TCONS:2017 Winter Project Week

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Domestic conference call number: 800-501-8979
Access code: 7327389

International conference call numbers
Access code: 7327389

Weekly, Tuesdays 10am, Boston time from November 22nd, 2016 to January 3rd, 2017

Tcon #6: January 3 2017

Agenda: tying loose ends

Tcon #5: December 13

  • 10am Boston time
  • Project Discussions with focus on Machine Learning and Web-based software for clinical research/trials


  1. Tina Kapur (BWH) - organizer
  2. Steve Pieper (Isomics/BWH)
  3. JC (Kitware)
  4. Krisztina Fischer (BWH)
  5. Sungmin (NYU, Guido Gerig's group)
  6. Padma Stridharan(Upenn)
  7. Nicole Aucoin

Tcon #4: December 6

  • 10am Boston time
  • Project Discussions with focus on Machine Learning and Web-based software for clinical research/trials


  1. Tina Kapur (BWH) - organizer
  2. Steve Pieper (Isomics/BWH)
  3. JC (Kitware)
  4. Beatriz(Kitware)
  5. James Fishbaugh (NYU, Guido's group) -- longitudinal shape analysis
  6. Andras Lasso (Queens)
  7. Andrey Fedorov (BWH)

Tcon #3: November 29

  • 10am Boston time
  • Project Discussions with focus on Machine Learning and Web-based software for clinical research/trials


  • Tina Kapur (MIT) - organizer; planning Nvidia webinars. Proposal to use Monday as a schedule for the deep learning workshop before workshop begins.
  • 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.
  • Padma (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
  • 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.
  • JC (Kitware) - integration of iPython and Slicer; Tina Suggested also Deep Infer framework to integrate with Slicer
  • 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.
  • Frank Preiswerk (BWH) - General GPU programming; experiment with rehosting algorithms has has previously developed to GPU.
  • Paolo, Italy - (Summer Project Week Host)
  • Mahboob (Old Dominion) - two possible projects, not certain yet - (1) smaller training datasets for medical images, (2) braining atlas segmentation integration with Slicer.
  • 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;
  • Eric Seigler - OHIS Cornerstone Lesion Tracker author; Integrating interactive segmentation into the web-based framework


  • Training deep learning networks with smaller datasets.
  • Integrating of projects with Slicer & architecture will be a discussion topic during the week.
  • 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.
  • OK to send info to the NA-MIC email list

Tcon #2: November 22

  • 10am Boston time
  • Topics: continue Deep Learning, Web-based software
  • Participants (interests)
  1. Tina Kapur, BWH (needle detection)
  2. Steve Pieper, Isomics (web-based software, GPU computing)
  3. 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)
  4. Siddiqi, Old Dominion
  5. Nicole Aucoin, BWH
  6. Abdul, NVIDIA Business Development (potential deep learning tutorials by web conference before the event, then at the event)
  7. Able Brown, NVIDIA
  8. JC, Kitware
  9. Krisztina Fischer, BWH
  10. Andrew Beard, MGH (deep learning, parameter estimation from MRI)
  11. Gordon Harris, MGH
  12. Laurent Chauvin, ETS Montreal (CNN, GPUs)
  13. John Toeber, Bremen U
  14. Lauren O'Donnell, BWH
  15. Fan Zhang, BWH
  16. Isaiah Norton, BWH
  17. Wu Ye, BWH
  18. 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.)
  19. Pete Anderson (Open source tracker)
  20. Guillaume Pernelle, Imperial College (CNNs, LSTMs, Deep Learning, GPUs)
  21. 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.)
  22. Louise, Oslo, Norway (high-speed pipelining of image processing for liver resections. )
  23. Paolo, Catanzaro, Italy (Multiple GPU system architecture)
  24. Salvatore, Catanzaro, Italy
  25. Daniel Rubin, Stanford
  26. 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)
  27. Charles Guttman, BWH (has MS data, wants to use Docker-based repository. (Boutique looks like a good repository)

Tcon #1: November 15

  • 10am Boston time
  • Emergent interest in the application of Deep Learning techniques to medical image analysis.

Participants and interests

    1. Tina Kapur, BWH -- needle detection
    2. Steve Pieper, Isomics - GPUs
    3. Andras Lasso, Queens - Slicer expert
    4. Frankie Preiswerk, BWH -- hybrid ultrasound and MRI, interested in NVIDIA workshop
    5. JC, Kitware -- Slicer expert
    6. Mike Halle, BWH -- image feature search using deep learning (w/ Sandy Wells)
    7. Peter Neher, DKFZ (filling in for Marco Nolden) -- experience with deep learning with face recognition
    8. Nicole Aucoin, BWH -- Slicer expert
    9. Alireza Mehrtash, UBC, BWH -- deep learning for prostate interventions, extension server for deep learning for Slicer
    10. Daniel Rubin deep learning
    11. Krisztina Fischer -- teaching