Events Bi Weekly Hangouts - QIICR/ProjectIssuesAndWiki GitHub Wiki

QIICR hangouts are scheduled every other Thursday on odd-numbered weeks at 10:00 Eastern time

TODO:

  • OLS vs Bioportals
  • transformation of the items that have a concept code into tabular form
  • prostate radiomics study encoding

Discussed:

2016

Oct 13

Attended: Andrey, Jasyashree, Andrew, David, Michael, Steve

Minutes:

  • AMIA submission
  • David saw it, looks ok, we should consider promoting DICOM4QI as the new name for the RSNA activity
  • David SEG viewer usage in the context of RSNA DICOM4QI
  • most likely, Andrey failed in earlier tests because image had to be converted to multiframe first
  • Andrey will try the workflow with multiframe conversion and will follow up with David if there are issues
  • Reporting and Terminology support demo and feedback
  • looks good overall, no specific feedback noted at this time
  • Reconciliation of the Slicer GenericAnatomy terminology https://github.com/QIICR/dcmqi/issues/95
  • David will work on this as part of developing an automated approach for generating this JSON from the standard directly
  • Handling of image slice spacing https://github.com/QIICR/dcmqi/pull/89
  • all in agreement that it makes sense to refuse acceptance of a SEG when neither SliceThickness or SpacingBetweenSlices is present
  • use of units in Slicer: https://github.com/Slicer/Slicer/pull/592#issuecomment-253240575
  • communication of dictionaries
  • abbreviations from category/type/modifier and units meaning to human readable
  • David suggested for now to use manually populated table with meaningful abbreviated tuples, in the future might consider adding to standard
  • for the segmentation category/type, Slicer label in most cases is just lower cased code meaning for the type, prefixed with the left/right modifier
  • David plans to review how laterality modifier is communicated; potentially, the structure of the dictionary can be simplified by specifying whether certain concept is paired or not

Sept 29

Attended: Andrey, Christian, Reinhard, Jayashree, Andrew, Karl

Minutes:

  • no demo of Reporting since David and Steve are away
  • Reinhard - discussion of DICOM encoding for ophtalmology applications - Andrey followed up with Andreas
  • Jayashree - updates on the segmentation workflow development, data sharing plans - Andrey followed up with email about the details

Sept 15

Attended: Andrey, Steve, Reinhard, Jayashree, Michael, Andrew

Minutes:

  • DWI parameters CP update
  • dcmqi update
  • discussion on the design of the revised Reporting module
  • update on running Slicer from Docker

Sept 1

Attended: Steve, Reinhard, David, Andrew, Karl, Andrey

Minutes:

  • follow up on the topics discussed last time
  • Steve will work with Andrew on the docker setup
  • Andrew will document the process in a tutorial
  • issues with QIN-HEADNECK segmentations reported by SFU
  • issue appears to have been introduced in the Reporting module (followup communication from Andrey)
  • dcmtk status updates
  • paramaps in the OFFIS testing branch
  • dcmqi status updates
  • tid1500 conversion documentation sent to Daniel Rubin

Open questions:

  • plans for MGH to release the data

Aug 18

Attended: Andrey, David, Steve, Ron, Reinhard, Jayashree, Andrew, Karl

Agenda:

  • MGH demo
  • dcmqi updates

Action items:

  • tutorial on how to set up VNC based Slicer (Steve and Jayashree)
  • followup demo of the contouring process by Elizabeth

June 9

Attended: Andrey, Steve, David, Jayashree, Karl, Michael, Reinhard, Christian

Agenda

April 14

Attended: Andrey, Steve, Ron, Reinhard, Karl

Minutes

  • Issues related to Slicer development raised by Reinhard
  • it is very limiting to not have notifications when a test breaks (see https://github.com/Kitware/CDash/issues/303)
  • preparation for a release: need to monitor slicer-devel
  • how to reference an extension? documentation wiki page is recommended
  • Steve: CIP use case - would be desirable to encode levelset in addition to the segmentation, distance parametric map?
  • How to save data? Ron: centralized location. Andrey: this works for advanced users, but for workflow-oriented users integrated or transparent save may be more desirable. Steve: syngo workflow - on exit ask the user to discard or save the results.
  • Steve discussed experiments with continuous capture of the scene operations at the level of individual nodes for the CaseHub NAC effort

March 31

Attended: Andrey, Steve, Ron, David, Reinhard, Jayashree, Xiao, Karl

Minutes

  • Raul use case
  • RSNA QIRR abstract
  • PeerJ revision updates
  • RSNA PI-RADS abstract
  • DICOM as a replacement for the Slicer MRML scene
  • new supplement 190 volumetric presentation states appears to be very relevant and capable (only limitation identified on the spot is that surface models cannot be composed with the VR state)
  • consider in conjunction with DICOM Hanging protocols and DICOM Structured display

Action items:

  • Andrey
  • share Raul's use case details with David
  • work on the overall project vision diagram
  • RSNA submission
  • discuss with Michael the reasons why QIICR development in DCMTK is low-prioritized and how this can be remedied
  • David
  • PeerJ revision review
  • Steve
  • review DICOM Supp 190 http://www.dclunie.com/dicom-status/status.html#supplement190
  • follow up on the work David did for converting SRs to CSV
  • Jayashree
  • follow up with Andrey to schedule a meeting to discuss MGH plans and timeline

Feb 4

Attended: Andrey, Steve, Jayashree, Xiao, Reinhard

Minutes

  • MGH
  • working on evaluation of DSC and comparison with NordicIce
  • will work on the outline of the testing/evaluation approach and communicate to Andrey before the next hangout
  • Iowa
  • agreed to apply the conversion tools to the QIN PET challenge; Andrey is working on the next iteration of the tools
  • follow up on Christian email
  • will share video tutorial

Jan 21

Attended: Andrey, Ron, Steve, Jayashree, David, Michael, Xiao, Reinhard

Agenda

  • Updates: RSNA, Project week, site updates
  • Next steps with the PeerJ Preprint
  • Questions to Iowa: reference to Med Phys, upload the video, any issue from Christian?

Minutes

  • QIICR session at the 2016 Project week: http://wiki.na-mic.org/Wiki/index.php/2016_Winter_Project_Week/Breakout_Sessions/QIICRTools
  • Support of fractional segmentations: not in the immediate scope of QIICR; all API should be in place in DCMTK to write a converter
  • DICOM-AIM harmonization: updates from David, actual work has not yet commenced
  • next steps with the Iowa data: Steve to work on web/Slicer integrated demo
  • next steps with the PeerJ Preprint; the group is leaning towards publishing quickly, PeerJ is a good destination
  • Ok to make the Iowa tutorial video public
  • Legacy enhanced MR: Michael is working on the implementation, the plan is to have the API ready within a month

2015

Oct 29

Agenda

  • Iowa paper updates
  • enhanced MR updates
  • other site updates

Oct 15

Agenda

  • site updates
  • discuss publishing venue for the Iowa article

Sep 3

Attended: Andrey, Reinhard, David, Steve, Michael, Jayashree, Karl, Xiao

Minutes

  • MGH updates
  • code for T1 mapping CPP, PkModeling + T1 mapping and DSC modeling is posted under Xiao's github account
  • agreed python version of T1 mapping should be removed and replaced by the CPP version, Xiao will make a pull request
  • discussed procedures for working with the code: agreed as a general principle code should be hosted under QIICR organization, commits should follow Slicer rules, and should be done regularly
  • DCMTK integration updates - integrated!
  • Integration of the new DCMTK with Slicer is on the way
  • Software provenance
  • discussed PROV diagram experiments
  • discussed application of TID xxx21 to the Iowa use case: David prepared a new iteration of the supplement, need to update instantiation, coordinate with a smaller group that should probably include Satra, Karl, Joerg
  • Steve will work on software package provenance SR for Slicer
  • TCIA Iowa data sharing updates/status
  • clinical data is limited access available (need to supply TCIA user ID to access)
  • SEG/RWVM/SR are on the way, small delay since they need to go over a different route while submitting
  • Iowa conversion scripts (follow up with Ethan)
  • agreed it makes sense to upload the scripts to github

Aug 20

Agenda

  • Software provenance
  • DCMTK status
  • TCIA data submission updates
  • other updates

July 23

Attended: Steve, Reinhard, Andrey, Ron, Jayashree, Xiao

Agenda

  • Iowa multiple time points dataset
  • relatively few patients (22?) had followup scans
  • can add the previously shared cases with ~4 followup scans
  • plan to push the data to TCIA as soon as possible, processing of clinical SRs may require extra time as TCIA staff needs to consider extra patient data issues
  • Experiments with SR conversion and visualization
  • Looked interesting to Reinhard, will discuss with the Iowa group

July 9

Attended: Steve, David, Andrey, Reinhard, Jayashree, Karl, Ron, Michael

Minutes:

  • discuss the topic of encoding measurements using TID 1419 https://groups.google.com/forum/#!topic/qiicr-team/Fct9g3mE6YI
  • David: there will be 2 types of users: those who use/slightly modify established tools like Slicer, and those that start from scratch; the first should be able to follow the examples and code, it would be hard to support the second group
  • Reinhard: how will this data be actually used? Could consider converters to CSV, utilize Chronicle to explore this data, can be used for challenges that include clinical data
  • finalize standing issues for Iowa use case (3 issues identified by David in email)
  • discussed and the updated plan has already been sent to Andrey by David
  • Slicer DCMTK private dictionary integration
  • Michael identified behavior that was not quite expected (dicom.dic is not read from file), will work to provide a fix that would enable to build in both standard and private dictionaries
  • integration of dcmtk/seg is in progress

June 11

Attended: Andrey, Jayashree, Michael, Steve, Xiao

Minutes:

  • DCMTK private dictionary handling
  • need to set DCMDICTPATH, can also set programmatically - can consider adding to CTK, Michael will follow up
  • clarify DSC data format
  • Xiao and Jayashree will follow up on the tag to be used for parsing for the "simple" case
  • Xiao will test Slicer DWIConvert on a Mosaic dataset, will coordinate with Steve if help is needed
  • Steve will investigate putting together a "proper format" using legacy enhanced multiframe MR object
  • Dockers discussion
  • Steve demonstrated some work done by Australia collaborators: Slicer running from a Docker container/virtual machine/VNC with the interface streaming into web browser
  • Jayashree will plan a demo of MGH Dockers work in the future
  • We will need to cancel the next hangout since people will be in Barcelona for the project week

April 16

Attended: Andrey, Ron, Steve, Xiao, Jayashree, Michael

Agenda

  • BWH updates
  • RSNA QIRR abstract submitted; participants: Slicer, ePAD, ClearCanvas AIM, BrainLab, Hermes Medical, Eigen
  • OpenConnections contract is established
  • Iowa updates
  • posting video materials online
  • MGH updates
  • T1 mapping ...

March 19

Attended: David, Andrey, Steve, Ethan, Xiao, Ron

  • Iowa use case encoding
  • David reviewed the dataset and provided suggestions for corrections
  • Ethan will generate another dataset with 1/more than 2 tumor sites, multiple timepoints
  • Planning of the QIRR submission: handling industry interactions
  • David: ideally should have hands-on with each platform
  • consider using Parallels
  • will discuss details with confirmed participants next week
  • Steve: matrix showing level of support for different platforms
  • need to find RSNA rules for scientific exhibits
  • DICOM and SNOMED discussion
  • MGH
  • Xiao contributed source code to QIICR community
  • Will work on studying the documentation, then will follow up with Andrey about meeting
  • Barcelona project week

March 5

Attended: Andrey, Ron, Steve, Michael, Reinhard, Ethan, David, Xiao

  • Iowa use case conversion update
  • derivation image sequence is not populated (Michael)
  • need to initialize Image library (Andrey)
  • verification (David)
  • Ethan will prepare a complete set of objects for testing of code functionality and verification of consistency of the objects
  • We should add DCMTK command line tools for SR to Slicer distribution
  • RSNA connectathon discussion
  • MGH update
  • Xiao is working on T1 mapping, will be checking with Jayashree about credits

February 19

  • Update on discussion with Siemens reporting group (Steve)

February 6

  • BWH updates
  • DCMTK issues resolved, SEG converted code updated, updates communicated to Ethan
  • SPL atlas MR DICOM encoding sharing: MultiframeGrayscaleWordSecondaryCaptureImageStorage
  • Adding support for loading referenced DICOM data in Slicer (e.g., offer user to load MR referenced by SEG) (joint work with SlicerRT group)

January 22

Attended: Andrey, David, Steve, Reinhard, Jayashree, Artem, Xiao, Karl

Agenda

  • Progress with the Iowa clinical data encoding (Reinhard/David)
  • David: very close to completion, required huge effort, need to think if we want to do this for all clinical projects, and whether harmonization across clinical projects is worthwhile; template documentation will be prepared before data is publicly released
  • NCI CDE Browser can be helpful: https://cdebrowser.nci.nih.gov/CDEBrowser/, but not well structured and difficult to use
  • Encoding clinical data of BWH and MGH: will be investigated based on Iowa use case once it is completed
  • Conversion using XSLT is a sensible approach that we will use for the Iowa data, no C++ converters will be developed, at least for now
  • Standing issues with the Iowa tumor segmentation extension (Christian/Andrey)
  • all resolved - extension is fully functional - great job Christian! https://plus.google.com/103730364707811819340/posts/Hew3eAo1LaA
  • Next steps for Iowa data encoding
  • open issues in DCMTK need to be fixed, Andrey will test converter once done, and then pass to Ethan to add handling of longitudinal data, refine encoding of tumor segmentations
  • Reinhard will organize a meeting about remaining issues about clinical data encoding
  • data will be released in steps - clinical first, then quantitative SR/SEG
  • Public sharing of SPL Atlas MR multiframe and SEG (Andrey/David)
  • David is fine
  • Andrey will do few more checks, and coordinate with David if any issues are identified
  • Branding of the DBP tools developed with participation of QIICR (Andrey)
  • Agreed QIICR grant is acknowledged, even though a different grant can be primary contributor (eg, PET segmentation primary contributor is Iowa QIN grant)
  • Standing issues in dcmtk/seg (Andrey/Michael, if Michael is present)
  • discussed with Michael; Michael will try to fix bugs identified shortly
  • Mathis from Siemens syngo team will be in Germany early February and will try to set up DICOM interoperability discussion (SEG, SR, etc) (Steve, David, Michael, Andrey)
  • Steve will coordinate meeting arrangements with Andrey and David
  • Quick question: DICOM for tracker coordinates? Should it be registration object with multiple matrices? (Steve, David)
  • David: can consider fiducials, surface objects (was considered as the starting point by the DTI folks); no ideal representation exists
  • Encoding of parametric maps
  • Steve and Jayashree will discuss and work on a solution using pydicom; Andrey is interested in participating in discussions and staying in the loop on how this is going
  • MGH updates
  • Jayashree will coordinate scheduling of a meeting to discuss integration of T1 mapping and PkModeling modules (Andrey and Steve to join)
  • Artem wants to use scipy in Slicer: Steve mentioned project by Jorge on packaging Anaconda python with Slicer - this is in the stage of experiment, status will be discussed when MGH team visits BWH

2014

October 30

Attended: Andrey, Steve, Ethan, Karl

Agenda

  • Iowa: discuss status and progress of the SEG conversion process
  • Ethan compiled DCMTK seg branch, making progress
  • discussed the situation where SliceThickness is present and is not equal to the computed spacing (ePAD lung segmentation example: SliceThickness carried from CT, which is 1.25, but computed is 1mm); unresolved situation: frames encoding a segmentation are not consecutive (this may not be detectable, inter-frame distances can still be consistent), and SliceThickness is present -- no right answer what to do. Warn if SpacingBetweenSlices (Type 3) is not present, and ask the user what to pick? Example: differences in prescribed segmentation slice thickness are not obvious as erroneous, left 1.25mm, right 1mm. http://slicer.kitware.com/midas3/download/item/162714/CT_seg_thickness_example.png

width=150px

  • Handling of geometric inconsistencies while converting segmentations into SEG: by default, agreed it makes sense follow the prescribed geometry by default, give extra options to "cleanup" by resampling, rounding based on prescribed tolerance

  • Handling RLE encoding for SEG: added to the agenda of CTK hackfest: http://www.commontk.org/index.php/CTK-Hackfest-Nov-2014#DICOM

  • DICOM Search: investigated the problem with delayed loading of images, this is due to modifications to image URLs after page load, need to add special handler to scroll after load is done.

October 16

Attended: Andrey, Steve, David, Reinhard, Michael, Jayashree

Agenda

October 2

Attended: Andrey, Ron, Jayashree, Reinhard, Ethan

Minutes

  • Iowa workshop preparations
  • event planning page http://wiki.na-mic.org/Wiki/index.php/Iowa2014
  • registration form
  • TODO: prepare a flyer
  • QIICR part: support for DICOM/advanced DICOM objects
  • Jayashree programmer may join
  • email David to book the time for this event
  • plan a hangout with Jayashree
  • TODO: segmentation code in October
  • Event OS: Linux
  • QIN segmentation challenge data conversion: discussion of outstanding issues
  • updates to the script and GUI behavior
  • tutorial on how to do the conversion for QIN
  • need input from users
  • different ways to save the same segmentation, which one?
  • support in Matlab
  • DCE validation
  • consider writing white (or non-white) validation paper, share validation results
  • comparison with other packages - maybe
  • Jayashree to update the group next hangout
  • Discuss sufficient data needed to recover volumetric information from segmentation images
  • http://dclunie.blogspot.com/2013/10/how-thick-am-i-sad-story-of-lonely-slice.html
  • CP-1427
  • DocBook DICOM: chunking and paragraph referencing

September 4

Attended: Steve, Ron, David, Reinhard, Andrey, Yanming, Michael

Notes

  • Iowa use case conversion
  • DCMTK API: converter round trip is working for Iowa use case, but not for SPL atlas dataset; Andrey thinks he knows what needs to be done! Michael provided the next update, the remaining issue of incorrect assignment of IPO group should be fixed
  • interoperability and testing of Iowa use case datasets: few products will be able to consume those; will look at ePAD and AIM ClearCanvas interoperability; will consider a connectathon for the next RSNA (can also try this RSNA, since both Daniel and Pat will likely be there)
  • David provided test datasets that were used in the ClearCanvas project: http://slicer.kitware.com/midas3/folder/2371
  • Steve will be working on some Siemens syngo.via interoperability aspects as part of the Siemens project at BWH; Steve shared Siemens project preliminary report with the group
  • DCMTK plans for the next year
  • Need to prioritize tasks: Andrey will follow up with Michael and all
  • Michael will suggest higher level API for DCMTK to handle segments/stacks etc, Andrey will try to help with the implementation
  • Iowa comments
  • max flow (?) optimizer is GPL; there seems to be an alternative in Boost, or can implement one from scratch (perhaps not as fast)
  • how to test? Slicer provides automated testing, there are many examples; can investigate those at the Winter project week and Iowa visit in November
  • BWH updates
  • demo of slice DICOM/corner/color bar annotations; David suggested providing higher level API for extracting DICOM information relevant for annotation display (Andrey will need to clarify a bit better)
  • Yanming MGH updates
  • Yanming is planning to work on DRAMMS integration with Slicer in September
  • Yanming will look into registration for prostate DWI distortion correction using DRAMMS

August 21

Attended: Andrey, Michael, Jayashree, Karl, Steve, Reinhard, Christian, David

Agenda

Notes

August 7

Agenda

July 14

  • Updates from BWH
  • Andrey is working with Michael's API on SEG support
  • Alireza is finishing Slicer infrastructure projects (corner annotations, color bar, slice orientation)
  • DCE bolus arrival time estimation project
  • TODO: arrange for time with Ethan to hand over Iowa SR conversion code
  • DCMTK FG/SEG API
  • clarify API/plans for initialization of per-frame functional groups, dimension organization, derivation image/referenced series sequences
  • discuss timeline/plans for merging with the DCMTK trunk and integration with Slicer

Attended: Andrey, Ron, Steve, Michael, David, Yangming, Karl

Notes

  • DCMTK SEG/FG API
  • multi-frame bit-packing: padding should be taken care of at DCMTK level
  • encoding SoftwareVersions (0018,1020): multivalue, but David suggests many tools do not use multivalue to improve compatibility; no convention how versions/repo should be encoded; decided to dedicate next QIICR hangout to this topic (also related link from Ron: http://www.w3.org/2005/Incubator/prov/wiki/W3C_Provenance_Incubator_Group_Wiki)
  • Michael estimates finishing the code and integration with DCMTK trunk by end of August
  • once API/examples are ready, we should make them visible to engage other communities; discussed neuro community efforts on JSON extensions (?) of NIFTI (relevant links: http://nipy.org/nibabel/, http://nipy.org/nibabel/dicom/dicom.html#dicom)
  • Integration of annotations with Slicer
  • would like to have it in the release (target end of July), but will depend on the level of maturity of code, will discuss with Alireza
  • Steve: integration of external/research applications with clinical systems (Centricity)
  • relevant documents from IHE: http://wiki.ihe.net/index.php?title=Invoke_Image_Display, http://en.wikipedia.org/wiki/Invoke_Image_Display
  • MGH update (Yangming)
  • joint estimation of DCE and motion correction work in progress; will be available in Slicer
  • DRAMMS integration with Slicer is underway; Yanming is working to substitute FSL registration with Slicer BRAINSFit this and next week, once this is done will coordinate next steps with Steve to have the tool available as an extension
  • Need feedback from Jayashree re CPs covering the DCE and DSC use cases

July 10

  • Follow up on NA-MIC Summer Project Week
  • Discussion of Siemens syngo.via collaboration with BWH and interface to QIICR (interoperability of SR and other objects)
  • Update on SR and SEG progress in DCMTK (the work of Michael and Jörg)
  • Site updates

Notes: Steve, Reinhardt, David, Michael, Ron

  • Suggestions from David and Reinhardt on the syngo evaluation (consulting time on syngo is covered by Siemens budget to BWH not by QIICR)
  • David suggested using QIBA DRO for MM Oncology experiments
  • Reinhardt provided data for physical phantom scanned at Iowa on Siemens
  • David suggests taking care to avoid cross-talk when doing test-retest since syngo sometimes fails to forget some things
  • Michael reported on SR and SEG work he and Jörg are doing
  • David says there is not (yet) a standard for SR XML, but he has a work item for that and for SR JSON
  • Discussed goal for vtkMRMLSegmentationNode in Slicer
  • Discussed next generation RT standard that will move more toward seg-like planning
  • Iowa progress report
  • Working through custom SUV calculations
  • Working on Slicer extensions (work on CLI and Editor Effect undo/redo...)
  • Need to make SEG objects and will study from work by Jayashree and Andrey from project week

June 9

  • progress reporting documents back to Rachana due tomorrow
  • moving phone call to Thursday 10am Eastern - confirm
  • MGH use case diagram
  • decoupling of structure color and structure code

May 12, 2014

Agenda

Attended: Andrey, Ron, Steve, David, John, Karl, Alireza, Michael, Jayashree, Reinhard

Minutes

  • DICOM provenance
  • David will work on developing template for capturing information about the reader observer
  • Steve and Andrey will review and generalize the software provenance information to not be Slicer-specific, then will iterate with David, and coordinate with WG23
  • David suggested to add information about taxonomy of the analysis tool
  • Provenance needs are present for the Iowa use case: multiple versions of software are used, multiple ROIs created using different software tools are encoded in the same SR, multiples readers
  • PROV model from W3C pointed by Karl: http://www.w3.org/TR/prov-dm/
  • Project week: Ethan (Iowa) and John (MGH) will participate; Jayashree and Yangming may join; Reinhard may join
  • dcmjs: Steve demoed the functionality on his Android phone! Plans to implement a client-side JS anonymization tool are considered by CTK community
  • related project pointed by David: https://github.com/chafey/dicomParser

April 28, 2014

Agenda

Attended: Ron, Andrey, Steve, Karl, Jayashree, David, John, Alireza

  • Slicer DICOM Module presentation: current status and ongoing improvements work (Alireza)

April 14, 2014

Agenda

Attended: Ron, Andrey, Steve, Michael, Reinhard, John, Karl, Jayashree

  • Courtesy request from Ron: please try to use your camera while on the call!
  • MGH updates
  • Iowa updates
  • Iowa use case workflow (single time point)
  • BWH updates
  • SUV RWVM output should be completed, git hash provenance added
  • terminology for Quantitative Indices: check status with David and Reinhard
  • updates on Slicer infrastructure projects (Alireza) -- postponed

Minutes

  • MGH updates:
  • issues related to converting intensity signal to concentration in DRO is resolved
  • poor Ktrans/ve fitted values for certain combination of parameters in DRO - resolved (?? confirm with Jayashree)
  • John confirmed the scale (peak) of the pAIF is not adjusted - should we consider doing this?
  • comparison done only qualitatively, internal code does not produce the quality of fit maps
  • next steps: implementation of the debugging features (see PkModeling issue #3), quantitative comparison with the internal tools
  • Iowa updates:
  • discussed the use case workflow diagram
  • next steps: confirm the quantitative indices terminology and template with David before implementing
  • BWH updates:
  • John's pAIF tested on prostate dataset - poor fit voxels observed, further investigation needed
  • infrastructure projects discussion
  • will review Slicer DICOM module and related issues next meeting
  • next steps: debugging PkModeling, discuss with David next steps re SR template and SUV quantitative indices

March 31, 2014

Agenda

  • Iowa updates
  • BWH updates
  • MGH updates
  • Michael/DCMTK updates
  • Discussion: Steve report from Germany

March 17, 2014

Agenda

  • BWH updates
  • MGH updates
  • Discussion: Slicer/QIICR presentation at QIN face to face meeting

Minutes

Attended: Andrey, Ron, David, John, Karl

  • BWH updates

  • TID 1411 code updated to address feedback from David and Joerg

  • RWVM code added to Iowa SUV calculation tool

  • DICOM CPs under development: discussed with Siemens, iCAD

  • MGH updates

  • John is working on the debugging and validation of the population AIF

  • Action items:

  • John/MGH

  • add the summary of the population AIF (citation, parameters) to the wiki

  • describe the process that was used for validation

  • Andrey

  • follow up with Ethan/Reinhard about the correctness of the SUV factors

  • test John population AIF implementation on prostate DCE MRI data

March 3, 2014

Agenda

  • MGH updates
  • Iowa updates
  • BWH updates
  • Discussion: DCMTK and automated generation of SR template code
  • Discussion: Parametric maps in DICOM - timing and some of the issues

Minutes

Attended: Andrey, Ron, David, Steve, Michael, Jayashree, John, Karl, Reinhard, Ethan

  • MGH updates
  • Parker population AIF implementation in PkModeling: work in progress, expect completion including validation within the next 1-2 weeks (https://github.com/QIICR/PkModeling)
  • specifics regarding the implementation strategy for the DCE processing components at MGH will be discussed upon completion of AIF implementation; Ron suggested to keep the scope limited to address the use case of QIICR, not answer all research questions
  • Iowa
  • SUV factor calculation: initial version done by Ethan (https://github.com/QIICR/Slicer-SUVFactorCalculator)
  • serialization as RWV next (Andrey will work on this initially, will report at next call and coordinate with Ethan as necessary)
  • David noted that the current RWV IE does not describe the quantity being measured directly, only the units (the quantity measured can be "sneaked in", but this may be sub-optimal); we may need to fix this in the future
  • discussed the level of detail needed to record in the process of image annotation; Reinhard will discuss the appropriate level of detail with the U01 team
  • BWH
  • code to save a measurement as SR following TID1411 (modified to be a root template) is re-factored, coordinated with David, Michael and Jörg Riesmeier (DCMTK)
  • TCIABrowser updated to support downloads in the background
  • DCMTK automated code generation from XML of SR templates
  • Michael: Jan Schlamelcher will finish the thesis in about 4 weeks, will present a summary to QIICR group
  • code most likely will be published in public domain (pending confirmation with OFFIS); plans for integration with DCMTK are not certain, it may be a standalone tool
  • Parametric maps supplement: work in progress, initiated by David
  • discussed the issue of encoding "what is being measured" explicitly in addition to the units of the entity being measured - agreed this is probably necessary
  • this supplement as well as the correction proposal for TID1411 are very likely interesting in the scope of work for BWH-Siemens collaboration; Andrey will communicate relevant documents to the Siemens collaborators in preparation to the meeting on Wed; David will try to join remotely

Feb 17, 2014

Agenda

Minutes

  • Attended: Ron, Andrey, Steve, Michael, David, Reinhard, Ethan
  • TCIABrowser
  • David: compare performance of the Java application vs REST API
  • Iowa use case
  • discussed the PET -> RWVM path, separate call w/ Iowa team to follow
  • SR experiments
  • David identified issues: wrong nesting level, need to keep information about the human observer (should probably be propagated from SEG)
  • correction proposals: will work on this once Iowa use case is formalized and we proceed with the SRs
  • provenance record for device observer: need to extend the level of detail currently captured in DICOM SR this page

Feb 3, 2014

Agenda/minutes

  • Items not discussed in the previous call
  • NCIP Hub updates
  • concerns related to longevity of the government-funded infrastructure, federal compliance such as 508k (?) have been raised
  • it was decided to keep the usage of NCIP Hub at the level of experimentation, at least for now
  • Iowa project and related infrastructure issues
  • scripted module that wraps CLI quantitative index calculation has been developed (Ethan); source code on QIICR github page
  • DICOM PET conversion ideas: conversion into SUV on import? generation of RWV mapping objects? (how to handle those in Slicer?)
  • RWV-related question to David: MRI Units for RWV not present in the standard?
    • need Rescale Type and codes for RWV output
    • for DCE-MRI, need units for concentration, T1 or R1 (time or 1/time), etc.
  • right now we only have DICOM plugins that interpret the data on load; does it make sense to have "DICOM import plugins", which would generate enhanced storage, RWV mapping objects, for recognized modalities?
  • Implementation strategy:
  • consider single time point, do SUV conversion in a standalone module producing one (or several) RWV objects, add handling of RWV objects as DICOM plugins in Slicer, store the result in a scalar volume; keep reference to RWV UID, explore what other improvements to scalar volume are needed; reference RWV from SR
  • Updates on SR TID 1411 (ftp://medical.nema.org/medical/dicom/final/cp1112_ft.pdf)
  • Example of encoding of mean over SEG-defined ROI on Midas, created using DCMTK SR
  • how to report measurements that are based on RVW-modified values?
  • correction proposals for TID 1411: fix relationships, root template
    • also probably need to add specific reference to RWV from SR template
  • measurement types, anatomical structures, equations for PET-related calculations: check for overlap with existing context groups, create new as need, based on Iowa requirements, see Iowa project page
    • consider multiple single lesions plus total
    • future work: across time, including splits and merges
  • next steps
  • For information/discussion: Brad Erikson and Dan Blezek of Mayo have released a research PACS called Notion under a BSD license.
  • Written in Java, it uses DCM4CHE and CTP and has a REST API to support a Single Page Application javascript web-based interface.
  • NITRIC: http://www.nitrc.org/projects/notion/
  • GitHub: https://github.com/dblezek/Notion

Minutes/Notes

  • NCIP Hub
  • concerns related to longevity of the government-funded infrastructure, federal compliance such as 508k (?) have been raised
  • it was decided to keep the usage of NCIP Hub at the level of experimentation, at least for now
  • Iowa use case
  • agreed upon strategy: consider single time point use case, do SUV conversion in a standalone module producing one (or several) RWV objects, add handling of RWV objects as DICOM plugins in Slicer, store the result in a scalar volume; keep reference to RWV UID, explore what other improvements to scalar volume are needed

Jan 20, 2014

Agenda

  • Updates from the project week
  • DCMTK/CMake fixes: discuss timeline for integration into DCMTK trunk
  • Enhanced vs Legacy converted enhanced: proposed approach: convert into "true" enhanced when possible (for example, heuristics for DCE), legacy enhanced as a fallback? - discuss
  • TCIA Browser: plan to release as Slicer extension this week
  • Quantitative index computation module from Iowa: discuss in relation to Label statistics module, image modalities concept in Slicer (also relevant for PK modeling support)
  • Fixes to SEG support in Slicer: need help with warnings, see here http://slicer.kitware.com/midas3/folder/2033; coordinate with Michael
  • Implementation of TID1411 using dcmsr in progress; question to David re Source Image for Segmentation - mandatory in template, but Derivation image sequence is not mandatory in SEG?
  • DICOM docbook reference initial experience, future plans
  • NCIP Hub updates, http://nciphub.org/groups/qiicr

Minutes

  • Attended: Andrey, Ron, Steve, Jayashree, David, Reinhard
  • Multiframe: agreed it is reasonable to create "true" enhanced objects even if they are not technically accurate because they have the desired encoding of attributes like diffusion gradient direction which is more likely to make them compatible with other tools. We may need to fall back to legacy in other cases. Advantages of legacy enhanced objects vs non-multiframe objects: single instance, can be archived to PACS, improved organization of attributes.
  • Iowa QI module: need access to DICOM database, not possible from CLI; it was not immediately clear there is a consensus that Slicer internal data model should be improved to represent at least some of the DICOM information (such as modality) directly.
  • Some of the other issues discussed:
  • SR template builder, browser of terminology vocabularies (eg http://bioportal.bioontology.org/)
  • all OK with switching to every other week for the bi-weekly call

Action items:

  • Steve: follow up with TCIA folks (Justin) re WADO/QIDO rest API to TCIA -- DONE
  • Andrey
  • w/ Alireza demo TCIABrowser to Justin and John, discuss limitations of REST interface
  • w/ Reinhard discuss next steps for QI calculation extension and related issues
  • send TID1411 SR object to David when ready
  • David: review seg object produced by Slicer re warnings -- DONE
  • Jayashree: send to David cc Andrey the requirements and AIM templates used by the MGH project
  • Steve: mark DICOMSearch demo as containing a draft version of the standard -- DONE
  • Steve: add David and Andrey to DICOMSearch and DICOMStandard github projects -- DONE

2013

Dec 16, 2013

Agenda

Minutes

Action items

  • Andrey and Jayashree to schedule a project week planning call after Dec 18
  • Andrey will email Jerry Li re our intent to try out NCIP hub
  • Multiframe sample data: Reinhard has phantom PET dataset, will look into sharing it after returning from vacation; Jayashree has some MF data from a multi-site trial, will look into sharing
  • David suggested a phone call to discuss specifics about using pixelmed tools for MF conversion; Andrey will get in touch after compiling and getting started with it
  • Reinhard: Iowa project page on the NA-MIC wiki (not discussed at the call)
  • Andrey: BWH project page(s) on the NA-MIC wiki (not discussed at the call)

Nov 18, 2013: Hangout 2

  • Go over action items from last call
  • Discuss ideas for site-specific DBP implementation/use case work
  • Discuss general use case template structure, with David's Clinical trial results template (pdf and doc) as a starting point. Abbreviated version/notes compiled by @fedorov are here

Questions:

  • The DICOM-2013-03-19 Minutes document topic 9 refers to XML encoded versions of Parts 3 and 16. Where are those files posted?
  • Does an XML or other computable version of the tables in ClinicalTrialsResults_20111123_QIBA exist?
  • Are SR Templates expressible as XML Schemas or Schematron?

Minutes

  • Attended: Andrey, Ron, Steve, Karl, Reinhard, John, Michael
  • discussed MGH sample datasets: Karl will coordinate with Jayashree to identify a suitable dataset, and will update the group at the next meeting
  • reviewed proposed deliverables from each DBP in sharing methods and data:
  • MGH
  • Tools: some of the possible projects considered (all related to PK processing) are listed at the MGH DBP page. Need to have a better understanding of the dependencies, implementation platform, to pick the method to be transitioned. Steve suggested registration toolkit (DRAMMS) from Yangming Ou can also be a nice deliverable, considering it can be cleaned from the dependencies, and Yanming will be working with Jayashree.
  • Data: to be finalized depending on the dataset selected for sharing.
  • Iowa
  • Tools: a module for computing various SUV-based metrics. Some of these can be computationally intensive, depending on the ROI size. Related classes in ITK: itkLabelStatisticsImageFilter and itkLabelGeometryImageFilter. Need better idea how various metrics can be exchanged between CLI and Slicer, or implemented in a scripted module. Label statistics module in Slicer. SUV calculation CLI from Markus here
  • Data: Image data shared in QIN-HEADNECK collection. Metadata exchange can augment these imaging datasets with the segmentation results and the quantitative indices calculated from those segmentations. Also related DICOM templates defined in DICOM CP 1112 ftp://medical.nema.org/medical/dicom/final/cp1112_ft.pdf.
  • BWH
  • Tools: interactive module to assist user in applying PkModeling extension (guide through the parameter selection steps, define ROIs, calculate summary statistics based on ROIs).
  • Data: augment the QIN-PROSTATE collection with the structured reports that will include ROI segmentations and computed indices.
  • Steve and Michael discussed XML versions of the DICOM spec and concluded that any existing files we know of are old and out of date with the spec.
  • Reviewed the possibility of using XML-Schema and Michael reported that Jorg has explored this and says that it is insufficiently expressive to handle SR templates, but that Schematron might work. Further investigation is required to know for sure. JSON-Schema should also be investigated.

Action items

  • @fedorov will arrange for one-on-one calls with Iowa and MGH
  • MGH to discuss and finalize the dataset to share and submit request to TCIA. Include more details (implementation language/platform, dependencies on proprietary libraries) for the tools considered for sharing.
  • Iowa and MGH to join one of the planning calls for project week in Salt Lake City (@fedorov will send TCON access information). Please let @fedorov know the meeting you are planning to join.
  • All: review the Clinical trial results structured reporting document discussed at the hangout and comment on what you think is relevant and what is missing.

Nov 4, 2013: Hangout 1

Agenda

  • all team members to review the kick-off meeting materials and the standing issues and be ready to discuss the deadlines
  • establish tentative deliverables for year 1 for all participants
  • review the structure of the wiki

Proposed 1st year deliverables:

  1. Site-specific workflow development: (1) in collaboration with the clinical user, develop a mock design of the workflow as it should be implemented in Slicer; (2) document describing the organization of the data produced by the workflow/analysis pipeline to drive the structured report development.

  2. Identify a small data exchange use case (a subset of the data captured: a segmentation, parametric map, QA support) and implement a DICOM compliant solution in 3D Slicer to support it.

  3. Identify an analysis component of the workflow and contribute as an extension to 3D Slicer.

Results

  • 1st year deliverables agreed upon
  • mock design: each DBP develops independently, review initial designs at SLC project week (Jan 6-11 2014)?
  • data organization document: @fedorov to work on the initial outline, will review at the next call
  • data exchange use case: will need support in Slicer/DCMTK; @michaelonken will need to know the details of the use case to estimate the work, DICOM Segmentation object support in DCMTK will definitely be needed
  • will update industry contacts as development progresses to stimulate support in commercial tools
  • Data sharing
  • ideally, would prefer to share data using TCIA as it undergoes rigorous curation procedure
  • can use XNAT Central for reduced delays in sharing data (easier submission process, no fees, Slicer interface is available)

Action items

  • BWH, MGH and Iowa: populate DBP wiki pages with initial content (follow BWH outline); prepare specific ideas about data exchange use case and processing step use case
  • @fedorov: prepare high-level outline for DBP use case description document; setup mailing list; fix links to the presentations on the kickoff event page; try to clarify the details about TCIA paid storage services; coordinate with Tina Kapur a QIICR dedicated phone call for SLC planning
  • @pieper: work on integrating DICOM header viewer into CTK/Slicer at CTK Hackfest in London