2008 Winter Project Week:fmri image analysis - Revision history

Fjanoos at 20:16, 19 December 2007

2007-12-19T20:16:44Z

2007-12-19T20:16:16Z

2007-12-19T20:13:58Z

2007-12-19T20:13:00Z

2007-12-19T20:10:42Z

2007-12-19T20:09:43Z

References

2007-12-19T20:09:19Z

June 2007 Project Week

2007-12-19T20:03:19Z

2007-12-19T19:59:24Z

2007-12-19T19:59:05Z

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 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.)
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 <h2>References</h2>
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 <li> J. Ashburner and K. J. Friston. <b>Multimodal image coregistration and partitioning - a unified framework.</b> NeuroImage, 6(3):209-217, 1997. 7 J. Ashburner and K. J. Friston. Voxel-based morphometry - the methods. NeuroImage, 11:805-821, 2000
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 <h2>References</h2>

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

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 <li> K.J. Friston, J. Ashburner, S.J. Kiebel, T.E. Nichols, and W.D. Penny, editors. <b>Statistical Parametric Mapping: The Analysis of Functional Brain Images</b>. Academic Press, 2007
 <li> J. Ashburner. <b>Computational Neuroanatomy</b>. PhD thesis, University College London, 2000.
+<li> K. J. Friston, J. Ashburner, C. D. Frith, J.-B. Poline, J. D. Heather, and R. S. J. Frackowiak. <b> Spatial registration and normalization of images.</b> Human Brain Mapping, 2:165-189, 1995.
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 <h1>Progress</h1>
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-====June 2007 Project Week====
+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.)
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-===References===
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 <h1>Approach, Plan </h1>
-Our approach is described by the references below.  Our challenge is to build the ITK infrastructure (such as new ITK iterators) to support this algorithm.  Our main purpose at the Project Week is to collaborate on new algorithms and clinical data to provide the best solutions for our DBP partners.
+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.
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 <h1>Objective</h1>
 To implement an fMRI analysis pipeline in the Slicer 3 framework including:
-a) Slice timing correction (open)
+<br>a) Slice timing correction (open)
-b) Inter-slice motion correction (done)
+<br>b) Inter-slice motion correction (done)
-c) Spatial normalization (open)
+<br>c) Spatial normalization (open)
-d) Co-registration of functional and structural data (open)
+<br>d) Co-registration of functional and structural data (open)
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