Advanced MRI data acquisition and management

Target group

The target audience is the current and/or future user of the MRI scanner at the GIfMI facility, either as a PI, PhD or postdoc. We also invite people from the Radiology Department (radiologists and ASO, radiographers) as we have a very valuable connection and indispensable cooperation with the University Hospital.


Magnetic Resonance Imaging (MRI) is a medical imaging technique used to produce high quality images of the body. This course will provide current/future PhD students and regular users of the MRI scanner available at GIfMI (Ghent Institute for Functional and Metabolic Imaging) with advanced knowledge about the sensitive balance and trade-offs between acquisition parameters, sequences available for research, data quality control and data conversion.  


This course will go deep into the details of MRI acquisition parameters, the balance between the parameters and their trade-offs with the aim of maximizing signal (coil use, TR, TE, flip angle, number of averages, bandwidth), contrast (TI, MTC, contrast agents), spatial resolution (slice thickness, image matrix, FOV, recFOV) in a reasonable acquisition time, resulting in 2D slices or 3D volumes. A showcase of sequences for structural, functional and qualitative imaging, their applications and limitations could lead to new insights for participants future research projects and co-operations. Participants will learn about what’s next immediately and later on after the process of acquisition: data quality control at the scanner and offline, decision making on whether or not to repeat sequences, good practice on data conversion. 

Objectives of the course

This course is aimed at those who would like to understand

  • Advanced data acquisition parameters, the balance between them and their trade-offs for image optimisation
  • The mechanism and extra pitfalls of 3D imaging
  • Advanced sequences for structural, functional and qualitative imaging and how to select the appropriate sequence for a research project
  • Good practices for quality control at the console and offline
  • Good practices for data conversion 

Knowledge of Basic MRI Physics is necessary.



Repeat session Basic MRI physics

  • MRI contrast (TR, TE, FA), MR signal, spatial encoding

Structural MRI: 

  • Optimizing structural image quality: parameters and trade-offs between SNR, spatial resolution, CNR and scan time.
  • Artefacts and quality control of structural MRI data.


  • Short introduction to DWI/DTI
  • Optimizing DTI
  • FAQ: Why do we acquire a PA scan? What are the b-values exactly? Why do I opt for a specific amount of directions and shells? What is the use of b=0? Why do we use GRAPPA in DTI and not in fMRI? The role of partial Fourier in DTI? How about denoising? How to model crossing fibers?  Coping with distortions? …
  • Artefacts and quality control of DTI data



  • Short introduction to fMRI.
  • Optimizing functional MRI: Effect of Fa, TR, TE, number of slices, bandwidth
  • FAQ: Why do we acquire a field map? The importance of distortion in fMRI? What is the effect of the multiband factor on the data, what are the pitfalls? …
  • Artefacts and quality control of fMRI data


  • Short introduction to ASL
  • Applications in the brain and kidney
  • Artefacts and quality control of ASL data

Data management

  • Data conversion
  • BIDS


  • Neurodesk
  • Qualitative and quantitative MRI: the sky is the limit!

Dates and Venue

8 & 9 February 2023 (9:00-17:30) - Ghent University Hospital – Aud C . 


Prof. Dr. Ir. Pim Pullens
Graduated in Biomedical Engineering in 2006 at TU Eindhoven, PhD in cognitive neuroscience in 2012, worked as a biomedical engineer/software developer for Brain Innovation BV (Maastricht) and as a consultant for Icometrix a spin-off company that offers advanced image processing for quantitative analysis of biomedical images. Currently at work as MRI physicist in UZ Gent. He has a network of MRI specialists all over the world.

Ing. Pieter Vandemaele 

Graduated as industrial engineer electronics (Vives) in 1998 and as MSc in computer Science (UGent) in 2000. He started working for the hospital’s radiology department right after graduating, teaching PhD students and MRI users how to safely use an MRI scanner since 2000.

Stephanie Bogaert MSc

Graduated as a professional Bachelor in medical imaging (Odisee) in 2007, started working in the clinical MRI department of UZ Gent that houses three MRI scanners and combined this with the Master in care management. Moved to the scientific environment of GIfMI in 2013 to support PhD Students in the practical and safe use of the MRI scanner. Former president of the Flemish Radiographer Society (VMBv) and guest lecturer at Odisee bachelor in medical imaging.

Dr. Patricia Clement 

Graduated as a PhD in 2022 and currently employed by UZ Gent as a neuroimaging researcher. First author of the systematic review of modifiers of the physiological brain perfusion in healthy subjects and the paper on ASL-BID. Science Communication Officer/Work group Leader GLiMR 2.0 (COST CA18206). 

Ing Luis Carlos Sanmiguel Serpa, PhD

Graduated as an electronic engineer at the Pontifical Javeriana University, former Staff Technical Support Engineer at NI (National Instruments) and currently PhD researcher at Ghent University with the aim to contribute in areas related to electronic and biomedical technology such. 


You can find the registration link here
Please read the cancellation policy.

Registration fee

Free of charge for Doctoral School members.

Number of participants

Maximum 100

Evaluation criteria (doctoral training programme)

GIfMI will award a certificate of attendance to successful candidates who attended a 100%.