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Activities completed this month
  1. Demo docker submissions to Emily Townley who is designing a MIDRC challenge. I should have a non-gpu and a gpu submission ready soon:
    1. Currently I am signed in to the DTI Azure Active Directory. I need this to access and create resources for the MIDRC challenge. Now that we intend to test gpus out we want to test on a non-MedICI subscription.
    2. Steps to complete:
      1. Deploy GPU VM through DTI subscription
      2. Test out submissions and have MIDRC folks test them as well
      3. Make some changes to UX workflow for dockersubmimssions
  2. Kheops report is finalized and we just received word from Joel (from Kheops) that OHIF only saves length measurements. I will add that detail to the report and hand off to Ulli.
  3. Didn't quite get around to fixing he codalab deployment on nci's network. A docker issue crept up again and I had to wait for Kevin Olexa to disable "cylancecsv", some sort of anti-virus software.
  4. Setup up highlight system on medici-challenges.org to indicate which challenges still accept submissions.
  5. Setup  Dr. David Newitt's BMMR2: Breast Multiparametric MRI for prediction of NAC Response challenge (https://qin-challenge-acrin.centralus.cloudapp.azure.com/competitions/2).
  6. Setup Dr. Mazurowski's 2nd part of his challenge (https://spie-aapm-nci-dair.westus2.cloudapp.azure.com/competitions/6).
Planned for next month
  1. Continue the Federated Learning Document about integrating MedICI and Federated Challenges.
    1. Document is pending some additional notes. We are currently working with ACR (American College of Radiology) to deploy some Federated Learning clients and servers and this will greatly help me understand the complexities involved with setting up Federated learning challenges. Next month hopefully I'll have a better idea of what goes into setting up a system like this. 
  2. Submit an ePoster to AAPM by the end of June.
MeetingDate
Bi-weekly Meeting #1

 

Bi-weekly Meeting #2

Milestones

DescriptionDate
  • Got access to DTI Azure Active Directory

 

  • BMMR Challenge has launched

 

  • DAIR Challenge has launched

 

Task in Progress

DescriptionStatusCreation DateClose Date

Investigated Kheops and am finishing the report. I met with Joël Spaltenstein from Kheops and he helped me setup a fully secured and working Kheops. I will be collecting more notes from this and talking more about it in the report.

In Progress

 

 

Continued ascertaining the validity of v2 codalab (codabench). I honestly haven't had too much time because of the covid challenge platform. I did get it to launch but there are some issues. I plan to get it all ready and deployed with the MICCAI challenge from last year. Once I have that we can scan it on the NCI platform and run challenges there. Deploy "develop" branch of codabench code to see if it is farther along and more bug free.

UPDATE: we will use old codalab ported to python3 with jQuery update.

Closed

 

 

Finishing setting up MedNIST and Basic Template sample challenges within the kubernetes deployment. This project is a collaboration with Microsoft that has been ongoing since July\August 2020. This should allow us to scale CodaLab up for more users to use and allow a robust docker submission platform. In Progress

 


Risks

DescriptionMitigationRankStatusCreation DateRealizationClose Date
Codabench could prove to be hard to setup and may be buggyNothing we can do but try and see what happens1In Progress

 

We will go with python3 port of codalab for now.

 

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