fMRIPrep Bootcamp
The CIBM Center for Biomedical Imaging is proud to announce its inaugural Bootcamp for fMRI researchers, focusing on the use of the fMRIPrep pipeline to prepare their fMRI data for analysis, including 7T fMRI.
This intensive 3-day bootcamp will cover all the steps of the preprocessing pipeline from BIDS and containers up to the interpretation of the analysis results. It will be led by two of the founders and principal developers of the fMRIPrep pipeline, Dr. Oscar Esteban and Dr. Chris Markiewicz. This is a unique opportunity to gain hands-on experience and deep insights directly from the experts who created the tool.
The fMRIPrep Bootcamp will be held from 9th to 11th September 2024 from 8:30am to 5:00pm at CMU, University of Geneva. The Bootcamp is designed for PhD students , post docs and research staff who are familiar with fMRI.
Registration is now closed
LEARNING OUTCOMES
At the end of this course, we expect to have provided you with the following skills and abilities:
- Upload large neuroimaging datasets into HPC systems
- Understand BIDS, data organization, and the implications of these topics on reproducibility
- Deploy a data management strategy to future-proof your analyses
- Process large datasets within HPC and desktop systems
- Master the basics of containerization as a way to make analyses more reproducible
- Execute fMRIPrep on large datasets, understand and finally resolve issues that emerge down the line
- Recognize and operate on the fMRIPrep outputs to build your final fMRI analyses
- Critically evaluate the outputs of fMRIPrep to determine the quality of the processing
- Assess the quality of unprocessed images with MRIQC
BOOTCAMP INSTRUCTORS
The Bootcamp will be taught by Dr Oscar Esteban (CHUV) and Dr Chris Markiewicz (Stanford University), two founders and main developers of the pipeline, so don’t miss out on this occasion!
Oscar Esteban
Lausanne University Hospital
Chris Markiewicz
Stanford University
PRELIMINARY PROGRAMME
DAY 1 : September 9, 2024
8h30: Welcome
9h00: Opening of the Workshop
9h30: Overview of the fMRI neuroimaging pipeline, fMRIPrep
10h30: Coffee Break
10h45: BIDS
11h30: Overview of the 7T fMRI dataset
12h00: Lunch Break
13h30: Hands-on – Access to data on HPC
14h30: Introduction to Containers
15h00: Coffee Break
15h15: Hands-on – first run of fMRIPrep on the 7T fMRI dataset
17h00: End
18h00: Welcome Dinner
DAY 2 : September 10, 2024
8h30: Arrival
9h00: Fixing common fMRIPrep errors, Parallelisation and Resource planning
10h30: Coffee Break
10h45: Analysing data processed with fMRIPrep
12h00: Lunch Break
13h30: Quality control
15h00: Coffee Break
15h15: Hands-on advanced processing using fMRIPrep, run fMRIPrep on own data
17h00: End
DAY 3 : September 11, 2024
8h30: Arrival
9h00: Hackathon project pitches
10h30: Coffee break
10h45: Hacking!
12h00: Lunch break
13h00: Hacking
15h00: Coffee break
15h15: Round table – showcase results.
16h30: End