_Events#Past_Project_Weeks|here]].<br />
<br />
Please make sure that you are on the NA-MIC Project Week [http://public.kitware.com/mailman/listinfo/na-mic-project-week mailing list]<br />
<br />
==Conference Calls for Preparation==<br />
<br />
Conference call phone number and notes are available [[TCONS:2017_Winter_Project_Week|here]].<br />
<br />
==Calendar==<br />
<br />
'''''<font color="maroon">The events are listed in the calendar below. Note that due to a current known limitation of our infrastructure, you will need to manually navigate to the week of January 8, 2017 to see the relevant events.</font>'''''<br><br />
<br />
<br />
{{#widget:Google Calendar<br />
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com<br />
|timezone=America/New_York&dates=20170108%2F20170114<br />
|title=NAMIC Winter Project Week<br />
|view=WEEK<br />
|dates=20170108/20170114<br />
}}<br />
<br />
iCal (.ics) link: https://calendar.google.com/calendar/ical/kitware.com_sb07i171olac9aavh46ir495c4%40group.calendar.google.com/public/basic.ics<br />
<br />
='''Projects'''=<br />
<br />
*Use this [[2017_Project_Week_Template | Updated Template for project pages]]<br />
<br />
== Deep Learning and GPUs ==<br />
#[[2017 Winter Project Week/Deep Learning for Medical Image Computation| Deep Learning for Medical Image Computing]] (Tina Kapur)<br />
#[[2017 Winter Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Tina Kapur, Ziyang Wang, Guillaume Pernelle, Paolo Zaffino)<br />
#[[2017 Winter Project Week/DeepInfer| DeepInfer: Open-source Deep Learning Deployment Toolkit]] (Alireza Mehrtash, Mehran Pesteie, Yang (Silvia) Yixin, Tina Kapur, Sandy Wells, Purang Abolmaesumi, Andriy Fedorov)<br />
#[[2017 Winter Project Week/Diffusely abnormal white matter segmentation with 3d U-net| Diffusely abnormal white matter segmentation with 3d U-net]] (Mohsen Ghafoorrian, Bram Platel, Sandy Wells, Tina Kapur, Charles Guttmann)<br />
# [[2017 Winter Project Week/OCM-MRI | Deep Learning for Synthetic MRI]] (Frank Preiswerk, Yaofei "Ada" Wang)<br />
#[[2017 Winter Project Week/An open-source tool to classify TMJ OA condyles | An open-source tool to classify TMJ OA condyles]] (Priscille de Dumast, Juan Carlos Prieto, Beatriz Paniagua)<br />
#[[2017 Winter Project Week/Evaluate Deep Learning for binary cancer legion classification | Evaluate Deep Learning for binary cancer lesion classification]] (Curt Lisle)<br />
#[[2017 Winter Project Week/Convolutional neural nets for lung cancer survival prediction | Convolutional neural nets for lung cancer survival prediction]] (Ahmed Hosny, Chintan Parmar, Roman Zeleznik, Hugo Aerts)<br />
#[[2017 Winter Project Week/Population Based Image Imputation | Population Based Image Imputation]] (Adrian Dalca, Katie Bouman, Mert Sabuncu, Polina Golland)<br />
<br />
== Web Technologies ==<br />
#[[2017_Winter_Project_Week/WebTechnologyAndSlicer| Web Technology and Slicer]] (Steve Pieper, Erik Zeigler, Curt Lisle, Satra Ghosh, Hans Meine) <br />
#[[2017 Winter Project Week/Slicer Qt5 and Python3 | Slicer Qt5 and Python3]] (Steve Pieper, Jean-Christophe Fillion-Robin, Andras Lasso, Andrey Fedorov)<br />
#[[2017 Winter Project Week/IPFS_NoSQL_Combination | IPFS and NoSQL for cloud databases]] (Hans Meine, Steve Pieper)<br />
#[[Explore integration of Web-based imaging workflows with Slicer | Explore integration of Web-based imaging workflows with Slicer ]] (Curt Lisle, Satra Gosh, Steve Peiper)<br />
#[[2017 Winter Project Week/Web-based system to federate biological, clinical and morphological data | Web-based system to federate biological, clinical and morphological data]] (Juan Carlos Prieto, Clément Mirabel)<br />
#[[2017_Winter_Project_Week/OAuth2SlicerPathology | OAuth2.0 authentication in SlicerPathology]] (Erich Bremer, Steve Pieper, Teodora Szasz)<br />
#[[2017 Winter Project Week/Electron App to add, navigate and visualize DICOM images | Electron App to add, navigate and visualize DICOM images]] (Smruti Padhy, Satrajit Ghosh, Mathias Goncalves)<br />
#[[2017 Winter Project Week/AMI: A 3D Medical Imaging Javascript Library | AMI: A 3D Medical Imaging Javascript Library]] (Rudolph Pienaar, Jorge Luis Bernal Rusiel, Nicolas Rannou)<br />
#[[2017_Winter_Project_Week/MedicalVisualizerUsingParaViewWeb | Medical Visualizer using ParaViewWeb]] (Teodora Szasz)<br />
<br />
== IGT: Navigation, Robotics, Surgical Planning ==<br />
#[[2017 Winter Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization III: The Refining]] (Andras Lasso, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Janne Beate Bakeng)<br />
#[[2017 Winter Project Week/ROS Surface Scan | ROS Surface Scan]] (Tobias Frank, Junichi Tokuda, Longquan Chen)<br />
#[[2017 Winter Project Week/Open_Source_Electromagnetic_Trackers | Open Source Electromagnetic Trackers]] (Peter Traneus Anderson)<br />
#[[2017 Winter Project Week/LiverResectionPlanning | Liver resection planning extension]] (Louise Oram, Andrey Fedorov, Christian Herz, Andras Lasso)<br />
#[[2017 Winter Project Week/3DSurgicalPlanningBreastReconstruction| 3D surgical planning solution for autologous breast reconstruction]] (Michael Chae, Andras Lasso, Julian Smith, Warren Rozen, David Hunter-Smith)<br />
#[[2017 Winter Project Week/Intraoperative_Functional_Visualization | Visualization Concept for Intraoperative Use of Functional Mapping Data ]] (Rebekka Lauer, Anna Roethe, Prashin Unadkat, Sarah Frisken)<br />
<br />
==dMRI==<br />
#[[2017 Winter Project Week/WhiteMatterAnalysis | Fiber endpoint analysis for neurosurgical planning]] (Fan Zhang, Shun Gong, Isaiah Norton, Ye Wu, Lauren J. O'Donnell)<br />
#[[2017 Winter Project Week/LORDWI | Density-based DMRI registration ]] (Henrik Groenholt Jensen, Lauren J. O'Donnell, Tina Kapur, Fan Zhang, Carl-Fredrik Westin)<br />
#[[2017 Winter Project Week/SlicerDMRIDocumentationAndTesting | SlicerDMRI Testing and Documentation]] (Shun Gong, Ye Wu, Isaiah Norton, Fan Zhang, Lauren J. O'Donnell)<br />
#[[2017 Winter Project Week/DiPy_in_Slicer | WMA & DiPy integration in Slicer]] (Isaiah Norton, Lauren J. O'Donnell)<br />
#[[2017 Winter Project Week/DWI_Similarity_Metrics | Identification of information-rich patches in Diffusion-Weighted Images]] (Laurent Chauvin, Fan Zhang, Lauren J. O'Donnell, Matthew Toews)<br />
<br />
==Quantitative Imaging Informatics==<br />
#[[2017 Winter Project Week/dcmqi | dcmqi library]] (Andrey Fedorov, Christian Herz, JC, Steve Pieper)<br />
#[[2017 Winter Project Week/QuantitativeReporting | DICOM QuantitativeReporting]] (Christian Herz, Andrey Fedorov, Andras Lasso, Csaba Pinter)<br />
#[[2017 Winter Project Week/PyRadiomics | PyRadiomics library ]] (Joost van Griethuysen, Hugo Aerts, Andrey Fedorov, Steve Pieper, Jean-Christophe Fillion-Robin)<br />
#[[2017 Winter Project Week/PkModeling | PkModeling - DCE Modeling Accuracy and UI/UX Update]] (Andrew Beers)<br />
#[[2017 Winter Project Week/SegWithSubtractionAndModel| Manual Segmentation Module w/ Subtraction Maps + Delaunay Models]] (Andrew Beers)<br />
<br />
== Shape Analysis, Segmentation ==<br />
#[[2017 Winter Project Week/SlicerShape | Slicer for Shape Analysis ]] (Beatriz Paniagua)<br />
#[[2017 Winter Project Week/MandibularRegression | Mandibular Shape Regression ]] (Beatriz Paniagua, James Fishbaugh)<br />
#[[2017 Winter Project Week/Slicer_HoloLens | Slicer & HoloLens]] (Adam Rankin, Andras Lasso)<br />
#[[2017 Winter Project Week/HyperspectralOpht | Slicer for Hyperspectral Ophthalmology Analysis ]] (Sungmin Hong)<br />
#[[2017 Winter Project Week/GeodesicSegmentationandLungtumorAnalysis| Geodesic Segmentation and Lung tumor Analysis]] (Patmaa S, Sarthak Pati, Ratheesh k, Mark B, Yong F, Despina K, Ragini V, Christos D)<br />
#[[2017 Winter Project Week/ProstateSectorSegmentation | Prostate Gland Sector Segmentation]] (Anneke Meyer, Andrey Fedorov, Alireza Mehrtash, Christian Hansen)<br />
#[[2017 Winter Project Week/Multi-ModalitySegmentationOfUSandMRImagesForGliomaSurgery | Multi-Modality Segmentation of US- and MR-Images for Glioma Surgery]] (Jennifer Nitsch)<br />
#[[2017 Winter Project Week/MeningiomaSegmentation | Segmentation of meningiomas in structural MR images]] (Satrajit Ghosh, Omar Arnaout)<br />
#[[2017 Winter Project Week/CoronarySegmentationTool| Automatic and Manual Segmentation Tool of Coronary Artery from CTA imaging]] (Haoyin Zhou, Jayender Jagadeesan)<br />
<br />
== Infrastructure ==<br />
#[[2017 Winter Project Week/SubjectHierarchyRefactoring | Subject hierarchy single-node refactoring]] (Csaba Pinter)<br />
#[[2017 Winter Project Week/ImprovementsToSegmentEditor | Improvements to Segment Editor]] (Csaba Pinter, Andras Lasso)<br />
#[[2017 Winter Project Week/Plastimatch19 | Upgrade Plastimatch extension ]] (Greg Sharp)<br />
#[[2017 Winter Project Week/UpdatingCommunityForums | Updating Community Forums (Discourse, GitHub, Gitter, ???)]] (Andrey Fedorov, Andras Lasso, Steve Pieper, Mike Halle, Isaiah Norton, and The Community)<br />
#[[2017 Winter Project Week/SlicerGeometryModifier | Slicer support for interactive modification of 3D models ]] (Johan Andruejol, Beatriz Paniagua, Andras Lasso)<br />
#[[2017 Winter Project Week/Support_for_volumetric_meshes | Support for volumetric meshes ]] (Alexis Girault, Curtis Lisle, Steve Pieper)<br />
#[[2017 Winter Project Week/Improve_Matlab_integration | Improve Matlab integration ]] (Alexis Girault, Andras Lasso)<br />
#[[2017 Winter Project Week/Integrative_Intraoperative_Interface | Integrative Interface for Intraoperative Software Applications ]] (Rebekka Lauer, Anna Roethe, Prashin Unadkat, Sarah Frisken)<br />
<br />
==Training and Dissemination==<br />
#[[2017 Winter Project Week/2017TutorialContest| Tutorial contest]] (Sonia Pujol)<br />
#[[2017 Winter Project Week/2017 NVIDIA Demo Contest|NVIDIA Demo Contest]] (Abdul Halabi, Abel Brown)<br />
<br />
==Next project week==<br />
#[[2017 Winter Project Week/Next project week| Next project week]] (Paolo Zaffino, Maria Francesca Spadea, Tina Kapur)<br />
<br />
= '''Registrants''' =<br />
<br />
Do not add your name to this list - it is maintained by the organizers based on your paid registration. To register, visit this [https://www.regonline.com/2017projectweek registration site].<br />
<br />
# Aman Shboul, Zaina :: Old Dominion University<br />
# Aerts, Hugo :: DFCI-Harvard<br />
# Alam, Mahbubul :: Old Dominion University<br />
# Anderson, Peter :: Retired<br />
# Andruejol, Johan :: Kitware, Inc.<br />
# Bakeng, Janne Beate :: SINTEF<br />
# Beers, Andrew :: Massachusetts General Hospital<br />
# Bernal Rusiel, Jorge Luis :: Boston Children's Hospital<br />
# Bremer, Erich :: Stony Brook University<br />
# Burke, Brice :: American University of Antigua College of Medicine<br />
# Cetin Karayumak, Suheyla :: Brigham and Women's Hospital<br />
# Chae, Michael :: Monash University<br />
# Chauvin, Laurent :: ETS<br />
# Dalca, Adrian :: Massachusetts Institute of Technology<br />
# DiPrima, Tammy :: Stony Brook University<br />
# Drouin, Simon :: Montreal Neurological Institute<br />
# Fan, Zhipeng :: Brigham and Women's Hospital<br />
# Fedorov, Andriy :: Brigham and Women's Hospital<br />
# Fillion-Robin, Jean-Christophe :: Kitware, Inc.<br />
# Fishbaugh, James :: New York University<br />
# Frank, Tobias :: Leibniz Universität Hannover<br />
# Frisken, Sarah :: Brigham and Women's Hospital<br />
# García Mato, David :: Queen´s University / Universidad Carlos III de Madrid<br />
# Ghafoorian, Mohsen :: Brigham and Women's Hospital<br />
# Ghosh, Satrajit :: Massachusetts Institute of Technology<br />
# Girault, Alexis :: Kitware, Inc.<br />
# Golland, Polina :: Massachusetts Institute of Technology<br />
# Gollub, Randy :: Massachusetts General Hospital<br />
# Goncalves, Mathias :: Massachusetts Institute of Technology<br />
# Gong, Shun :: Brigham and Women's Hospital<br />
# Guerrier de Dumast, Priscille :: University of Michigan<br />
# Halle, Michael :: Brigham and Women's Hospital<br />
# Harris, Gordon :: Massachusetts General Hospital<br />
# Helba, Brian :: Kitware, Inc.<br />
# Herz, Christian :: Brigham and Women's Hospital<br />
# Hong, Sungmin :: New York University<br />
# Hosny, Ahmed :: Dana-Farber<br />
# Jagadeesan, Jayender :: Brigham and Women's Hospital<br />
# Jarecka, Dorota :: Massachusetts Institute of Technology<br />
# Jensen, Henrik G. :: University of Copenhagen<br />
# Kaczmarzyk, Jakub :: Massachusetts Institute of Technology<br />
# Kapur, Tina :: Brigham and Women's Hospital<br />
# Kennedy, David :: UMass Medical School<br />
# Kikinis, Ron :: Brigham and Women's Hospital<br />
# Lasso, Andras :: PerkLab, Queen's University<br />
# Lauer, Rebekka :: Humboldt University Berlin<br />
# Lisle, Curtis :: KnowledgeVis, LLC<br />
# Mastrogiacomo, Katie :: Brigham and Women's Hospital<br />
# Mateus, D. :: TUM<br />
# Mehrtash, Alireza :: Brigham and Women's Hospital<br />
# Meine, Hans :: University of Bremen<br />
# Meyer, Anneke :: University of Magdeburg<br />
# Miller, James :: GE Research<br />
# Mirabel, Clement :: University of Michigan<br />
# Nitsch, Jennifer :: University of Bremen<br />
# Norton, Isaiah :: Brigham and Women's Hospital<br />
# O'Donnell, Lauren :: Brigham and Women's Hospital<br />
# Oram, Louise :: The Intervention Centre-Oslo University Hospital<br />
# Padhy, Smruti :: Massachusetts Institute of Technology<br />
# Paniagua, Beatriz :: Kitware, Inc.<br />
# Parmar, Chintan :: DFCI-Harvard Medical School<br />
# Peled, Sharon :: Brigham and Women's Hospital<br />
# Pieper, Steve :: Isomics, Inc.<br />
# Pinter, Csaba :: Queen's University<br />
# Preiswerk, Frank :: Brigham and Women's Hospital/Harvard Medical School<br />
# Prieto, Juan :: NIRAL<br />
# Pujol, Sonia :: Brigham and Women's Hospital/Harvard Medical School<br />
# Rankin, Adam :: Robarts Research Institute<br />
# Rheault, Francois :: Université de Sherbrooke<br />
# Roethe, Anna :: Humboldt University / Charité University Hospital Berlin<br />
# Szczepankiewicz, Filip :: Lund University<br />
# Sharp, Gregory :: Massachusetts General Hospital<br />
# Sridharan, Patmaa :: University of Pennsylvania-CBICA<br />
# Szasz, Teodora :: University of Chicago<br />
# Unadkat, Prashin :: Brigham and Women's Hospital<br />
# Van Griethuysen , Joost :: Netherlands Cancer Institute<br />
# Vidyaratne, Lasitha :: Old Dominion University<br />
# Wang, Yaofei :: Brigham and Women's Hospital<br />
# Wang, Ziyang :: Brigham and Women's Hospital<br />
# Wei, Dawei :: Brigham and Women's Hospital<br />
# Westin, Carl-Fredrik :: Brigham and Women's Hospital, Harvard Medical School<br />
# Xu, Wanxin :: Brigham and Women's Hospital<br />
# Yang, Yixin :: Brigham and Women's Hospital<br />
# Ye, Wu :: Brigham and Women's Hospital<br />
# Zaffino, Paolo :: Magna Graecia University of Catanzaro, Italy<br />
# Zeleznik, Roman :: DFCI<br />
# Zhang, Fan :: Brigham and Women's Hospital<br />
# Zhang, Miaomiao :: Massachusetts Institute of Technology<br />
# Zhang, Yuqian :: Brigham and Women's Hospital<br />
# Zhou, Haoyin :: Brigham and Women's Hospital<br />
# Ziegler, Erik :: Open Health Imaging Foundation/Mass General Hospital</div>Pinterhttps://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/Dinner&diff=943952017 Winter Project Week/Dinner2017-01-06T17:44:14Z<p>Pinter: /* RSVPs */</p>
<hr />
<div>==Dinner Specs==<br />
<br />
*Date and Time: Thursday, January 12, 6pm<br />
*Location: Desi Dhaba, 401 Massachusetts Ave, Cambridge (about 10 minute walk from MIT)<br />
*Food: Indian. (Veg and non-veg options, naan, rice)<br />
*Cost: (TBD, last year was $25)<br />
*Drinks: tap water is included in this price. Beyond that each person pays individually for their drinks.<br />
<br />
==RSVPs==<br />
<br />
#Curt Lisle<br />
#Tina Kapur<br />
# Andrey Fedorov<br />
# Csaba Pinter</div>Pinterhttps://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week&diff=943622017 Winter Project Week2017-01-05T20:06:38Z<p>Pinter: </p>
<hr />
<div>__NOTOC__<br />
[[image:PW-Winter2017.png|300px]]<br />
<br />
=Welcome to the web page for the 24th Project Week!=<br />
<br />
The 24th NA-MIC Project Week open source hackathon is being held during the week of January 9-13, 2017 at MIT. Please go through this page for information, and if you have questions, please contact [https://www.spl.harvard.edu/pages/People/tkapur Tina Kapur, PhD].<br />
<br />
==Logistics==<br />
<br />
*'''Dates:''' January 9-13, 2017.<br />
*'''Location:''' [https://www.google.com/maps/place/MIT:+Computer+Science+and+Artificial+Intelligence+Laboratory/@42.361864,-71.090563,16z/data=!4m2!3m1!1s0x0:0x303ada1e9664dfed?hl=en MIT CSAIL], Cambridge, MA. (Rooms: [[MIT_Project_Week_Rooms#Kiva|Kiva]], R&D)<br />
*'''Transportation:''' Public transportation is highly encouraged, as no parking permits will be issued by MIT. For a list of local garages, please see [[http://web.mit.edu/facilities/transportation/parking/visitors/public_parking.html here]]<br />
*'''REGISTRATION:''' Register [https://www.regonline.com/2017projectweek here]. Registration Fee: $330.<br />
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.<br />
*'''Next Project Week:'''' [http://wiki.na-mic.org/Wiki/index.php/2017_Summer_Project_Week June 26-30, 2017, Catanzaro, Italy]<br />
<br />
== Introduction ==<br />
The National Alliance for Medical Image Computing (NAMIC), was founded in 2005 and chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], enhancements to the underlying building blocks [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an open source hackathon event called Project Week.<br />
<br />
[[Engineering:Programming_Events|Project Week]] is a semi-annual open source hackathon which draws 60-120 researchers. As of August 2014, it is a [http://www.miccai.org/organization MICCAI] endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event. <br />
<br />
Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.<br />
<br />
Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO]. <br />
<br />
A summary of all previous Project Events is available [[Project_Events#Past_Project_Weeks|here]].<br />
<br />
Please make sure that you are on the NA-MIC Project Week [http://public.kitware.com/mailman/listinfo/na-mic-project-week mailing list]<br />
<br />
==Conference Calls for Preparation==<br />
<br />
Conference call phone number and notes are available [[TCONS:2017_Winter_Project_Week|here]].<br />
<br />
==Calendar==<br />
<br />
'''''<font color="maroon">The events are listed in the calendar below. Note that due to a current known limitation of our infrastructure, you will need to manually navigate to the week of January 8, 2017 to see the relevant events.</font>'''''<br><br />
<br />
<br />
{{#widget:Google Calendar<br />
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com<br />
|timezone=America/New_York&dates=20170108%2F20170114<br />
|title=NAMIC Winter Project Week<br />
|view=WEEK<br />
|dates=20170108/20170114<br />
}}<br />
<br />
iCal (.ics) link: https://calendar.google.com/calendar/ical/kitware.com_sb07i171olac9aavh46ir495c4%40group.calendar.google.com/public/basic.ics<br />
<br />
='''Projects'''=<br />
<br />
*Use this [[2017_Project_Week_Template | Updated Template for project pages]]<br />
<br />
== Learning and GPUs ==<br />
<br />
* [[2017 Winter Project Week/Needle Segmentation from MRI | Needle Segmentation from MRI]] (Ziyang Wang, Guillaume Pernelle, Paolo Zaffino, Tina Kapur)<br />
* [[2017 Winter Project Week/OCM-MRI | Deep Learning for Synthetic MRI]] (Frank Preiswerk, Yaofei "Ada" Wang)<br />
* [[2017 Winter Project Week/An open-source tool to classify TMJ OA condyles | An open-source tool to classify TMJ OA condyles]] (Priscille de Dumast, Juan Carlos Prieto, Beatriz Paniagua)<br />
* [[2017 Winter Project Week/DeepInfer| DeepInfer: Open-source Deep Learning Deployment Toolkit]] (Alireza Mehrtash, Mehran Pesteie, Yang (Silvia) Yixin, Tina Kapur, Sandy Wells, Purang Abolmaesumi, Andriy Fedorov)<br />
<br />
== Web Technologies ==<br />
* [[2017_Winter_Project_Week/WebTechnologyAndSlicer| Web Technology and Slicer]] (Steve Pieper, Erik Zeigler, Curt Lisle, Satra Ghosh, Hans Meine)<br />
* [[2017 Winter Project Week/Slicer Qt5 and Python3 | Slicer Qt5 and Python3]] (Steve Pieper, Jean-Christophe Fillion-Robin, Andras Lasso, Andrey Fedorov)<br />
* [[2017_Winter_Project_Week/OAuth2SlicerPathology | OAuth2.0 authentication in SlicerPathology]] (Erich Bremer, Steve Pieper)<br />
* [[Explore integration of Web-based imaging workflows with Slicer | Explore integration of Web-based imaging workflows with Slicer ]] (Curt Lisle, Satra Gosh, Steve Peiper)<br />
* [[2017 Winter Project Week/IPFS_NoSQL_Combination | IPFS and NoSQL for cloud databases]] (Hans Meine, Steve Pieper)<br />
* [[2017 Winter Project Week/Web-based system to federate biological, clinical and morphological data | Web-based system to federate biological, clinical and morphological data]] (Juan Carlos Prieto, Clément Mirabel)<br />
*[[2017 Winter Project Week/Electron App to add, navigate and visualize DICOM images | Electron App to add, navigate and visualize DICOM images<br />
]] (Smruti Padhy, Satrajit Ghosh, Mathias Goncalves)<br />
<br />
== IGT: Navigation, Robotics, Surgical Planning ==<br />
* [[2017 Winter Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization III: The Refining]] (Andras Lasso, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Janne Beate Bakeng)<br />
* [[2017 Winter Project Week/ROS Surface Scan | ROS Surface Scan]] (Tobias Frank, Junichi Tokuda, Longquan Chen)<br />
* [[2017 Winter Project Week/Open_Source_Electromagnetic_Trackers | Open Source Electromagnetic Trackers]] (Peter Traneus Anderson)<br />
* [[2017 Winter Project Week/OpenIGTLink for the Communications of Robotics Devices: Adding Kuka LWR connection to MeVisLab | OpenIGTLink for the Communications of Robotics Devices: Adding Kuka LWR connection to MeVisLab ]] (Scheherazade Kraß (Shery), Junichi Tokuda, Longquan Chen, )<br />
* [[2017 Winter Project Week/LiverResectionPlanning | Liver resection planning extension]] (Louise Oram, Andrey Fedorov, Christian Herz, Andras Lasso)<br />
* [[2017 Winter Project Week/ProstateSectorSegmentation | Prostate Gland Sector Segmentation]] (Anneke Meyer, Andrey Fedorov)<br />
* [[2017 Winter Project Week/Multi-ModalitySegmentationOfUSandMRImagesForGliomaSurgery | Multi-Modality Segmentation of US- and MR-Images for Glioma Surgery]] (Jennifer Nitsch)<br />
* [[2017 Winter Project Week/MeningiomaSegmentation | Segmentation of meningiomas in structural MR images]] (Satrajit Ghosh, Omar Arnaout)<br />
<br />
==dMRI==<br />
* [[2017 Winter Project Week/WhiteMatterAnalysis | WhiteMatterAnalysis New Module and Documentation]] (Fan Zhang, Shun Gong, Isaiah Norton, Ye Wu, Lauren J. O'Donnell)<br />
* [[2017 Winter Project Week/LORDWI | Density-based DMRI registration ]] (Henrik Groenholt Jensen, Lauren J. O'Donnell, Tina Kapur, Fan Zhang, Carl-Frederik Westin)<br />
* [[2017 Winter Project Week/SlicerDMRIDocumentationAndTesting | SlicerDMRI Testing and Documentation]] (Isaiah Norton, Fan Zhang, Shun Gong, Ye Wu, Lauren J. O'Donnell)<br />
* [[2017 Winter Project Week/DiPy_in_Slicer | DiPy integration in Slicer]] (Isaiah Norton, Lauren J. O'Donnell)<br />
* [[2017 Winter Project Week/DWI_Similarity_Metrics | Identification of information-rich patches in Diffusion-Weighted Images]] (Laurent Chauvin, Fan Zhang, Lauren J. O'Donnell, Matthew Toews)<br />
<br />
==Quantitative Imaging Informatics==<br />
* [[2017 Winter Project Week/dcmqi | dcmqi library and DICOM QuantitativeReporting]] (Andrey Fedorov, Christian Herz, JC, Steve Pieper)<br />
* [[2017 Winter Project Week/PyRadiomics | PyRadiomics library ]] (Joost van Griethuysen, Hugo Aerts, Andrey Fedorov, Steve Pieper, Jean-Christope Fillion-Robin)<br />
<br />
== Visualization ==<br />
* [[2017 Winter Project Week/Slicer_HoloLens | Slicer & HoloLens]] (Adam Rankin, Andras Lasso)<br />
== Infrastructure ==<br />
* [[2017 Winter Project Week/SubjectHierarchyRefactoring | Subject hierarchy single-node refactoring]] (Csaba Pinter)<br />
* [[2017 Winter Project Week/SlicerGeometryModifier | Slicer support for interactive modification of 3D models ]] (Johan Andruejol, Beatriz Paniagua, Andras Lasso)<br />
* [[2017 Winter Project Week/PkModeling | PkModeling - DCE Modeling Accuracy and UI/UX Update]] (Andrew Beers)<br />
* [[2017 Winter Project Week/SegWithSubtractionAndModel| Manual Segmentation Module w/ Subtraction Maps + Delaunay Models]] (Andrew Beers)<br />
* [[2017 Winter Project Week/UpdatingCommunityForums | Updating Community Forums (Discourse, GitHub, Gitter, ???)]] (Andrey Fedorov, Andras Lasso, Steve Pieper, Mike Halle, Isaiah Norton, and The Community)<br />
<br />
==To be Categorized==<br />
<br />
* [[2017 Winter Project Week/Support_for_volumetric_meshes | Support for volumetric meshes ]] (Alexis Girault, Curtis Lisle, Steve Piper)<br />
* [[2017 Winter Project Week/Improve_Matlab_integration | Improve Matlab integration ]] (Alexis Girault, Andras Lasso)<br />
* [[2017 Winter Project Week/HyperspectralOpht | Slicer for Hyperspectral Ophthalmology Analysis ]] (Sungmin Hong)<br />
* [[2017 Winter Project Week/SlicerShape | Slicer for Shape Analysis ]] (Beatriz Paniagua)<br />
* [[2017 Winter Project Week/MandibularRegression | Mandibular Shape Regression ]] (Beatriz Paniagua, James Fishbaugh)<br />
* [[2017 Winter Project Week/Plastimatch19 | Upgrade Plastimatch extension ]] (Greg Sharp)<br />
* [[2017 Winter Project Week/2017TutorialContest| Tutorial contest]] (Sonia Pujol)<br />
<br />
= '''Registrants''' =<br />
<br />
Do not add your name to this list - it is maintained by the organizers based on your paid registration. To register, visit this [https://www.regonline.com/2017projectweek registration site].<br />
<br />
# A, Zeina :: SHBOUL<br />
# Aerts, Hugo :: DFCI-Harvard<br />
# Alam, Mahbubul :: Old Dominion University<br />
# Anderson, Peter :: Retired<br />
# Andruejol, Johan :: Kitware, Inc.<br />
# Bakeng, Janne Beate :: SINTEF<br />
# Beers, Andrew :: Massachusetts General Hospital<br />
# Bernal Rusiel, Jorge Luis :: Boston Children's Hospital<br />
# Bremer, Erich :: Stony Brook University<br />
# Burke, Brice :: American University of Antigua College of Medicine<br />
# Cetin Karayumak, Suheyla :: Brigham and Women's Hospital<br />
# Chae, Michael :: Monash University<br />
# Chauvin, Laurent :: ETS<br />
# Dalca, Adrian :: Massachusetts Institute of Technology<br />
# Fedorov, Andriy :: Brigham and Women's Hospital<br />
# Fillion-Robin, Jean-Christophe :: Kitware, Inc.<br />
# Fishbaugh, James :: New York University<br />
# Frank, Tobias :: Leibniz Universität Hannover<br />
# García Mato, David :: Queen´s University / Universidad Carlos III de Madrid<br />
# Girault, Alexis :: Kitware, Inc.<br />
# Golland, Polina :: Massachusetts Institute of Technology<br />
# Gollub, Randy :: Massachusetts General Hospital<br />
# Gong, Shun :: Brigham and Women's Hospital<br />
# Guerrier de Dumast, Priscille :: University of Michigan<br />
# Harris, Gordon :: Massachusetts General Hospital<br />
# Herz, Christian :: Brigham and Women's Hospital<br />
# Hong, Sungmin :: New York University<br />
# Hosny, Ahmed :: Dana-Farber<br />
# Jagadeesan, Jayender :: Brigham and Women's Hospital<br />
# Jensen, Henrik G. :: University of Copenhagen<br />
# Kapur, Tina :: Brigham and Women's Hospital<br />
# Kikinis, Ron :: Brigham and Women's Hospital<br />
# Lasso, Andras :: PerkLab, Queen's University<br />
# Lauer, Rebekka :: Humboldt University Berlin<br />
# Lisle, Curtis :: KnowledgeVis, LLC<br />
# Mastrogiacomo, Katie :: Brigham and Women's Hospital<br />
# Mateus, D. :: TUM<br />
# Mehrtash, Alireza :: Brigham and Women's Hospital<br />
# Meine, Hans :: University of Bremen<br />
# Meyer, Anneke :: University of Magdeburg<br />
# Miller, James :: GE Research<br />
# Mirabel, Clement :: University of Michigan<br />
# Nitsch, Jennifer :: University of Bremen<br />
# Norton, Isaiah :: Brigham and Women's Hospital<br />
# O'Donnell, Lauren :: Brigham and Women's Hospital<br />
# Oram, Louise :: The Intervention Centre-Oslo University Hospital<br />
# Paniagua, Beatriz :: Kitware, Inc.<br />
# Parmar, Chintan :: DFCI-Harvard Medical School<br />
# Peled, Sharon :: Brigham and Women's Hospital<br />
# Pieper, Steve :: Isomics, Inc.<br />
# Pinter, Csaba :: Queen's University<br />
# Preiswerk, Frank :: Brigham and Women's Hospital/Harvard Medical School<br />
# Pujol, Sonia :: Brigham and Women's Hospital/Harvard Medical School<br />
# Rankin, Adam :: Robarts Research Institute<br />
# Rheault, Francois :: Université de Sherbrooke<br />
# Roethe, Anna :: Humboldt University / Charité University Hospital Berlin<br />
# Sharp, Gregory :: Massachusetts General Hospital<br />
# Sridharan, Patmaa :: University of Pennsylvania-CBICA<br />
# Vidyaratne, Lasitha :: Old Dominion University<br />
# Wang, Yaofei :: Brigham and Women's Hospital<br />
# Westin, Carl-Fredrik :: Brigham and Women's Hospital, Harvard Medical School<br />
# Yang, Yixin :: Brigham and Women's Hospital<br />
# Ye, Wu :: Brigham and Women's Hospital<br />
# Zaffino, Paolo :: Magna Graecia University of Catanzaro, Italy<br />
# Zeleznik, Roman :: DFCI<br />
# Zhang, Fan :: Brigham and Women's Hospital<br />
# Zhang, Miaomiao :: Massachusetts Institute of Technology<br />
# Zhang, Yuqian :: Brigham and Women's Hospital<br />
# Ziegler, Erik :: Open Health Imaging Foundation/Mass General Hospital</div>Pinterhttps://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/SubjectHierarchyRefactoring&diff=941502017 Winter Project Week/SubjectHierarchyRefactoring2017-01-02T18:59:51Z<p>Pinter: /* Project Description */</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]<br />
<!-- Use the "Upload file" link on the left and then add a line to this list like "File:MyAlgorithmScreenshot.png" --><br />
</gallery><br />
<br />
==Key Investigators==<br />
* Csaba Pinter (Queen's)<br />
* ? (JC, Steve, Andras)<br />
<br />
==Project Description==<br />
{| class="wikitable"<br />
! style="text-align: left; width:27%" | Objective<br />
! style="text-align: left; width:27%" | Approach and Plan<br />
! style="text-align: left; width:27%" | Progress and Next Steps<br />
|- style="vertical-align:top;"<br />
|<br />
<!-- Objective bullet points --><br />
Although the subject hierarchy mechanism is in place and is already used, there are several issues and limitations that cannot be addressed in its current form:<br />
* Subject hierarchy needs to be disabled by default, because<br />
** A second node is created for each data node and the scene can grow very large in case of many data nodes<br />
** Model hierarchies and subject hierarchies are not fully compatible, so problems may arise in case of complex model hierarchies (such as atlases)<br />
** Because of this, a popup is shown to the user, which is confusing for users. It prevents some from using SH, and is annoying for the others<br />
* Expanded state is reset to all extended when switching to another module and back. This can be very frustrating when there are many subjects or folders, because the user sees it very differently after returning to SH<br />
* Manual re-ordering of nodes is not possible<br />
* Node selector based on subject hierarchy (e.g. where it's possible to start selecting by patient in some way) cannot be implemented without major changes<br />
These issues are due to<br />
* The overly complex Qt MRML scene model infrastructure, which is rigid in some ways, and bloated in others<br />
** Can only show nodes, so if an item is needed to be shown, a new node needs to be created (thus the lot of SH nodes and the virtual branches, see below). Also pointer tracking of nodes complicates things.<br />
** Index calculation is very complex and gets even more complex in the sub classes.<br />
** The features that are needed for specific models but are implemented in the base model overcomplicate the implementation (e.g. pre- and post items)<br />
* Unstable workarounds implemented in the current subject hierarchy infrastructure to accommodate certain use cases<br />
** Nested associations that use the MRML hierarchy associations in a nested way so that the same nodes can be added both to model and subject hierarchies<br />
** Virtual branches to accommodate data that do not correspond to MRML nodes one-on-one (segments contained by segmentations, fiducials contained by markups)<br />
** Postfixes of the SH nodes to differentiate them from the associated data nodes<br />
This necessitates a re-design of the subject hierarchy mechanism. The proposed solution is to store the whole subject hierarchy tree in one node, the internals of which are synchronized with the data nodes of the scene. A new Qt item model needs to be implemented for this node that supplies the information to the tree view and the future node selectors.<br />
|<br />
<!-- Approach and Plan bullet points --><br />
* Store the whole tree in one vtkMRMLSubjectHierarchy node<br />
** Items have unique identifier numbers that is strictly incremental<br />
** Item information can be accessed using accessors, the item class itself is private<br />
* Automatically populate from added nodes (as before), observe modified and removed events<br />
* Implement new Qt item model that is synchronized with the subject hierarchy node instead of the scene<br />
* Import model hierarchies to SH node on entering SH module if new detected (thus model hierarchies can be fully used from <br />
* Subject hierarchy logic makes sure there is only one SH node and it is valid (at import, deletion, potential undo, etc.)<br />
|<br />
<!-- Progress and Next steps bullet points (fill out at the end of project week) --><br />
*<br />
|}<br />
<br />
==Background and References==<br />
<!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --></div>Pinterhttps://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/SubjectHierarchyRefactoring&diff=941492017 Winter Project Week/SubjectHierarchyRefactoring2017-01-02T18:58:44Z<p>Pinter: </p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]<br />
<!-- Use the "Upload file" link on the left and then add a line to this list like "File:MyAlgorithmScreenshot.png" --><br />
</gallery><br />
<br />
==Key Investigators==<br />
* Csaba Pinter (Queen's)<br />
* ? (JC, Steve, Andras)<br />
<br />
==Project Description==<br />
{| class="wikitable"<br />
! style="text-align: left; width:27%" | Objective<br />
! style="text-align: left; width:27%" | Approach and Plan<br />
! style="text-align: left; width:27%" | Progress and Next Steps<br />
|- style="vertical-align:top;"<br />
|<br />
<!-- Objective bullet points --><br />
Although the subject hierarchy mechanism is in place and is already used, there are several issues and limitations that cannot be addressed in its current form:<br />
* Subject hierarchy needs to be disabled by default, because<br />
** A second node is created for each data node and the scene can grow very large in case of many data nodes<br />
** Model hierarchies and subject hierarchies are not fully compatible, so problems may arise in case of complex model hierarchies (such as atlases)<br />
** Because of this, a popup is shown to the user, which is confusing for users. It prevents some from using SH, and is annoying for the others<br />
* Expanded state is reset to all extended when switching to another module and back. This can be very frustrating when there are many subjects or folders, because the user sees it very differently after returning to SH<br />
* Manual re-ordering of nodes is not possible<br />
* Node selector based on subject hierarchy (e.g. where it's possible to start selecting by patient in some way) cannot be implemented without major changes<br />
These issues are due to<br />
* The overly complex Qt MRML scene model infrastructure, which is rigid in some ways, and bloated in others<br />
** Can only show nodes, so if an item is needed to be shown, a new node needs to be created (thus the lot of SH nodes and the virtual branches, see below). Also pointer tracking of nodes complicates things.<br />
** Index calculation is very complex and gets even more complex in the sub classes.<br />
** The features that are needed for specific models but are implemented in the base model overcomplicate the implementation (e.g. pre- and post items)<br />
* Unstable workarounds implemented in the current subject hierarchy infrastructure to accommodate certain use cases<br />
** Nested associations that use the MRML hierarchy associations in a nested way so that the same nodes can be added both to model and subject hierarchies<br />
** Virtual branches to accommodate data that do not correspond to MRML nodes one-on-one (segments contained by segmentations, fiducials contained by markups)<br />
** Postfixes of the SH nodes to differentiate them from the associated data nodes<br />
This necessitates a re-design of the subject hierarchy mechanism. The proposed solution is to store the whole subject hierarchy tree in one node, the internals of which are synchronized with the data nodes of the scene. A new Qt item model needs to be implemented for this node that supplies the information to the tree view and the future node selectors to show the information.<br />
|<br />
<!-- Approach and Plan bullet points --><br />
* Store the whole tree in one vtkMRMLSubjectHierarchy node<br />
** Items have unique identifier numbers that is strictly incremental<br />
** Item information can be accessed using accessors, the item class itself is private<br />
* Automatically populate from added nodes (as before), observe modified and removed events<br />
* Implement new Qt item model that is synchronized with the subject hierarchy node instead of the scene<br />
* Import model hierarchies to SH node on entering SH module if new detected (thus model hierarchies can be fully used from <br />
* Subject hierarchy logic makes sure there is only one SH node and it is valid (at import, deletion, potential undo, etc.)<br />
|<br />
<!-- Progress and Next steps bullet points (fill out at the end of project week) --><br />
*<br />
|}<br />
<br />
==Background and References==<br />
<!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --></div>Pinterhttps://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week/SubjectHierarchyRefactoring&diff=939622017 Winter Project Week/SubjectHierarchyRefactoring2016-12-12T20:13:52Z<p>Pinter: Created page with "__NOTOC__ <gallery> Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|Projects List <!-- Use the "Upload file" link on the l..."</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Winter2017.png|link=2017_Winter_Project_Week#Projects|[[2017_Winter_Project_Week#Projects|Projects List]]<br />
<!-- Use the "Upload file" link on the left and then add a line to this list like "File:MyAlgorithmScreenshot.png" --><br />
</gallery><br />
<br />
==Key Investigators==<br />
* Csaba Pinter (Queen's)<br />
* ? (JC, Steve, Andras)<br />
<br />
==Project Description==<br />
{| class="wikitable"<br />
! style="text-align: left; width:27%" | Objective<br />
! style="text-align: left; width:27%" | Approach and Plan<br />
! style="text-align: left; width:27%" | Progress and Next Steps<br />
|- style="vertical-align:top;"<br />
|<br />
<!-- Objective bullet points --><br />
Although the subject hierarchy mechanism is in place and is already used, there are several issues and limitations that cannot be addressed in its current form:<br />
* Subject hierarchy needs to be disabled by default, because<br />
** A second node is created for each data node and the scene can grow very large in case of many data nodes<br />
** Model hierarchies and subject hierarchies are not fully compatible, so problems may arise in case of complex model hierarchies (such as atlases)<br />
** Because of this, a popup is shown to the user, which is confusing for users. It prevents some from using SH, and is annoying for the others<br />
* Expanded state is reset to all extended when switching to another module and back. This can be very frustrating when there are many subjects or folders, because the user sees it very differently after returning to SH<br />
* Manual re-ordering of nodes is not possible<br />
* Node selector based on subject hierarchy (e.g. where it's possible to start selecting by patient in some way) cannot be implemented without major changes<br />
These issues are due to<br />
* The extremely complex Qt MRML scene model infrastructure, which is quite rigid in various ways, and has unstable features<br />
* Unstable workarounds implemented in the current subject hierarchy infrastructure to accommodate certain use cases, e.g.<br />
** Nested associations that use the MRML hierarchy associations in a nested way so that the same nodes can be added both to model and subject hierarchies<br />
** Virtual branches to accommodate data that do not correspond to MRML nodes one-on-one (segments contained by segmentations, fiducials contained by markups)<br />
** Postfixes of the SH nodes to differentiate them from the associated data nodes<br />
This necessitates a re-design of the subject hierarchy mechanism. The proposed solution is to store the whole subject hierarchy tree in one node, the internals of which are synchronized with the data nodes of the scene. A new Qt item model needs to be implemented for this node that supplies the information to the tree view and the future node selectors to show the information.<br />
|<br />
<!-- Approach and Plan bullet points --><br />
* Store the whole tree in one vtkMRMLSubjectHierarchy node<br />
** Items have unique identifier numbers that is strictly incremental<br />
** Item information can be accessed using accessors, the item class itself is private<br />
* Automatically populate from added nodes (as before), observe modified and removed events<br />
* Implement new Qt item model that is synchronized with the subject hierarchy node instead of the scene<br />
* Import model hierarchies to SH node on entering SH module if new detected (thus model hierarchies can be fully used from <br />
* Subject hierarchy logic makes sure there is only one SH node and it is valid (at import, deletion, potential undo, etc.)<br />
|<br />
<!-- Progress and Next steps bullet points (fill out at the end of project week) --><br />
*<br />
|}<br />
<br />
==Background and References==<br />
<!-- Use this space for information that may help people better understand your project, like links to papers, source code, or data --></div>Pinterhttps://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week&diff=939612017 Winter Project Week2016-12-12T19:51:50Z<p>Pinter: /* Infrastructure */</p>
<hr />
<div>__NOTOC__<br />
[[image:PW-Winter2017.png|300px]]<br />
<br />
=Welcome to the web page for the 24th Project Week!=<br />
<br />
The 24th NA-MIC Project Week open source hackathon is being held during the week of January 9-13, 2017 at MIT. Please go through this page for information, and if you have questions, please contact [https://www.spl.harvard.edu/pages/People/tkapur Tina Kapur, PhD].<br />
<br />
==Logistics==<br />
<br />
*'''Dates:''' January 9-13, 2017.<br />
*'''Location:''' [https://www.google.com/maps/place/MIT:+Computer+Science+and+Artificial+Intelligence+Laboratory/@42.361864,-71.090563,16z/data=!4m2!3m1!1s0x0:0x303ada1e9664dfed?hl=en MIT CSAIL], Cambridge, MA. (Rooms: [[MIT_Project_Week_Rooms#Kiva|Kiva]], R&D)<br />
*'''REGISTRATION:''' Register [https://www.regonline.com/2017projectweek here]. Registration Fee: $330.<br />
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.<br />
<br />
<br />
== Introduction ==<br />
The National Alliance for Medical Image Computing (NAMIC), was founded in 2005 and chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], enhancements to the underlying building blocks [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an open source hackathon event called Project Week.<br />
<br />
[[Engineering:Programming_Events|Project Week]] is a semi-annual open source hackathon which draws 60-120 researchers. As of August 2014, it is a [http://www.miccai.org/organization MICCAI] endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event. <br />
<br />
Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.<br />
<br />
Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO]. <br />
<br />
A summary of all previous Project Events is available [[Project_Events#Past_Project_Weeks|here]].<br />
<br />
This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.<br />
<br />
Please make sure that you are on the NA-MIC Project Week [http://public.kitware.com/mailman/listinfo/na-mic-project-week mailing list]<br />
<br />
==Conference Calls for Preparation==<br />
<br />
Domestic conference call number: 800-501-8979 <br><br />
Access code: 7327389 <br><br />
<br />
[[media:TollFree.png|International conference call numbers]] <br><br />
Access code: 7327389 <br><br />
<br />
Weekly, Tuesdays 10am, Boston time from November 22nd, 2016 to January 3rd, 2017.<br />
<br />
<br />
===Tcon #4: December 6 ===<br />
*10am Boston time<br />
*Project Discussions with focus on Machine Learning and Web-based software for clinical research/trials<br />
<br />
Participants<br />
* Tina Kapur (MIT) - organizer<br />
* Steve Pieper (Isomics/BWH)<br />
* Beatriz, JC (Kitware) <br />
<br />
===Tcon #3: November 29 ===<br />
*10am Boston time<br />
*Project Discussions with focus on Machine Learning and Web-based software for clinical research/trials<br />
Participants<br />
* Tina Kapur (MIT) - organizer; planning Nvidia webinars. Proposal to use Monday as a schedule for the deep learning workshop before workshop begins. <br />
*Steve Pieper (Isomics/BWH) - NVidia update; met with Abdul at NVidia (Medical applications of deep learning). Positive meeting and Slicer might be a reference platform. NVIdia will host a Monday Afternoon session at Project Week and hold outside webinars for basic deep learning information. Considering two or three days of a few hours each for webinar. Discussion of a prize board awarded for demonstrations that Nvidia could use. <br />
*Patmal (Univ. of Pennsylvania Biomedical Group) Showcase some of their capability: cancer & phenomics toolkit; facilitate integration from their toolkit to/from Slicer; They have a few applications that might be interesting to others during project week - (1) fibre tracking in brain, (2) lung tumor segmentation, (3) density estimation<br />
*Beatriz, Alexis, and JC (Kitware) - Slicer support and 3 other projects (1) customized childrern's medical, (1) Alex submitted volumetric meshing project in Slicer idea to the NA-MIC email list; have a discussion on Meshing; the goal is for Finite Element analsis and light imaging (2), better MATLAB integration (use Python-like interface). (3) Beatrix - shape analysis algorithms to be added to Slicer based on recently-funded grant. <br />
*JC (Kitware) - integration of iPython and Slicer; Tina Suggested also Deep Infer framework to integrate with Slicer<br />
*Louise Oram (Stockholm) - Specialization of Slicer for Liver surgery, possibly using SliceLet approach or other way to tailor the Slicer UI. Currently customizations need to be in the Extension catalog. Also interested in Liver vessel segmentation project and other Liver segmentation tasks. This might complement with MeVIS lab capability focused on liver. Separate modules for liver surgery that might be integrated together later. <br />
*Frank Pricework (BWH) - General GPU programming; experiment with rehosting algorithms has has previously developed to GPU. <br />
*Paolo, Italy - (Summer Project Week Host) <br />
*Naboo (Old Dominion) - two possible projects, not certain yet - (1) smaller training datasets for medical images, (2) braining atlas segmentation integration with Slicer.<br />
*Curt Lisle (KnowledgeVis) - (1) web-based transition of subset of Slicer capability, (2) Iowa Meshing Module move from 3.6 to 4.7 (with Alex from Kitware); (3) possible integration of web-based volume rendering; <br />
*Patmal (Univ. of Pennsylvania Biomedical Group) Showcase some of their capability: cancer & phenomics toolkit; facilitate integration from their toolkit to/from Slicer; They have a few applications that might be interesting to others during project week - (1) fibre tracking in brain, (2) lung tumor segmentation, (3) density estimation<br />
*Eric Seigler - OHIS Cornerstone Lesion Tracker author; Integrating interactive segmentation into the web-based framework<br />
<br />
Discussions<br />
*Training deep learning networks with smaller datasets. <br />
*Integrating of projects with Slicer & architecture will be a discussion topic during the week.<br />
*Everybody, be sure to register on the Wiki for the workshop; come up with a title and short description of the project(s) you will work on.<br />
*OK to send info to the NA-MIC email list<br />
<br />
===Tcon #2: November 22 ===<br />
*10am Boston time<br />
*Topics: continue Deep Learning, Web-based software<br />
*Participants (interests)<br />
# Tina Kapur, BWH (needle detection)<br />
# Steve Pieper, Isomics (web-based software, GPU computing)<br />
#Mahbub, Old Dominion University (creating architectures for deep learning networks in matlab, bridge to Slicer, MICCAI challenge code into Slicer, make learning faster and with less training)<br />
#Siddiqi, Old Dominion <br />
#Nicole Aucoin, BWH<br />
#Abdul, NVIDIA Business Development (potential deep learning tutorials by web conference before the event, then at the event)<br />
#Able Brown, NVIDIA<br />
#JC, Kitware<br />
#Krisztina Fischer, BWH<br />
#Andrew Beard, MGH (deep learning, parameter estimation from MRI)<br />
#Gordon Harris, MGH<br />
#Laurent Chauvin, ETS Montreal (CNN, GPUs)<br />
#John Toeber, Bremen U<br />
#Lauren O'Donnell, BWH<br />
#Fan Zhang, BWH<br />
#Isaiah Norton, BWH<br />
#Wu Ye, BWH<br />
#Erik Siegler, MGH (Slicer / ePad connection with LesionTracker; more web-based technologies; discussion of ePad custom widget that will send out connections to remote jobs., PET/CT Lymphoma workshop as extension to lesion tracker.)<br />
#Pete Anderson (Open source tracker)<br />
#Guillaume Pernelle, Imperial College (CNNs, LSTMs, Deep Learning, GPUs)<br />
#Mike Halle, BWH (slicer cross-platform architecture to work for hardware-specific; proxy running cloud that can support interface, Atlas browser is an active project for web-based interface. Slicer success is primarily application-level tools. The community could benefit with architectural study.)<br />
#Louise, Oslo, Norway (high-speed pipelining of image processing for liver resections. )<br />
#Paolo, Catanzaro, Italy (Multiple GPU system architecture)<br />
#Salvatore, Catanzaro, Italy<br />
#Daniel Rubin, Stanford<br />
#Curt Lisle, Knowledgevis (has image web-based workflow systems; Deeply interested in web transition of imaging technologies. Also interested (but not experienced) in deep learning application; particularly feature recognition; small animal imaging applications)<br />
#Charles Guttman, BWH (has MS data, wants to use Docker-based repository. (Boutique looks like a good repository)<br />
<br />
===Tcon #1: November 15 ===<br />
*10am Boston time<br />
*Emergent interest in the application of Deep Learning techniques to medical image analysis.<br />
<br />
Participants and interests<br />
*#Tina Kapur, BWH -- needle detection<br />
*#Steve Pieper, Isomics - GPUs<br />
*#Andras Lasso, Queens - Slicer expert<br />
*#Frankie Preiswerk, BWH -- hybrid ultrasound and MRI, interested in NVIDIA workshop <br />
*#JC, Kitware -- Slicer expert<br />
*#Mike Halle, BWH -- image feature search using deep learning (w/ Sandy Wells)<br />
*#Peter Neher, DKFZ (filling in for Marco Nolden) -- experience with deep learning with face recognition<br />
*#Nicole Aucoin, BWH -- Slicer expert<br />
*#Alireza Mehrtash, UBC, BWH -- deep learning for prostate interventions, extension server for deep learning for Slicer<br />
*#Daniel Rubin deep learning<br />
*#Krisztina Fischer -- teaching<br />
<br />
==Agenda==<br />
<br />
{|border="1"<br />
|-style="background:#b0d5e6;color:#02186f" <br />
!style="width:10%" |Time<br />
!style="width:18%" |Monday, January 9<br />
!style="width:18%" |Tuesday, January 10<br />
!style="width:18%" |Wednesday, January 11<br />
!style="width:18%" |Thursday, January 12<br />
!style="width:18%" |Friday, January 13<br />
|-<br />
|<br />
|bgcolor="#dbdbdb"|'''Project Presentations''' <br />
|bgcolor="#6494ec"| '''Work on Projects'''<br />
|bgcolor="#6494ec"| '''Work on Projects'''<br />
|bgcolor="#6494ec"| '''Work on Projects'''<br />
|bgcolor="#faedb6"| '''Reporting Day'''<br />
|-<br />
|bgcolor="#ffffdd"|'''8:30am'''<br />
|rowspan="2"|<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast <br />
|-<br />
|bgcolor="#ffffdd"|'''9:00am-10:30am'''<br />
|bgcolor="#88aaae"|Clinical Topics<br />
|bgcolor="#88aaae"|Clinical Topics<br />
|bgcolor="#88aaae"|Clinical Topics<br />
|bgcolor="#88aaae"|Clinical Topics<br />
|-<br />
|bgcolor="#ffffdd"|'''10:30am-12pm:'''<br />
|'''Talk (Sebastian Ourselin, PhD, UCL)'''<br />
|<br />
|<br />
|<br />
|Project Reporting<br />
|-<br />
|bgcolor="#ffffdd"|'''12:00pm-1:00pm'''<br />
|bgcolor="#ffffaa"|Lunch <br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm<br />
|-<br />
|bgcolor="#ffffdd"|'''1:00-5:30pm'''<br />
|'''1:00pm-2:30pm:''' Project Presentations<br />
|<br />
|<br />
|<br />
|'''1:30-2:30pm:''' [[AMIGO_TourPW2017Winter|AMIGO Tour]]<br />
|-<br />
|bgcolor="#ffffdd"|'''5:30pm'''<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day <br> [[2017_Winter_Project_Week/Dinner|Dinner on Thursday Night]] (Optional)<br />
|<br />
|}<br />
<br />
==Calendar==<br />
<br />
'''''<font color="maroon">The events are listed in the calendar below. Note that due to a current known limitation of our infrastructure, you will need to manually navigate to the week of January 8, 2017 to see the relevant events.</font>'''''<br><br />
<br />
<br />
{{#widget:Google Calendar<br />
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com<br />
|timezone=America/New_York&dates=20170108%2F20170114<br />
|title=NAMIC Winter Project Week<br />
|view=WEEK<br />
|dates=20170108/20170114<br />
}}<br />
<br />
iCal (.ics) link: https://calendar.google.com/calendar/ical/kitware.com_sb07i171olac9aavh46ir495c4%40group.calendar.google.com/public/basic.ics<br />
<br />
='''Projects'''=<br />
<br />
*Use this [[2017_Project_Week_Template | Updated Template for project pages]]<br />
<br />
== Learning and GPUs ==<br />
<br />
== Web Technologies ==<br />
<br />
== Visualization ==<br />
* [[2017 Winter Project Week/Slicer_HoloLens | Slicer & HoloLens]] (Adam Rankin)<br />
<br />
== IGT ==<br />
* [[2017 Winter Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization III: The Refining]] (Andras Lasso, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Janne Beate Bakeng)<br />
* [[2017 Winter Project Week/WhiteMatterAnalysis | WhiteMatterAnalysis New Module and Documentation]] (Fan Zhang, Isaiah Norton, Ye Wu, Lauren J. O'Donnell)<br />
* [[2017 Winter Project Week/ROS Surface Scan | ROS Surface Scan]] (Tobias Frank, Junichi Tokuda, Longquan Chen)<br />
<br />
== Craniofacial == <br />
<br />
<br />
== Infrastructure ==<br />
* [[2017 Winter Project Week/Slicer Qt5 and Python3 | Slicer Qt5 and Python3]] (Steve Pieper, Jean-Christophe Fillion-Robin, Andras Lasso, Andrey Fedorov)<br />
* [[2017 Winter Project Week/SlicerDMRIDocumentationAndTesting | SlicerDMRI Testing and Documentation]] (Isaiah Norton, Fan Zhang, Shun Gong, Ye Wu, Lauren J. O'Donnell)<br />
* [[2017 Winter Project Week/SubjectHierarchyRefactoring | Subject hierarchy refactoring]] (Csaba Pinter)<br />
<br />
== DICOM ==<br />
<br />
= '''Registrants''' =<br />
<br />
Do not add your name to this list - it is maintained by the organizers based on your paid registration. To register, visit this [https://www.regonline.com/2017projectweek registration site].</div>Pinterhttps://www.na-mic.org/w/index.php?title=2017_Winter_Project_Week&diff=939602017 Winter Project Week2016-12-12T19:51:27Z<p>Pinter: Added SH refactoring to projects</p>
<hr />
<div>__NOTOC__<br />
[[image:PW-Winter2017.png|300px]]<br />
<br />
=Welcome to the web page for the 24th Project Week!=<br />
<br />
The 24th NA-MIC Project Week open source hackathon is being held during the week of January 9-13, 2017 at MIT. Please go through this page for information, and if you have questions, please contact [https://www.spl.harvard.edu/pages/People/tkapur Tina Kapur, PhD].<br />
<br />
==Logistics==<br />
<br />
*'''Dates:''' January 9-13, 2017.<br />
*'''Location:''' [https://www.google.com/maps/place/MIT:+Computer+Science+and+Artificial+Intelligence+Laboratory/@42.361864,-71.090563,16z/data=!4m2!3m1!1s0x0:0x303ada1e9664dfed?hl=en MIT CSAIL], Cambridge, MA. (Rooms: [[MIT_Project_Week_Rooms#Kiva|Kiva]], R&D)<br />
*'''REGISTRATION:''' Register [https://www.regonline.com/2017projectweek here]. Registration Fee: $330.<br />
*'''Hotel:''' Similar to previous years, no rooms have been blocked in a particular hotel.<br />
<br />
<br />
== Introduction ==<br />
The National Alliance for Medical Image Computing (NAMIC), was founded in 2005 and chartered with building a computational infrastructure to support biomedical research as part of the NIH funded [http://www.ncbcs.org/ NCBC] program. The work of this alliance has resulted in important progress in algorithmic research, an open source medical image computing platform [http://www.slicer.org 3D Slicer], enhancements to the underlying building blocks [http://www.vtk.org VTK], [http://www.itk.org ITK], [http://www.cmake.org CMake], and [http://www.cdash.org CDash], and the creation of a community of algorithm researchers, biomedical scientists and software engineers who are committed to open science. This community meets twice a year in an open source hackathon event called Project Week.<br />
<br />
[[Engineering:Programming_Events|Project Week]] is a semi-annual open source hackathon which draws 60-120 researchers. As of August 2014, it is a [http://www.miccai.org/organization MICCAI] endorsed event. The participants work collaboratively on open-science solutions for problems that lie on the interfaces of the fields of computer science, mechanical engineering, biomedical engineering, and medicine. In contrast to conventional conferences and workshops the primary focus of the Project Weeks is to make progress in projects (as opposed to reporting about progress). The objective of the Project Weeks is to provide a venue for this community of medical open source software creators. Project Weeks are open to all, are publicly advertised, and are funded through fees paid by the attendees. Participants are encouraged to stay for the entire event. <br />
<br />
Project Week activities: Everyone shows up with a project. Some people are working on the platform. Some people are developing algorithms. Some people are applying the tools to their research problems. We begin the week by introducing projects and connecting teams. We end the week by reporting progress. In addition to the ongoing working sessions, breakout sessions are organized ad-hoc on a variety of special topics. These topics include: discussions of software architecture, presentations of new features and approaches and topics such as Image-Guided Therapy.<br />
<br />
Several funded projects use the Project Week as a place to convene and collaborate. These include [http://nac.spl.harvard.edu/ NAC], [http://www.ncigt.org/ NCIGT], [http://qiicr.org/ QIICR], and [http://ocairo.technainstitute.com/open-source-software-platforms-and-databases-for-the-adaptive-process/ OCAIRO]. <br />
<br />
A summary of all previous Project Events is available [[Project_Events#Past_Project_Weeks|here]].<br />
<br />
This project week is an event [[Post-NCBC-2014|endorsed]] by the MICCAI society.<br />
<br />
Please make sure that you are on the NA-MIC Project Week [http://public.kitware.com/mailman/listinfo/na-mic-project-week mailing list]<br />
<br />
==Conference Calls for Preparation==<br />
<br />
Domestic conference call number: 800-501-8979 <br><br />
Access code: 7327389 <br><br />
<br />
[[media:TollFree.png|International conference call numbers]] <br><br />
Access code: 7327389 <br><br />
<br />
Weekly, Tuesdays 10am, Boston time from November 22nd, 2016 to January 3rd, 2017.<br />
<br />
<br />
===Tcon #4: December 6 ===<br />
*10am Boston time<br />
*Project Discussions with focus on Machine Learning and Web-based software for clinical research/trials<br />
<br />
Participants<br />
* Tina Kapur (MIT) - organizer<br />
* Steve Pieper (Isomics/BWH)<br />
* Beatriz, JC (Kitware) <br />
<br />
===Tcon #3: November 29 ===<br />
*10am Boston time<br />
*Project Discussions with focus on Machine Learning and Web-based software for clinical research/trials<br />
Participants<br />
* Tina Kapur (MIT) - organizer; planning Nvidia webinars. Proposal to use Monday as a schedule for the deep learning workshop before workshop begins. <br />
*Steve Pieper (Isomics/BWH) - NVidia update; met with Abdul at NVidia (Medical applications of deep learning). Positive meeting and Slicer might be a reference platform. NVIdia will host a Monday Afternoon session at Project Week and hold outside webinars for basic deep learning information. Considering two or three days of a few hours each for webinar. Discussion of a prize board awarded for demonstrations that Nvidia could use. <br />
*Patmal (Univ. of Pennsylvania Biomedical Group) Showcase some of their capability: cancer & phenomics toolkit; facilitate integration from their toolkit to/from Slicer; They have a few applications that might be interesting to others during project week - (1) fibre tracking in brain, (2) lung tumor segmentation, (3) density estimation<br />
*Beatriz, Alexis, and JC (Kitware) - Slicer support and 3 other projects (1) customized childrern's medical, (1) Alex submitted volumetric meshing project in Slicer idea to the NA-MIC email list; have a discussion on Meshing; the goal is for Finite Element analsis and light imaging (2), better MATLAB integration (use Python-like interface). (3) Beatrix - shape analysis algorithms to be added to Slicer based on recently-funded grant. <br />
*JC (Kitware) - integration of iPython and Slicer; Tina Suggested also Deep Infer framework to integrate with Slicer<br />
*Louise Oram (Stockholm) - Specialization of Slicer for Liver surgery, possibly using SliceLet approach or other way to tailor the Slicer UI. Currently customizations need to be in the Extension catalog. Also interested in Liver vessel segmentation project and other Liver segmentation tasks. This might complement with MeVIS lab capability focused on liver. Separate modules for liver surgery that might be integrated together later. <br />
*Frank Pricework (BWH) - General GPU programming; experiment with rehosting algorithms has has previously developed to GPU. <br />
*Paolo, Italy - (Summer Project Week Host) <br />
*Naboo (Old Dominion) - two possible projects, not certain yet - (1) smaller training datasets for medical images, (2) braining atlas segmentation integration with Slicer.<br />
*Curt Lisle (KnowledgeVis) - (1) web-based transition of subset of Slicer capability, (2) Iowa Meshing Module move from 3.6 to 4.7 (with Alex from Kitware); (3) possible integration of web-based volume rendering; <br />
*Patmal (Univ. of Pennsylvania Biomedical Group) Showcase some of their capability: cancer & phenomics toolkit; facilitate integration from their toolkit to/from Slicer; They have a few applications that might be interesting to others during project week - (1) fibre tracking in brain, (2) lung tumor segmentation, (3) density estimation<br />
*Eric Seigler - OHIS Cornerstone Lesion Tracker author; Integrating interactive segmentation into the web-based framework<br />
<br />
Discussions<br />
*Training deep learning networks with smaller datasets. <br />
*Integrating of projects with Slicer & architecture will be a discussion topic during the week.<br />
*Everybody, be sure to register on the Wiki for the workshop; come up with a title and short description of the project(s) you will work on.<br />
*OK to send info to the NA-MIC email list<br />
<br />
===Tcon #2: November 22 ===<br />
*10am Boston time<br />
*Topics: continue Deep Learning, Web-based software<br />
*Participants (interests)<br />
# Tina Kapur, BWH (needle detection)<br />
# Steve Pieper, Isomics (web-based software, GPU computing)<br />
#Mahbub, Old Dominion University (creating architectures for deep learning networks in matlab, bridge to Slicer, MICCAI challenge code into Slicer, make learning faster and with less training)<br />
#Siddiqi, Old Dominion <br />
#Nicole Aucoin, BWH<br />
#Abdul, NVIDIA Business Development (potential deep learning tutorials by web conference before the event, then at the event)<br />
#Able Brown, NVIDIA<br />
#JC, Kitware<br />
#Krisztina Fischer, BWH<br />
#Andrew Beard, MGH (deep learning, parameter estimation from MRI)<br />
#Gordon Harris, MGH<br />
#Laurent Chauvin, ETS Montreal (CNN, GPUs)<br />
#John Toeber, Bremen U<br />
#Lauren O'Donnell, BWH<br />
#Fan Zhang, BWH<br />
#Isaiah Norton, BWH<br />
#Wu Ye, BWH<br />
#Erik Siegler, MGH (Slicer / ePad connection with LesionTracker; more web-based technologies; discussion of ePad custom widget that will send out connections to remote jobs., PET/CT Lymphoma workshop as extension to lesion tracker.)<br />
#Pete Anderson (Open source tracker)<br />
#Guillaume Pernelle, Imperial College (CNNs, LSTMs, Deep Learning, GPUs)<br />
#Mike Halle, BWH (slicer cross-platform architecture to work for hardware-specific; proxy running cloud that can support interface, Atlas browser is an active project for web-based interface. Slicer success is primarily application-level tools. The community could benefit with architectural study.)<br />
#Louise, Oslo, Norway (high-speed pipelining of image processing for liver resections. )<br />
#Paolo, Catanzaro, Italy (Multiple GPU system architecture)<br />
#Salvatore, Catanzaro, Italy<br />
#Daniel Rubin, Stanford<br />
#Curt Lisle, Knowledgevis (has image web-based workflow systems; Deeply interested in web transition of imaging technologies. Also interested (but not experienced) in deep learning application; particularly feature recognition; small animal imaging applications)<br />
#Charles Guttman, BWH (has MS data, wants to use Docker-based repository. (Boutique looks like a good repository)<br />
<br />
===Tcon #1: November 15 ===<br />
*10am Boston time<br />
*Emergent interest in the application of Deep Learning techniques to medical image analysis.<br />
<br />
Participants and interests<br />
*#Tina Kapur, BWH -- needle detection<br />
*#Steve Pieper, Isomics - GPUs<br />
*#Andras Lasso, Queens - Slicer expert<br />
*#Frankie Preiswerk, BWH -- hybrid ultrasound and MRI, interested in NVIDIA workshop <br />
*#JC, Kitware -- Slicer expert<br />
*#Mike Halle, BWH -- image feature search using deep learning (w/ Sandy Wells)<br />
*#Peter Neher, DKFZ (filling in for Marco Nolden) -- experience with deep learning with face recognition<br />
*#Nicole Aucoin, BWH -- Slicer expert<br />
*#Alireza Mehrtash, UBC, BWH -- deep learning for prostate interventions, extension server for deep learning for Slicer<br />
*#Daniel Rubin deep learning<br />
*#Krisztina Fischer -- teaching<br />
<br />
==Agenda==<br />
<br />
{|border="1"<br />
|-style="background:#b0d5e6;color:#02186f" <br />
!style="width:10%" |Time<br />
!style="width:18%" |Monday, January 9<br />
!style="width:18%" |Tuesday, January 10<br />
!style="width:18%" |Wednesday, January 11<br />
!style="width:18%" |Thursday, January 12<br />
!style="width:18%" |Friday, January 13<br />
|-<br />
|<br />
|bgcolor="#dbdbdb"|'''Project Presentations''' <br />
|bgcolor="#6494ec"| '''Work on Projects'''<br />
|bgcolor="#6494ec"| '''Work on Projects'''<br />
|bgcolor="#6494ec"| '''Work on Projects'''<br />
|bgcolor="#faedb6"| '''Reporting Day'''<br />
|-<br />
|bgcolor="#ffffdd"|'''8:30am'''<br />
|rowspan="2"|<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast<br />
|bgcolor="#ffffaa"|Breakfast <br />
|-<br />
|bgcolor="#ffffdd"|'''9:00am-10:30am'''<br />
|bgcolor="#88aaae"|Clinical Topics<br />
|bgcolor="#88aaae"|Clinical Topics<br />
|bgcolor="#88aaae"|Clinical Topics<br />
|bgcolor="#88aaae"|Clinical Topics<br />
|-<br />
|bgcolor="#ffffdd"|'''10:30am-12pm:'''<br />
|'''Talk (Sebastian Ourselin, PhD, UCL)'''<br />
|<br />
|<br />
|<br />
|Project Reporting<br />
|-<br />
|bgcolor="#ffffdd"|'''12:00pm-1:00pm'''<br />
|bgcolor="#ffffaa"|Lunch <br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch<br />
|bgcolor="#ffffaa"|Lunch boxes; Adjourn by 1:30pm<br />
|-<br />
|bgcolor="#ffffdd"|'''1:00-5:30pm'''<br />
|'''1:00pm-2:30pm:''' Project Presentations<br />
|<br />
|<br />
|<br />
|'''1:30-2:30pm:''' [[AMIGO_TourPW2017Winter|AMIGO Tour]]<br />
|-<br />
|bgcolor="#ffffdd"|'''5:30pm'''<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day<br />
|bgcolor="#f0e68b"|Adjourn for the day <br> [[2017_Winter_Project_Week/Dinner|Dinner on Thursday Night]] (Optional)<br />
|<br />
|}<br />
<br />
==Calendar==<br />
<br />
'''''<font color="maroon">The events are listed in the calendar below. Note that due to a current known limitation of our infrastructure, you will need to manually navigate to the week of January 8, 2017 to see the relevant events.</font>'''''<br><br />
<br />
<br />
{{#widget:Google Calendar<br />
|id=kitware.com_sb07i171olac9aavh46ir495c4@group.calendar.google.com<br />
|timezone=America/New_York&dates=20170108%2F20170114<br />
|title=NAMIC Winter Project Week<br />
|view=WEEK<br />
|dates=20170108/20170114<br />
}}<br />
<br />
iCal (.ics) link: https://calendar.google.com/calendar/ical/kitware.com_sb07i171olac9aavh46ir495c4%40group.calendar.google.com/public/basic.ics<br />
<br />
='''Projects'''=<br />
<br />
*Use this [[2017_Project_Week_Template | Updated Template for project pages]]<br />
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== Learning and GPUs ==<br />
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== Web Technologies ==<br />
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== Visualization ==<br />
* [[2017 Winter Project Week/Slicer_HoloLens | Slicer & HoloLens]] (Adam Rankin)<br />
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== IGT ==<br />
* [[2017 Winter Project Week/Tracked Ultrasound Standardization | Tracked Ultrasound Standardization III: The Refining]] (Andras Lasso, Simon Drouin, Junichi Tokuda, Longquan Chen, Adam Rankin, Janne Beate Bakeng)<br />
* [[2017 Winter Project Week/WhiteMatterAnalysis | WhiteMatterAnalysis New Module and Documentation]] (Fan Zhang, Isaiah Norton, Ye Wu, Lauren J. O'Donnell)<br />
* [[2017 Winter Project Week/ROS Surface Scan | ROS Surface Scan]] (Tobias Frank, Junichi Tokuda, Longquan Chen)<br />
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== Craniofacial == <br />
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== Infrastructure ==<br />
* [[2017 Winter Project Week/Slicer Qt5 and Python3 | Slicer Qt5 and Python3]] (Steve Pieper, Jean-Christophe Fillion-Robin, Andras Lasso, Andrey Fedorov)<br />
* [[2017 Winter Project Week/SlicerDMRIDocumentationAndTesting | SlicerDMRI Testing and Documentation]] (Isaiah Norton, Fan Zhang, Shun Gong, Ye Wu, Lauren J. O'Donnell)<br />
* [[2017 Winter Project Week/SubjectHierarchyRefactoring | Subject hierarchy refactoring]]<br />
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== DICOM ==<br />
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= '''Registrants''' =<br />
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Do not add your name to this list - it is maintained by the organizers based on your paid registration. To register, visit this [https://www.regonline.com/2017projectweek registration site].</div>Pinterhttps://www.na-mic.org/w/index.php?title=2016_Summer_Project_Week/Segmentations_Integration&diff=934282016 Summer Project Week/Segmentations Integration2016-06-25T08:33:45Z<p>Pinter: Added progress</p>
<hr />
<div>__NOTOC__<br />
<gallery><br />
Image:PW-Summer2016.png|[[2016_Summer_Project_Week#Projects|Projects List]]<br />
Image:SegmentationHighlights01s.png|Highlights of segmentations 1<br />
Image:SegmentationHighlights02s.png|Highlights of segmentations 2<br />
Image:20160526_SegmentationObject.PNG|Segmentation object<br />
Image:20160526_ConversionGraph.PNG|Conversion graph for automated conversions<br />
Image:20160526_SegmentationsArchitecture.png|Segmentations architecture<br />
Image:ContourRepresentations_201507.png|Representations<br />
</gallery><br />
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==Key Investigators==<br />
* Csaba Pinter<br />
* Andras Lasso<br />
* Steve Pieper<br />
* Jean-Christophe Fillion-Robin (to be consulted remotely)<br />
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==Project Description==<br />
<div style="margin: 20px;"><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Objective</h3><br />
* Integration of the Segmentation infrastructure into Slicer core<br />
* The infrastructure contains the following components:<br />
** SegmentationCore: Pure VTK implementation of the segmentation object, oriented VTK image data and utilities, and the automated conversion mechanism<br />
** Segmentation MRML: Segmentation MRML node, display node, storage node, displayable managers<br />
** Segmentations module: Slicer module for handling segmentation nodes, various re-usable widgets, and subject hierarchy plugins<br />
** Segment Editor: Slicer module for editing segmentation nodes directly. Similar to Editor, but has a C++ core, and extended functionality that makes use of the advanced Segmentations features<br />
** Segment Morphology: Slicer module for performing expand/shrink and logical operations (union, intersection, subtraction) on segments. Its logic can be used in Segment Editor effects<br />
** Segment Registration (?): Distance map based registration of segmentations (from SlicerProstate::DistanceMapBasedRegistration, integration TBD)<br />
* [https://www.slicer.org/slicerWiki/index.php/File:20160526_Segmentations.pptx Presentation slides] explaining the motivation, features, and details of the infrastructure<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Approach, Plan</h3><br />
* Move classes into Slicer core<br />
** Convert to Slicer core coding conventions (curly brackets in line with the contained block)<br />
** vtkSegmentationCore -> vtkAddon'''?'''<br />
** Segmentations/MRML -> Libs/MRML/Core<br />
** Segmentations/MRMLDM -> Libs/MRML/DisplayableManager<br />
** Segmentations/Widgets -> MRML/Widgets'''?'''<br />
** Segmentations/EditorEffects -> '''?'''<br />
** Segmentations -> Modules/Loadable<br />
** SegmentEditor -> Modules/Scripted<br />
* Discuss possible integration vtkOrientedImageData to VTK core<br />
</div><br />
<div style="width: 27%; float: left; padding-right: 3%;"><br />
<h3>Progress</h3><br />
* Code moved from SlicerRT to Slicer core<br />
** vtkSegmentationCore to Libs/vtkAddon<br />
** Segmentations module (MRML, MRMLDM, Widgets, EditorEffects, Logic) to Modules/Loadable<br />
** SegmentEditor module to Modules/Scripted<br />
* [https://github.com/Slicer/Slicer/pull/542 Pull request] sent<br />
** Waiting for the CircleCI test to pass, then Jc's and Steve's nod<br />
* Outstanding issues<br />
** One tests fails due to usage of DICOM-RT, need to switch to a scene<br />
** Add subject hierarchy plugin for Segment Editor<br />
** Add disclaimer to Editor that there is an updated version of the module and offer a button that takes the user there<br />
</div><br />
</div></div>Pinter