Thursday, 18 January 2018 10:51

FULLY BOOKED! Ph.D. Course in 'Anatomical and physiological fingerprinting of the human brain with multi-modal MRI'


THE PHD COURSE IS NOW FULLY BOOKED! An update with course material will be uploaded on this page. 

The participating students who are signed up for the course have to bring their own laptop to do the exercises, and they need to install Thinlic client on their computer. Instructions will appear on this website.

UPDATE: You will be working on our DRCMR cluster and for that you will need to install the thinlinc client which is downloaded from Cendios' webpage ( If problems appear with the downloading, it will be fixed when the exercises are being held.

Please note that reading material will be uploaded on this page on a regular basis, listed according to topic. A login password will be sent in a separate e-mail to the participants.


Basic MRI





Available reading material can be uploaded here.


We are getting closer to the start date of the PhD Course and we hope that you are ready. If you are not familiar with Hvidovre Hospital, and the linked map under Course Location seems confusing, please look at this version (click here). Also, you are welcome to ask the people in the information booth at the main entrance. They will know where the PhD Course is being held.  


Learning objectives

A student who has met the objectives of the course will be able to:

  1. Describe and understand the basic principles of an MRI scanner and the possibilities in using ultra-high-field MRI.
  2. Explain and understand central sequences and experimental concepts for neurovascular MRI, quantitative MRI, diffusion MRI and spectroscopy.
  3. Characterize the MRI signal contrast obtained from neurovascular MRI, quantitative MRI, diffusion MR and spectroscopy in relation to the true underlying physiological and microstructural environment.
  4. Justify multimodal MRI experiments and identify relevant data analysis and modelling strategies to map a biological functional, microstructural and metabolic feature in tissue.


The PhD course provides an overview on how Magnetic Resonance Imaging (MRI) can be used in neuroimaging. Four cutting edge MRI topics will be introduced, addressing the increasing need for combining several MRI modalities. It covers how to 1) improve the specificity for mapping anatomical features for precision medicine, and 2) create a better link between brain structure and function, which is partly missing today. The four MRI topics covered are: Neurovascular contrast imaging, Quantitative MRI, Diffusion MRI and Spectroscopy. The possibilities of using the Danish National Ultra-High Field human 7T MRI will be integrated within the lectures. The course combines lectures and practical hands-on exercises for introducing the participants to the state-of-art experimental designs within each of the topics, their possibilities and challenges. Exercise presentations and discussions between participants are emphasized. International keynote speakers will inspire the discussions of multi-modal imaging within the four MRI topics.

With emphasis on each of the MRI modalities we will cover the topics:

  • Introduction to MRI: How does a MRI scanner work? Basic tissue contrast mechanisms, T1 and T2 relaxation useful for tissue characterization, Ultra-High Field MRI  (7 tesla) and MR safety.
  • Functional MRI: Blood-oxygen-level dependent contrast imaging (BOLD) and Arterial Spin labelling (ASL) for hemodynamic assessment of changes in CBF, CBV, OEF and CMRO2 during neural activation, potential and analysis.
  • Quantitative MRI: T1/T2/T2* relaxations, magnetization transfer, susceptibility weighted imaging, analysis and tissue compartment modelling.
  • Diffusion MRI: Basic diffusion concepts, non-parametric (diffusion tensor and kurtosis imaging) and parametric tissue compartment models e.g. axon diameters, diffusion sequences, tractography, pre-processing pipeline.
  • Spectroscopy: Basic spectroscopy concepts, detectable metabolites and their significance, acquisition strategies (water suppression, single voxel, spectroscopic imaging), data processing/analysis, quantification, multinuclear spectroscopy.


The target participants are PhD students with interest in neuroscience, clinical research as well as those more technically interested in neuroimaging. It is beneficial but not required having insights into basic MRI. Students need to study provided material in advance to follow the introductory MRI lectures.




Lectures and practical hands-on sessions and discussions


Monday 26th February – Friday 2nd March 2018

Course location

Copenhagen University Hospital Hvidovre, Danish Research Centre for Magnetic Resonance, MR Conference Room, Section 340, Hvidovre, Denmark. For a map, please click here.

You can find the program for the course here.


Karam Sidaros

Tel.: +45 3862 3330
DRCMR, MR-forskning, Afs. 714
Copenhagen Hvidovre Hospital
Kettegard Alle 30
DK-2650 Hvidovre