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fMRI in NAMIC

fMRI in NAMIC. Polina Golland. With slides borrowed from AHM. Goals. Not to replicate existing analysis tools To identify problems that are important to Core 3 interesting to Core 1 Use NAMIC to create new collaborations. fMRI Status Update. Basic analysis functions in ITK (GE/Kitware)

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fMRI in NAMIC

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  1. fMRI in NAMIC Polina Golland With slides borrowed from AHM

  2. Goals • Not to replicate existing analysis tools • To identify problems that are • important to Core 3 • interesting to Core 1 • Use NAMIC to create new collaborations

  3. fMRI Status Update • Basic analysis functions in ITK (GE/Kitware) • User Interface in Slicer (BWH) • Current research: • Advanced detection • Exploratory analysis of fMRI • Integrated visualization of structure & function

  4. Findings from our discussions • Some of the “problems” have already been “solved” • Many items on the “wish list” are in reach • Especially with help of Core 2 • There are some really hard and interesting problems

  5. Major Themes • Integration with anatomical and DTI: • Registration • Joint analysis • Characterizing fMRI activation areas: • Represent “interesting” areas • Describe how they interact during an experiment • Characterize changes across experiments

  6. Multimodal Registration • Registration of fMRI, DTI and anatomic MR • individual and group data • Easy mapping between atlas space and native scan space • Permit warping from native space to atlas space or vice versa • Automated parcellation of cortical surface and subcortical gray matter structures • Generate label maps • Extract quantitative data from labeled ROIs or fROIs • e.g. examine atrophy within functionally derived ROI

  7. Multimodal Registration (contd) • Integrate measures of connectivity • Voxel by voxel and labeled ROI measures of connectivity within single subject time series • Resting & Task-induced connectivity • Changes in strength of connectivity over time • important for learning and habituation experiments • Relation to existing work • PLS, SEM, DCM, POI, other? • Visualization tool to display strength of connectivity including functional and neuroanatomic (tractography)

  8. Characterizing fMRI results • fMRI activation cluster utility • Represent ROIs for use in longitudinal/group analyses • Extract data from these clusters • What do we mean by ROI?

  9. QA for fMRI • Spatiotemporal browser designed for quality control during preprocessing of single subject time series data or contrasts • Easy loading of raw scan formats • Easy navigation through time & space • Quantify signal to noise • Identify temporal spikes  optional smoothing • Identify spatial distortion • B0 field map and phantom  optional adjustment • Also feature to identify outliers in group data • Tom Nichols at U. Michigan has a tool in Matlab that could be a nice basis.

  10. Major Themes for Discussion • Integration with anatomical and DTI: • Registration • Joint analysis • Characterizing fMRI activation areas: • Represent “interesting” areas • Describe how they interact during an experiment • Characterize changes across experiments

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