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, postdoc, assisting master-student. 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, about sequences available for research and about quality control, data transfer and storage of MRI research data.


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 transfer and data storage, and an introduction to data processing environments.

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 transfer and storage

Knowledge of Basic MRI Physics is necessary.



  • 9u15-10u15  Repeat session MRI contrast, MRI signal and spatial encoding
  • 10u15-11u00 Quantitative vs qualitative MRI
  • 11u15-13u00  Optimizing image quality: parameters and trade-offs

Part I) Maximizing signal (SNR) 

- Influence of field strength 

- Influence of coil type and position

- Influence of tissue type

- Voxel volume: slice thickness, image matrix, FOV

- TR, TE, flip angle

- Number of signal averages

- Receive bandwidth 

  • 13u45-15u30 PIM

Part II) Maximizing  spatial resolution 

- Slice thickness, image matrix, FOV

- Spatial resolution and pixel dimension

- Rectangular FOV

- Volume imaging

Part III) Maximizing contrast (CNR) 

- TR, TE

- TI


- Use of contrast agents 

  • 15u45 – 16u30 

Part IV) Minimizing scan time 

- TR

- Phase matrix

- Number of signal averages

- Readout strategies

- Minimizing artefacts        

  • 16u30 -17u00  Wrap-up - Decision making in image qualitythe pentagon 
  • 17u00 – 17u30 Q&A: From research question to sequence selection 


  • AM: Quality Control

Online Quality Control at the console

- Patient preparation

- Artefact or not?

- Decision making: data usable or not?

- Feedback to GIfMI

Phantom scanning

Looking at your data

- Stand-alone viewers

- Processing environments

- Resources / tools for QC  

Offline Quality Control PIM/PTR 

- Case studies 

  • PM: Data management: from RAW to MAP PTR

Raw Data formats 

- MRI Dicom

- Dicom tags

- Dicom header 

- Physiological data

Data transfer 

- Offline/online

- Dicom nodes

Data conversion 

- Nifti


- Other formats

Data storage 

- Location

- Volume

- Long-term/short-term

Data retrieval 

Pitfalls in data transfer and storage 

- Loss of metadata

- Changes in raw data

- Effects on analysis  

Dates and Venue

10 & 11 February 2022 - Ghent University Hospital – Aud C  


Dr. Ir. Pim Pullens
Affiliation: UZ Gent MRI physicist / UGent voluntary employee (will be guest professor around September 2021 at the Faculty of Biomedical Engineering)
Short biography: 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.

Ir. Pieter Vandemaele
Affiliation: UGent Dep. Diagnostic Sciences
Short biography: 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
Affiliation: UZ Gent MRI radiographer/MRI research assistant
Short biography: 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.


Please follow this link:
If the courses are fully booked, please send an e-mail to In case of cancellations you can take the open place. PhD students who asked to be on the waiting list will have priority to register in the next course.

Please read the cancellation policy.

Registration fee

Free of charge for Doctoral School members.

Number of participants

Maximum 40.

Evaluation criteria (doctoral training programme)

GIfMI will award a certificate to successful candidates with 100% attendance which gives permission to scan at the GIfMI facility after an additional practical training and a safety training on site by the GIfMI research assistant.