Brainstem fMRI (FSL) - May 28, 2017

New in 2017: join the premiere!

The brainstem is the most important part of the brain, when it comes to our daily survival. It is the location of multiple nuclei that control or modulate a vast array of functions, including homeostasis, consciousness and reflexive behaviors. These include the specialized neuromodulatory systems, that are involved in a range of widely studied processes such pain, reward and arousal. Additionally there is emerging evidence for the early involvement of brainstem nuclei in several neurodegenerative disorders, which precede the clinical syndromes by many years. Functional magnetic resonance imaging (fMRI) of the brainstem is a relatively young field that is rapidly evolving. Despite the significant problems that fMRI faces in this complicated brain region, the past few years have seen a number of important advances that bring us closer to routine application of this method.

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How to successfully prepare, analyze, and interpret brainstem-fMRI

  • brainstem anatomy
  • suitable tasks to activate brainstem nuclei, optimized imaging sequences
  • spatial normalization techniques
  • approaches for physiological noise reduction (PNM, FIX, masked ICA)
  • functional connectivity analysis within the brainstem as well as between brainstem and cortex
  • and the use of brainstem atlases
  • We will also briefly cover fMRI of the hypothalamus.


  • Basic understanding of fMRI pre-processing and analysis
  • The main software used in the course is FSL
  • For the practicals you should bring a laptop running Linux with FSL
  • the MICA toolbox is a crucial requirement
  • Important notice: only a limited number of people can participate!

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Instructor: Florian Beissner