fMRIPrep Bootcamp

bannerfMRIPrep

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 fee (includes coffee breaks, lunches and welcome dinner):
  • PhD Students: 450 CHF
  • Post-docs and research staff : 600 CHF
Deadline for registration: September 1st, 2024 

You will find the registration form at the bottom of the page. Places are limited, don’t miss your spot!

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

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 

REGISTRATION FORM

EV - fmriPrep bootcamp
Will you be attending the Welcome dinner?
Payment will be requested following confirmation of the registration

Date

09 - 11 Sep 2024

Time

All Day

Location

Centre Médical Universitaire, University of Geneva
Category
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