Data organization & processing for neuroimaging research w/BIDS & BIDS Apps

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Data organization & processing for neuroimaging research w/BIDS & BIDS Apps

fMRI Workshop: Data organization and processing for neuroimaging research with BIDS and BIDS Apps

When and where

Date and time



About this event

Workshop Overview:

Over the past decade, the neuroimaging field has produced (and continues to produce) incredible amounts of data. As a result, the scientific community has developed a diverse set of tools to facilitate the FAIRness of these data. This workshop will introduce the Brain Imaging Data Structure (BIDS) and BIDS Apps as well as a few other tools.

Workshop Objectives:

The workshop is designed to help attendees:

  • Understand how MRI data are organized
  • Learn the benefits of BIDS
  • Convert MRI data to BIDS in some hands-on exercises
  • Run reproducible pipelines that take BIDS data as input (BIDS Apps)
  • Use the tools discussed during the workshop on Rotman Servers, including the GRID, and the SciNet computing cluster

Attendee Requirements:

This workshop assumes that attendees have some familiarity with the different MRI modalities. The workshop will also use both the Unix shell and Python to demonstrate certain objectives. A working knowledge of both may aid in understanding.

No software installation is required prior to this workshop. The workshop will involve demonstrations using Jupyter notebooks that can be accessed at

Workshop Instructors:

Jacob Matthews is the MRI Specialist for the Rotman Research Institute. He completed his MSc in Medical Biophysics at the University of Western Ontario. In his current role, he maintains a variety of hardware and software environments for the Rotman MRI, as well as provides acquisition and analysis support to Rotman MRI Users. He is also involved in a handful of ongoing technical development projects with several Rotman scientists.

Michael Joseph is a Research Methods Specialist in the TIGR Lab at CAMH. He assists with improving the lab’s MRI data management and quality control software and provides technical support for the lab’s trainees. Michael’s primary interests lie in developing reproducible software to automate MRI data analysis and understanding the statistical techniques involved. To this end, he is involved in the development of dMRIPrep, a BIDS App for pre-processing diffusion MRI data.