Difference between revisions of "Events:Computational Methods for Radiation Oncology"

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==Summary==
 +
 +
[[Image:2011_May_UNC_NA-MIC_Radonc_Meeting.jpg|800px]]
 +
 +
25 researchers attended this meeting from UNC, BWH, MGH, Harvard, and U Michigan.  Several collaboration ideas have emerged and have been enumerated below.
  
 
==Date and Location==
 
==Date and Location==
 
Date: Thursday, May 5, 2011
 
Date: Thursday, May 5, 2011
  
−
Location: Shapiro Boardroom, 70 Francis Street, Boston
+
Location: Surgery Education Office, Room CA-034, Carrie Hall, 15 Francis Street.  ([[Media:Directions to CA-034 Carrie Hall 15 Francis Street Boston.doc|Directions]])
  
 +
In addition, the following information is useful for first time visitors to the hospital:
 +
*http://www.brighamandwomens.org/about_bwh/locations/directions/default.aspx
 +
*On the "Pike map" PDF link (bottom of page), the Carrie Hall building is closest to the 15 Francis St entrance -- enter through the columns.
 +
*On Google Street View/Map, the Carrie Hall building is near the label "Howard Hughes Medical Institute".
  
 
==Agenda==
 
==Agenda==
  
−
To brainstorm radonc computational methods between UNC, NA-MIC, BWH.
+
To brainstorm computational methods for radiation oncology between UNC, NA-MIC, BWH.
  
  
 
*8am: Breakfast
 
*8am: Breakfast
 
*8:30-10:30am: UNC -presentations about capabilities of current projects, short term and longer term plans  
 
*8:30-10:30am: UNC -presentations about capabilities of current projects, short term and longer term plans  
−
**Julian Rosenman PLUNC 18 minutes
+
**'''Julian Rosenman''' PLUNC 18 minutes
−
**Gregg Tracton Software for PLUNC, segmentation, registration  10 minutes
+
**'''Gregg Tracton''' Software for PLUNC, segmentation, registration  10 minutes
−
**Stephen Pizer Registration by regression (2 methods), Segmentation via posterior optimization, training probability distributions on s reps and quantile functions, segmentation via correspondence-preserving warps, ant aliasing 23 minutes
+
**'''Stephen Pizer''' Registration by regression (2 methods), Segmentation via posterior optimization, training probability distributions on s reps and quantile functions, segmentation via correspondence-preserving warps, ant aliasing 23 minutes
−
**Sha Chang Nanotube imaging, incl. for IGRT 10 minutes
+
**'''Sha Chang''' Nanotube imaging, incl. for IGRT 10 minutes
−
**Brandon Frederick Iterative tomographic reconstruction, CTs at treatment time, gpu’s 15 minutes
+
**'''Brandon Frederick''' Iterative tomographic reconstruction, CTs at treatment time, gpu’s 15 minutes
−
**Derek Merck 3D visualization via model-guided rendering, 3D visualization in PLUNC for RTP 15 minutes
+
**'''Derek Merck''' 3D visualization via model-guided rendering, 3D visualization in PLUNC for RTP 15 minutes
−
**Ilknur Kabul Texturing of surfaces, onion skins, and cut planes; interpolation of textures 10 minutes
+
**'''Ilknur Kabul''' Texturing of surfaces, onion skins, and cut planes; interpolation of textures 10 minutes
−
**Hina Shah Registration of endoscopic cine and CT of throat,fused displays of these two registered sources 8 minutes
+
**'''Hina Shah''' Registration of endoscopic cine and CT of throat,fused displays of these two registered sources 8 minutes
−
**Ron Alterovitz Planning for brachytherapy with curved needles, FEM software 12 minutes
+
**'''Ron Alterovitz''' Planning for brachytherapy with curved needles, FEM software 12 minutes
 
*10:30 am: Break  
 
*10:30 am: Break  
−
*10:50am-12pm: NA-MIC/Harvard presentations about capabilities of current projects, short term and longer term plans
+
*11:50am-2:30pm NA-MIC/Harvard presentations about capabilities of current projects, short term and longer term plans
−
**Slicer3 to Slicer 4, Radiation Therapy support today, and plans for the next year (Steve Pieper) (20 minutes)
+
**AMIGO (Tina Kapur) (5 minutes)
−
**Head and Neck Cancer NA-MIC DBP (Greg Sharp) (20 minutes)
+
**Slicer3 to Slicer 4, Radiation Therapy support today, and plans for the next year [[media:Pieper-CMRO-2011-05-05.ppt|(slides)]] ('''Steve Pieper''') (30 minutes)
−
**Gynecologic Cancer Brachytherapy Plans (Tina Kapur) (20 minutes)
+
**SPARKit, Canadian grant for providing open source software platform for radiotherapy, potentially based on NA-MIC Kit [[Media:SparKitIntroBostonRadOnc2011.pdf|(slides)]] ('''Andras Lasso''') (10minutes)
−
**Shadie, shading language for volume visualization(Hanspeter Pfister, Milos Hasan, George Chen, John Wolfgang) (20 minutes)
+
**Head and Neck Cancer NA-MIC DBP ([[Media:2011-CMRO-Sharp.pdf|slides]]) ('''Greg Sharp''') (15 minutes)
−
*12pm pm: Lunch
+
**Gynecologic Cancer Brachytherapy Plans ('''Tina Kapur''') (10 minutes)
−
*1pm: Intro of afternoon objectives (Julian Rosenman)  
+
**Shadie, shading language for volume visualization [[media:Shadie-BW-2011.pdf|(slides)]] ('''Hanspeter Pfister, Milos Hasan, George Chen, John Wolfgang''') (20 minutes)
−
*1:10pm: What UNC/Boston system combinations ought to be developed -- the Boston perspective (Tina Kapur)
+
*Continue presentations...
−
*1:30pm: What Boston/UNC system combinations ought to be developed -- the UNC perspective (Steve Pizer)
+
*2:30pm: Intro of afternoon objectives ('''Julian Rosenman''')  
−
*2:00-2:45pm: Comments from Kitware about their capabilities relevant to proposed combinations
+
*2:45pm: What UNC/Boston system combinations ought to be developed -- the Boston perspective ('''Tina Kapur''')
−
*245pm: Break and subgroup formation (e.g., merging surgical and radiation treatment planning system; 3D visualization software for treatment planning; image analysis software for treatment planning)
+
*3pm: What Boston/UNC system combinations ought to be developed -- the UNC perspective ('''Steve Pizer''')
−
*3:00-4pm: Subgroups sketch out mechanics for collaborations
+
*3:30pm: Comments from Kitware about their capabilities relevant to proposed combinations ('''Brad Davis''')
−
*4:00-5:0pm: Summary: what we do next?
+
*4-5pm
−
 
+
** Break and subgroup formation (e.g., merging surgical and radiation treatment planning system; 3D visualization software for treatment planning; image analysis software for treatment planning)
−
'''Agenda items from UNC'''
+
** Subgroups sketch out mechanics for collaborations (http://grants.nih.gov/grants/guide/pa-files/PAR-11-028.html?)
−
 
+
**Summary: what we do next?
−
#PLUNC: An open source complete radiation treatment planning system
 
−
##State of the art, GPU-based dose calculation
 
−
##Fast IMRT engine
 
−
##Image registration of unlimited number of images
 
−
##Manual segmentations in axial, coronal, and sagittal slices
 
−
##User interface via dials and other continuous controls
 
−
##Available on many operating systems and computers
 
−
##Used by ~100 institutions for research
 
−
##iHERO-compatible
 
−
##3D visualization (see item 2)
 
−
#3D visualization in radiation treatment planning
 
−
##Integrated within PLUNC
 
−
##User interface: fully interactive pose and slice control, display entity control
 
−
### Single-GPU-based
 
−
##Methods:
 
−
##MGRview:
 
−
###Combinations of volume rendering, surface rendering, dose painting, beam outlines and views, …
 
−
###Object-coordinate based visualization operations for 3D visualization of multiple entities (objects, beams, dose, etc.) supported by texturing (2D and 3D)
 
−
###Illustration of object shape and position variations across days
 
−
#Image analysis
 
−
##Skeletal model fitting to anatomic objects
 
−
##Skeletal model analysis into eigenmodes of variation and principal variances
 
−
##Segmentation via skeletal models and statistical models of image appearance (Pablo)
 
−
##Atlas to patient diffeomorphism calculation from corresponding reference object boundary points with correspondence maintenance
 
−
##Fluid-flow and control-theoretic greyscale diffeomorphism calculation
 
−
##IGRT from 2D projections to 3D CTs
 
−
###Registration
 
−
###CT reconstructions at treatment time therefrom
 
−
#Utilities: Anti-aliased manual segmentations
 
−
#Applications: Endoscopy/CT fusion in head and neck: registration and visualization (early stages)
 
−
 
 
−
'''Agenda items from NA-MIC'''
 
−
#Works in Progress on RT
 
−
##DICOM RT Support Roadmap and Head and Neck Cancer Application Summary(Greg Sharp)
 
−
##Pelvic Applications Summary (Tina)
 
−
#Slicer Roadmap and its relevance to RT
 
−
 
 
−
'''Agenda items from Harvard, MGH'''
 
  
 
==Participants==
 
==Participants==
  
−
People who indicated availability on May 5th (http://doodle.com/imkmfnshgmwwtw2a):
+
#Julian Rosenman, Radiation Oncology, UNC
 +
#Gregg Tracton, Radiation Physics UNC
 +
#Stephen Pizer, CS and Rad Onc UNC
 +
#Sha Chang, Radiation Physics UNC
 +
#Brandon Frederick, UNC
 +
#Derek Merck, UNC
 +
#Ilknur Kabul UNC
 +
#Hina Shah UNC
 +
#Ron Alterovitz UNC
 +
#Ron Kikinis BWH
 +
#Clare Tempany BWH
 +
#Ferenc Jolesz BWH
 +
#Sandy Wells BWH
 +
#Steve Pieper Isomics
 +
#Andras Lasso Queens
 +
#Greg Sharp MGH
 +
#Tina Kapur BWH
 +
#Hanspeter Pfister Harvard
 +
#George Chen MGH
 +
#Petter Risholm BWH
 +
#Andrey Fedorov BWH
 +
#James Balter U Michigan
 +
#Brad Davis Kitware
 +
#Andinet Enquobahrie Kitware
 +
#Firdaus Janoos BWH
  
−
#Julian Rosenman, UNC
+
==Potential Areas of Collaboration==
−
#Stephen Pizer
 
−
#Derek Merck
 
−
#Hina Shah
 
−
#Brandon Frederick
 
−
#Ilknur Kabul
 
−
#Gregg Tracton
 
−
#Sandy Wells
 
−
#James Balter
 
−
#Hanspeter Pfister
 
−
#Ron Kikinis
 
−
#Clare Tempany
 
−
#John Wolfgang
 
−
#Steve Pieper
 
−
#Andrey Fedorov
 
−
#George Chen
 
−
#Tina Kapur
 
  
−
 
+
#Multimodal registrations from BWH with PLUNC
−
This is the list of invited people:
+
#ITK needs GPU codes
−
 
+
#How to put UNC code into the open source world (from BWH experience)
−
#Steve Pizer, UNC
+
#Visual bookmarks as cf. Slicer (scene views)
−
#Sha Chang, UNC
+
#Tolerance and other surface color washes on textured objects
−
#Dave Lalush, UNC
+
#Endoscopy and 3D MR segmentation: cervix
−
#Ron Alterovitz, UNC
+
#AMIGO w/ endoscopy
−
#Derek Merck, UNC
+
#AMIGO w/ curved needles
−
#Ilknur Kaynar-Kabul, UNC
+
#Curved needles for biopsies
−
#Hina Shah, UNC
+
#Optical CT inclusion
−
#Chen-Rui Chou, UNC
+
#FEM modeling sharings between BWH and UNC
−
#Lei Pan, UNC
+
#Robotics and device tracking sharing: BWH has device tracking expertise: OPENIGT
−
#Brandon Frederick, UNC
+
#Shadie/MGRView or 3D PLUNC or 3D Slicer integration
−
#Clare Tempany, BWH
+
#Adding cmake/software process to PLUNC
−
#Robert Cormack, BWH
+
#Problem: how to integrate object-based coordinate systems into object models and integrate UI controls within those coordinate systems?
−
#Greg Sharp, MGH
+
#MGRView w/ ray-cast volume rendering a la volview/vtk
−
#Andrey Federov, BWH
+
#Inclusion of Ontario ARKit/SparKit? (adaptive RT)
−
#Ron Kikinis, BWH
+
#What can be taken from PLUNC into Slicer right away?
−
#Hans Peter Pfister, Harvard
+
#There needs to be a remodeling of PLUNC licensing to meet the Slicer sharing philosophy
−
#George Chen, MGH
+
#US-to-MR or -CT registration brought to RT
−
#John Wolfgang MGH
+
#Visualize uncertainty by painting over texture (Pfister/UNC)
−
#Milos Hasan MGH alum/Berkeley
+
#Combine Shadie language with MGRView/PLUNC 3Dview capabilities
−
#Tina Kapur, BWH
+
#Image analysis and visualization via Slicer (selected modules in use) into PLUNC into MOSAIQ, etc.
−
#James Balter, Michigan
+
#PLUNC Need: Flexibility/refactor?. Multimodal registration. Including context; annotations
−
#Gabor Fichtinger, Queens
+
#Is there a role for python, numpy?
−
#Terry Yoo, NLM
+
#Note: WashU CERR has a simple dose engine.  Do we integrate that?
−
#Dave Chen, NLM
+
#2d-3d Registration for IGRT using Nanotube Stationary Tomosynthesis  from Siemens, Xinray
−
#James Deye, NCI
+
#Head and Neck Segmentation by registration and refinement
−
#Stephen Aylward, Kitware
+
#Antialiasing algorithm
−
#Steve Pieper, Isomics
+
##How will antialiasing impact DVHs? What is the drift in the dose distribution
 +
##Morphomics Segmentation software for Prostate and Cervix maybe
 +
#James balter collaboration  LA problem
 +
#ITK should have GPU support
 +
#Potential tools from UNC:
 +
##Antialiasing software (potential project week project -- steve pizer, brad davis, petter risholm, andriy fedorov)
 +
##Iterative reconstruction software is shareable
 +
##General GPU tools
 +
##Manual Editing of alignment
 +
##Dose accumulation calculation
 +
#Mechanisms
 +
##Software maintenance R01
 +
##BRP collaborative grant
 +
#Registration of endoscopic images with CT for IGRT: Gyn colposcopy
 +
#Steerable needle planning for gyne brachytherapy
 +
#How to close the loop with feedback for needle insertion and steering for prostate brachy?
 +
#Open FEM standard for RT
 +
#Slicer License for UNC review: http://www.slicer.org/pages/LicenseText
 +
#http://wiki.na-mic.org/Wiki/index.php/2011_Summer_Project_Week

Latest revision as of 16:24, 6 May 2011

Home < Events:Computational Methods for Radiation Oncology
 Back to Events

Summary

2011 May UNC NA-MIC Radonc Meeting.jpg

25 researchers attended this meeting from UNC, BWH, MGH, Harvard, and U Michigan. Several collaboration ideas have emerged and have been enumerated below.

Date and Location

Date: Thursday, May 5, 2011

Location: Surgery Education Office, Room CA-034, Carrie Hall, 15 Francis Street. (Directions)

In addition, the following information is useful for first time visitors to the hospital:

Agenda

To brainstorm computational methods for radiation oncology between UNC, NA-MIC, BWH.


  • 8am: Breakfast
  • 8:30-10:30am: UNC -presentations about capabilities of current projects, short term and longer term plans
    • Julian Rosenman PLUNC 18 minutes
    • Gregg Tracton Software for PLUNC, segmentation, registration 10 minutes
    • Stephen Pizer Registration by regression (2 methods), Segmentation via posterior optimization, training probability distributions on s reps and quantile functions, segmentation via correspondence-preserving warps, ant aliasing 23 minutes
    • Sha Chang Nanotube imaging, incl. for IGRT 10 minutes
    • Brandon Frederick Iterative tomographic reconstruction, CTs at treatment time, gpu’s 15 minutes
    • Derek Merck 3D visualization via model-guided rendering, 3D visualization in PLUNC for RTP 15 minutes
    • Ilknur Kabul Texturing of surfaces, onion skins, and cut planes; interpolation of textures 10 minutes
    • Hina Shah Registration of endoscopic cine and CT of throat,fused displays of these two registered sources 8 minutes
    • Ron Alterovitz Planning for brachytherapy with curved needles, FEM software 12 minutes
  • 10:30 am: Break
  • 11:50am-2:30pm NA-MIC/Harvard presentations about capabilities of current projects, short term and longer term plans
    • AMIGO (Tina Kapur) (5 minutes)
    • Slicer3 to Slicer 4, Radiation Therapy support today, and plans for the next year (slides) (Steve Pieper) (30 minutes)
    • SPARKit, Canadian grant for providing open source software platform for radiotherapy, potentially based on NA-MIC Kit (slides) (Andras Lasso) (10minutes)
    • Head and Neck Cancer NA-MIC DBP (slides) (Greg Sharp) (15 minutes)
    • Gynecologic Cancer Brachytherapy Plans (Tina Kapur) (10 minutes)
    • Shadie, shading language for volume visualization (slides) (Hanspeter Pfister, Milos Hasan, George Chen, John Wolfgang) (20 minutes)
  • Continue presentations...
  • 2:30pm: Intro of afternoon objectives (Julian Rosenman)
  • 2:45pm: What UNC/Boston system combinations ought to be developed -- the Boston perspective (Tina Kapur)
  • 3pm: What Boston/UNC system combinations ought to be developed -- the UNC perspective (Steve Pizer)
  • 3:30pm: Comments from Kitware about their capabilities relevant to proposed combinations (Brad Davis)
  • 4-5pm
    • Break and subgroup formation (e.g., merging surgical and radiation treatment planning system; 3D visualization software for treatment planning; image analysis software for treatment planning)
    • Subgroups sketch out mechanics for collaborations (http://grants.nih.gov/grants/guide/pa-files/PAR-11-028.html?)
    • Summary: what we do next?

Participants

  1. Julian Rosenman, Radiation Oncology, UNC
  2. Gregg Tracton, Radiation Physics UNC
  3. Stephen Pizer, CS and Rad Onc UNC
  4. Sha Chang, Radiation Physics UNC
  5. Brandon Frederick, UNC
  6. Derek Merck, UNC
  7. Ilknur Kabul UNC
  8. Hina Shah UNC
  9. Ron Alterovitz UNC
  10. Ron Kikinis BWH
  11. Clare Tempany BWH
  12. Ferenc Jolesz BWH
  13. Sandy Wells BWH
  14. Steve Pieper Isomics
  15. Andras Lasso Queens
  16. Greg Sharp MGH
  17. Tina Kapur BWH
  18. Hanspeter Pfister Harvard
  19. George Chen MGH
  20. Petter Risholm BWH
  21. Andrey Fedorov BWH
  22. James Balter U Michigan
  23. Brad Davis Kitware
  24. Andinet Enquobahrie Kitware
  25. Firdaus Janoos BWH

Potential Areas of Collaboration

  1. Multimodal registrations from BWH with PLUNC
  2. ITK needs GPU codes
  3. How to put UNC code into the open source world (from BWH experience)
  4. Visual bookmarks as cf. Slicer (scene views)
  5. Tolerance and other surface color washes on textured objects
  6. Endoscopy and 3D MR segmentation: cervix
  7. AMIGO w/ endoscopy
  8. AMIGO w/ curved needles
  9. Curved needles for biopsies
  10. Optical CT inclusion
  11. FEM modeling sharings between BWH and UNC
  12. Robotics and device tracking sharing: BWH has device tracking expertise: OPENIGT
  13. Shadie/MGRView or 3D PLUNC or 3D Slicer integration
  14. Adding cmake/software process to PLUNC
  15. Problem: how to integrate object-based coordinate systems into object models and integrate UI controls within those coordinate systems?
  16. MGRView w/ ray-cast volume rendering a la volview/vtk
  17. Inclusion of Ontario ARKit/SparKit? (adaptive RT)
  18. What can be taken from PLUNC into Slicer right away?
  19. There needs to be a remodeling of PLUNC licensing to meet the Slicer sharing philosophy
  20. US-to-MR or -CT registration brought to RT
  21. Visualize uncertainty by painting over texture (Pfister/UNC)
  22. Combine Shadie language with MGRView/PLUNC 3Dview capabilities
  23. Image analysis and visualization via Slicer (selected modules in use) into PLUNC into MOSAIQ, etc.
  24. PLUNC Need: Flexibility/refactor?. Multimodal registration. Including context; annotations
  25. Is there a role for python, numpy?
  26. Note: WashU CERR has a simple dose engine. Do we integrate that?
  27. 2d-3d Registration for IGRT using Nanotube Stationary Tomosynthesis from Siemens, Xinray
  28. Head and Neck Segmentation by registration and refinement
  29. Antialiasing algorithm
    1. How will antialiasing impact DVHs? What is the drift in the dose distribution
    2. Morphomics Segmentation software for Prostate and Cervix maybe
  30. James balter collaboration LA problem
  31. ITK should have GPU support
  32. Potential tools from UNC:
    1. Antialiasing software (potential project week project -- steve pizer, brad davis, petter risholm, andriy fedorov)
    2. Iterative reconstruction software is shareable
    3. General GPU tools
    4. Manual Editing of alignment
    5. Dose accumulation calculation
  33. Mechanisms
    1. Software maintenance R01
    2. BRP collaborative grant
  34. Registration of endoscopic images with CT for IGRT: Gyn colposcopy
  35. Steerable needle planning for gyne brachytherapy
  36. How to close the loop with feedback for needle insertion and steering for prostate brachy?
  37. Open FEM standard for RT
  38. Slicer License for UNC review: http://www.slicer.org/pages/LicenseText
  39. http://wiki.na-mic.org/Wiki/index.php/2011_Summer_Project_Week
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