Life Sciences Life Sciences

DTI Science Case: Diffusion Tensor Imaging helps understand brain connectivity 


Life Sciences, Neuroscience

Workflow Links

DTI Preprocessing:
FSL BedpostX: 
DTI Population Registration:


Diffusion tensor imaging (DTI) is a magnetic resonance imaging (MRI) modality that enables in-vivo study of brain structure and function. It helps understand the integrity and shape of the white matter fiber tracts that connect different brain regions. The analysis of DTI data requires various specialized and complex steps using a large number of tools. All the necessary steps have been encapsulated into a workflow to facilitate data analysis for the neuroscientists. This workflow is offered to the users from a science gateway with intuitive interface, and it runs on the Dutch grid infrastructure.

Scientific Merit

Brain function and structure is fundamental to understand changes in the brain due to disease or other (external) factors. DTI data is widely used by neuroscientists and clinical researchers in studies that attempt to correlate patient symptoms to measurable modifications in brain function and structure. Much on-going research in neurosciences today aims at establishing DTI- and other MRI-based biomarkers of brain disease.


The analysis of DTI data involves various steps from data pre-processing, calculation of diffusion properties such as FA (fractional anisotropy), and finally to determination of white matter fiber bundles with some kind of fiber tracking algorithm.
In the example presented below the first two steps were executed as shown in the Figure below. All steps are encapsulated in one single job that is executed in a parameter sweep workflow for each DTI dataset.


Note: The text below is based on an article from EGI Case Studies:
It illustrates the most prestigious study done so far based on data analysed with the DTI workflows.
Veterans returning from active duty endure many challenges to readapt to a civilian life. For some there is the added complication of combat stress, which affects their memory, attention span and other cognitive functions. But how? And for how long?
Neuroscientist Guido van Wingen and colleagues at the Academic Medical Centre (AMC) in Amsterdam monitored a group of soldiers from before their first deployment to Afghanistan until 18 months after their return to civilian life. The idea was to look how combat stress affects brain areas supporting cognitive functions such as memory and attention. The team used the grid-enabled e-bioinfra science gateway to process and analyse 118 brain scans from 33 soldiers and 26 civilians used as controls. Thanks to a friendly user interface and the computing power of the grid, a workload of several weeks was condensed into two days.
The conclusions, published in the Proceedings of the National Academy of Sciences, show that combat stress impairs cognition by affecting the midbrain and its link with the prefrontal cortex, and that this is largely reversible but could have an impact on future social and cognitive functions.

Related Publications

These publications have been produced based on data analysis realized with the execution of workflows for DTI data analysis on the Dutch grid infrastructure. 
  1. Guido A. van Wingen, Elbert Geuze, Matthan W.A. Caan, Tamás Kozicz, Silvia D. Olabarriaga, Damiaan Denys, Eric Vermetten, Guillén Fernández (2012). Persistent and reversible consequences of combat stress on the mesofrontal circuit and cognition. Proceedings of the National Academy of Sciences of the USA. PNAS September 18, 2012 vol. 109 no. 38 pp. 15508-15513
  2. B. de Kwaasteniet, E. Ruhe, M. Caan, M. Rive, S. Olabarriaga, M. Groefsema, L. Heesink, G. van Wingen, and D. Denys, Relation between structural and functional connectivity in major depressivedis- order Biological Psychiatry, no. 0, 2013.
  3. Bart D. Peters, M.D., Marise Machielsen, Wendela Hoen, M.D., Matthan W. Caan, Philip R. Szeszko, Anil K. Malhotra, Silvia D. Olabarriaga, Lieuwe de Haan. Polyunsaturated Fatty Acid Concentration Predicts Myelin Integrity in Early Psychosis.. Schizophrenia Bulletin, Schizophr Bull. 2012 Aug 27 (epub ahead)
The neuroscience gateway where the DTI application is available is described in the following publication:
  1. Shayan Shahand, Ammar Benabdelkader,  Mahdi Jaghouri, Jordi Huguet, Mostapha Al Mourabit, Matthan Caan, Antoine van Kampen and Silvia Olabarriaga. A Data-Centric Science Gateway for Computational Neuroscience. Concurrency and Computation: Practice and Experience, epub 14 April 2014



   This project has received funding from the European Union's Seventh Framework Programme for research, technological development and demonstration under grant agreement no 312579.