ISMRM25 - Hands-On Open-Source MR: From Pulse Sequence Programming to Reconstruction & Analysis

ISMRM & ISMRT Annual Meeting & Exhibition • 10-15 May 2025 • Honolulu, Hawai'i

Hands-On Open-Source MR: From Pulse Sequence Programming to Reconstruction & Analysis

Weekend Course

ORGANIZERS: Berkin Bilgic, Li Feng, Rita Nunes, Yogesh Rathi

Sunday, 11 May 2025

313A

13:15 - 17:10

Moderators: Lipeng Ning & Maxim Zaitsev

Skill Level: Basic to Intermediate

Session Number: WE-29

CME Credit

Session Number: WE-29

Overview
The course will provide hands-on experience in basic pulse sequence programming, MRI reconstruction and analysis of MR images. Simulation tools for evaluating MR acquisition and reconstruction methods will also be covered.

Audience Members are asked to install requisite software as described in each speaker's synopsis and listed below.

Anais Artiges:
• Attendees may install mtrk from its github (https://github.com/mtrk-dev), which will include specific material for this session: https://github.com/mtrk-dev/ISMRM-2025-Surfing-School-Hands-On-Open-Source-MR.

Zora Kikinis:
• Attendees may download and install 3DSlicer ( https://download.slicer.org/ ), the 3D Slicer Extensions Manager ( https://dmri.slicer.org/download/) and use the link for test data (https://github.com/SlicerDMRI/SlicerDMRI/releases/download/v1.0.0/Dti_tutorial_data.zip) on the documentation page (https://dmri.slicer.org/docs/ )

Pablo Irarrazaval:
• Attendees are referred to juliahealth.org/KomaMRI.jl/getting-started/.

Qingping Chen, Andreia Gaspar:
• Attendees are referred to the GitHub repository: https://github.com/pulseq/ISMRM-2025-Surfing-School-Hands-On-Open-Source-MR

Onur Afacan:
• Attendees are encouraged to use:
https://gadgetron.readthedocs.io/en/latest/
https://github.com/yarra-framework/yarraclient
https://github.com/kspaceKelvin/python-ismrmrd-server

Target Audience
Students, post-doctoral fellows and researchers who are new to open source MRI sequence acquisition, reconstruction, and analysis.

Educational Objectives
As a result of attending this course, participants should be able to:
• Implement basic pulse sequences using open-source development environments;
• Use open-source tools for simple MR reconstruction tasks; and
• Employ open-source image analysis tools to process and analyze MR data.

13:15		MR Sequence Fundamentals Using Pulseq View Presentation Video Andreia Gaspar Impact: Pulseq is an open-source framework for MR pulse sequence design. This course will show how Pulseq can be used to create MR pulse sequences by combining different building blocks such as RF pulses and gradients, along with useful tools to implement different acquisition strategies.
13:45		k-Space Readout Strategies View Presentation Video Anaïs Artiges Impact: This course introduces several open-source tools to design k-space readout strategies and focuses on mtrk to implement echo-planar, radial, and spiral trajectories.
14:15		Offline Open Source Data Reconstruction View Presentation Video Qingping Chen, Maxim Zaitsev Impact: This lecture introduces multiple offline open-source data reconstruction approaches and the ISMRMRD data format. Through hands-on exercises, participants will learn how to convert Pulseq-based data into ISMRMRD format and perform offline reconstruction using manual methods and BART.
14:45		Hands-On Demo I
15:05		Break & Meet the Teachers
15:20		Online Open Source MRI Reconstruction Platforms View Presentation Video Onur Afacan Impact: This talk explores online open-source MRI reconstruction platforms, showcasing tools for efficient, vendor-independent data processing. Learn how these platforms enhance reproducibility, collaboration, and innovation in MRI research.
15:50		MR Simulation Tools View Presentation Video Pablo Irarrazaval, Carlos Castillo Impact: MRI simulation is key for research and teaching, enhancing understanding of MRI physics, sequence optimization, and acquisition testing. This course covers signal models, software solutions, and open-source tools. Using KomaMRI (Julia), we’ll explore its GUI and coding features.
16:20		Analysis of MRI Data Using the 3D Slicer Tool View Presentation Video Zora Kikinis, Ron Kikinis Impact: This presentation showcases 3D Slicer, an open-source MRI analysis tool, highlighting its applications in whole-body mapping, segmentation, AI-assisted diagnostics, and brain white matter tractography.
16:50		Hands-On Demo II