2008 Winter Project Week:fmri image analysis

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fMRI Image of the Brain after Inter-slice Motion Correction

Key Investigators

  • Ohio State University: Firdaus Janoos, Raghu Machiraju
  • BWH: Steve Pieper, Wendy Plesniak
  • Kitware: Luis Ibanez


To implement an fMRI analysis pipeline in the Slicer 3 framework including:
a) Slice timing correction (open)
b) Inter-slice motion correction (done)
c) Spatial normalization (open)
d) Co-registration of functional and structural data (open)

Approach, Plan

Our approach is based upon SPM (Statistical Parametric Mapping) toolkit widely used in the fMRI community. Our challenge is to build these algorithms into the Slicer3 infrastructure. Our main purpose at the Project Week is to work with our collaborators in order to define the scope of this project, decide upon the details of the fMRI framework in Slicer3, and identify other open problems with respect to fMRI analysis.


We have implemented the inter-slice motion correction module for Slicer3 and are now testing it on various data-sets. We are currently working on inter-volume registration and spatial normalization to a reference space (viz. Talairach and MNI.)


  • K.J. Friston, J. Ashburner, S.J. Kiebel, T.E. Nichols, and W.D. Penny, editors. Statistical Parametric Mapping: The Analysis of Functional Brain Images. Academic Press, 2007
  • P. Jezzard, P. M. Matthews, Stephen M. Smith, Functional MRI: An Introduction to Methods, Oxford Univ. Press, 2001
  • K. J. Friston, J. Ashburner, C. D. Frith, J.-B. Poline, J. D. Heather, and R. S. J. Frackowiak. Spatial registration and normalization of images. Human Brain Mapping, 2:165-189, 1995.
  • J. Ashburner and K. J. Friston. Multimodal image coregistration and partitioning - a unified framework. NeuroImage, 6(3):209-217, 1997. 7 J. Ashburner and K. J. Friston. Voxel-based morphometry - the methods. NeuroImage, 11:805-821, 2000