NA-MIC Project Weeks

MONAI Label Workshop / Tutorial

Workshop will be WAS held: January 25, 2023 9-11am EST

A recording of the workhop is here: https://www.youtube.com/watch?v=KtPE8m0LvcQ

Space will be limited so sign up by January 22th 2023

The goal of this workshop is to prepare users and developers to make use of MONAI and MONAI Label in their work at Project Week 38.

To request participation, please fill out this registration form.

Each participant will be allocated a cloud-hosted GPU workstation provided by AWS AppStream. Instances will be allocated in the US an EU based on the location of the participant. See this information about bandwidth considerations.

Background information

Please refer to the information and watch the videos of the previous workshops. The current workshop will serve as a refresher and update of the previous ones.

• January 12, 2022 (video)
• June 22, 2022 (video)

MONAILabel itself is described in this paper.

Agenda

• Intro and welcome (Steve Pieper - 1 minute)
• Overview of MONAI Events: workshop and bootcamp (Michael Zeyphyr - 1 minute)
• Overview of MONAI Label (Andres Diaz-Pinto) 15 minutes)
  • Intro for first time attendees / refresher for return attendees
  • What’s new in MONAI / MONAI Label since the last workshops?
  • What’s the overall architecture for MONAI model from training to deployment (e.g. considerations for someone doing project planning)
• 3D Slicer and MONAI on AWS (2 minutes, Rudolf Bumm / Steve Pieper)
• Preparation for Hands-on session on AWS (8 minutes, Qing Liu, Alex Lemm)
• What clinical/research applications developing with MONAI Label and what’s the general status of them (10 minutes each)
  • Lungs: Rudolf Bumm
  • Stroke: Ken Butcher
  • Cancer spines: Ron Alkalay
• Deeper dive into application example use cases (15 minutes Andres Diaz-Pinto)
  • data format and preparation
  • python code needs to be edited
  • what decisions need to be made
  • how to organize the training, etc.
• Hands-on session with pre-trained models + Q&A discussions (remainder of the time)

Note that right after this workshop starting at 11am EST, Nvidia is holding two longer MONAI Bootcamp sessions on the 25th and 26th of January: see information here.

Event logistics

• The zoom link info is: https://us06web.zoom.us/s/85353009880

• We will use the Project Week discord for tech support and discussion during the workshop. Please sign up here: https://discord.gg/d5Q6b5ug8u

• Please use the same email for discord that you used to sign up for the workshop and also please use your first and last names and organization in your discord name.

• The workshop will be recorded and made available.

Big thanks in advance to the AWS, NVIDIA, IDC, and Slicer teams for providing this activity!