VL-fMRI Homepage

Virtual Laboratory for fMRI

The Virtual Lab for fMRI (VL-fMRI) was one of the activities of the ``Medical Diagnosis and Imaging'' subprogram of the Virtual Laboratory for e-Sciences Project . It consisted of an attempt to face logistics problems experienced by neuroscientists who share the 3.0 Tesla Philips MRI (3T MRI) scanning facilities available the Academic Medical Centre (AMC) of the UvA. These facilities are used for research and advanced clinical applications, in particular for functional MRI (50%). This activity was completed with the end of the VL-e project (Dec 2009).

The VL-fMRI provides a computational infrastructure to facilitate the storage, analysis and sharing of fMRI data. The basis of this infrastructure is the VL-e Proof-Of-Concept (VL-e Poc) environment. Its main components are: acquisition devices located at the AMC; computational resources (data storage and computing) located at the SARA and NIKHEF; low level services provided by standard grid middleware; generic virtual laboratory (web and grid) services; and application-specific (web and grid) services for data acquisition, storage, analysis and access.

Figure 1: Components of VL-fMRI: acquisition devices, computing and storage resources, and services at the low, virtual laboratory and application-specific levels.

Figure 2: Connectivity of computational resources of VL-fMRI.

Current Status

The VL-fMRI has been used in production since 2008 to perform large fMRI experiments. In 2009 its usage became broader, also for other medical imaging applications (DTI image analysis) and next generation sequecing (DNA sequence alignment). The activities are now performed in the scope of the AMC e-Bioscience Infrastructure (e-BioInfra).

Phase 2

The VBrowser has been extended to run parameter sweep experiments and workflows for fMRI analysis. Three main plug-ins provide functionality that hides the complexity of job submission, monitoring and workflow enactment from the user:

The "Fear Runner" plugin enables users to start large parameter sweep functional MRI analysis experiments with the FSL Feat package from a comfortable and friendly front end. Image analysis jobs are submitted with gLite middleware. Metadata and provenance of the experiment is stored in a directory tree generated automatically.
The "Job monitoring" plugin enables interactive monitoring of jobs submitted via the gLite middleware. Logical job names are associated to the gLite "job ids" to facilitate the identification of individual jobs. Output files are automatically retrieved to any directory upon user request.
The "MOTEUR" plug-in interfaces the VBrowser with a (remote) MOTEUR Workflow Management System to enact workflows described in SCUFL (see Taverna) with gLite middleware.

In all cases, files (input data, results, workflow description, etc) are stored in (remote) data resources that can be interactively and directly manipulated by the user with the VBrowser.

Phase 1

The first phase has been completed. Using the Virtual Resource Browser (VBrowser), the data is transferred from the scanner into the SRB at the SARA using GT4.0 Reliable File Transfer (Web)Service. Firewall roadblocks have been removed by installing in the AMC a Grid Access Point (GAP), which is a privileged system running the VL-e PoC software distribution. The data analysis for individual scans is run on the SARA and NIKHEF computing nodes, using EGEE job submission utilities. Nimrod/G is used to run large experiments (parameter and image sweeps).

Team

VL-fMRI was carried out by a large multidisciplinary team of collaborating researchers in several Dutch institutions:

Academic Medical Center, University of Amsterdam (SP 1.3):
S. Olabarriaga, T. Glatard, K. Boulebiar, Martin Stam
A. Nederveen, R. Soleman, D.J. Veltman, S. Gevers, J. Snel, J. Alkemade
Institute of Informatics, University of Amsterdam :
R. Bakker, R. Belleman, A. Ozsoy, K. Maheshwari, T. Flanitzer , R. Marques, B. O' Nuallain, G. van Noordende, M. Koot, P. de Boer , A. Belloum
SARA Computing and Networking Services (SP 4)
M. Bouwhuis, B. Heupers, J. Engbers, grid-support@sara.nl
Dutch Institute for Nuclear Physics and High Energy Physics (NIKHEF) (SP 4)
D. van Dok, J. J. Keijser, J. Templon, O. Koeroo, grid-support@nikhef.nl

Related Publications ( see more details )

S.D. Olabarriaga, T. Glatard, P.T. de Boer, "A Virtual Laboratory for Medical Image Analysis", IEEE Transactions on Information Technology In Biomedicine (TITB), (in-press), 2010.

T. Glatard, Remi S. Soleman, Dick J. Veltman, Aart Nederveen, and Silvia Olabarriaga. Large scale functional MRI study on a production grid. Future Generation Computer Systems, vol. 26, no. 4, pp. 685-692, 2010.
abstract

R.S. Soleman, T. Glatard, D.J. Veltman, A. Nederveen, S. Olabarriaga. "Large scale fMRI parameter study on a production grid". Proceedings of the MICCAI Workshop on Medical imaging on grids: achievements and perspectives (MICCAI-Grid), New-York, 6 September 2008
pdf

T. Glatard, S. Olabarriaga. "From gridified scripts to workflows: the FSL Feat case". Proceedings of the MICCAI Workshop on Medical imaging on grids: achievements and perspectives (MICCAI-Grid), New-York, 6 September 2008
pdf

T. Glatard, K. Boulebiar and S. D. Olabarriaga. "Workflow integration in VL-e medical", in Proceedings of the 21st IEEE International Symposium on Computer-Based Medical Systems (CBMS'08), Jyväskylä, Finland, 17--19 June 2008
abstract pdf

S.D. Olabarriaga, T. Glatard, K. Boulebiar, and P. de Boer. "From 'low-hanging' to 'user-ready': initial steps into a healthgrid", Healthgrid, Chicago, June 2008. Best paper award.
abstract pdf

G. van Noordende, M. Koot, S.D. Olabarriaga, C. de Laat "Privacy and Trust for Grid-based Medical Applications", First Workshop on Security, Trust and Privacy in Grid Environments , 8th IEEE International Symposium on Cluster Computing and the Grid (CCGrid'08), , Lyon, June 2008
abstract pdf

T. Glatard, K. Boulebiar, P. de Boer and S.D. Olabarriaga. "fMRI analysis on EGEE with the VBrowser and MOTEUR", demo presented at the 3rd EGEE User Forum, 2008.
abstract

K. Boulebiar, S.D. Olabarriaga "The Experiment Dashboard for medical applications" poster presented at the 3rd EGEE User Forum, 2008
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S.D. Olabarriaga, A.J. Nederveen, Breanndan O' Nuallain, "Parameter Sweeps for Functional MRI Research in the Virtual Laboratory for e-Science Project", Fifth International Workshop on Biomedical Computations on the Grid (BioGrid'07), as part of the 7th IEEE International Symposium on Cluster Computing and the Grid (CCGrid'07), Rio de Janeiro, May 2007, pp. 685-690
pdf

S.D. Olabarriaga, P.T. de Boer, K. Maheshwari, A. Belloum, J.G. Snel, A.J. Nederveen, M. Bouwhuis, "Virtual Lab for fMRI: Bridging the Usability Gap", 2nd IEEE Conference on e-Science and Grid Computing, Amsterdam, December 2006
abstract pdf

S.D.Olabarriaga, A. Nederveen, J.G. Snel, R.G. Belleman, "Towards a Virtual Laboratory for fMRI Data Management and Analysis", HealthGrid 2006, Valencia, June 2006
abstract pdf

S.D.Olabarriaga, A. Nederveen, J.G. Snel, R.G. Belleman, "A Virtual Laboratory for fMRI Data Management and Analysis", poster presented at Human Brain Mapping 2006, Florence, June 2006
pdf

Contact

Silvia Delgado Olabarriaga, PhD
Academic Medical Center (+31 20 566 4660)
University of Amsterdam, The Netherlands

S -dot- D -dot- Olabarriaga -at- amc -dot- uva -dot- nl

See more information here.

Acknowledgment

This work is carried out in the context of the VLe project, which is supported by a BSIK grant from the Dutch Ministry of Education, Culture and Science (OC&W) and is part of the ICT innovation program of the Ministry of Economic Affairs (EZ).