1. National Alliance for Medical Image Computing http://na-mic.org Slicer fMRI introduction

2. National Alliance for Medical Image Computing http://na-mic.org Todo: stress that the current effort is basic infrastructure…

3. National Alliance for Medical Image Computing http://na-mic.org Goal… augment slicer to be a platform for fMRI analysis

4. National Alliance for Medical Image Computing http://na-mic.org strong coupling to anatomical analysis situate fMRI results in anatomy of individual make ROIs for use in fMRI analysis

5. National Alliance for Medical Image Computing http://na-mic.org workflow / human factors easy to use Wendy Plesniak

6. National Alliance for Medical Image Computing http://na-mic.org open source Matlab $$$ buy in from research community –distributed development

7. National Alliance for Medical Image Computing http://na-mic.org Slicer workshop: prototype tools for fMRI and multi-volume applications Functional Magnetic Resonance Imaging & fMRI data Protocols and modeling Analysis and inference Visualization Tools: Ibrowser, fMRIEngine (hands-on demos) Wendy Plesniak, Haiying Liu

8. National Alliance for Medical Image Computing http://na-mic.org Slicer workshop: prototype tools for fMRI and multi-volume applications What is BOLD-fMRI? BOLD-fMRI is a technique for determining which parts of the brain are activated by different types of sensation (sight, sound), activity (tapping a finger), or by performing cognitive tasks. This functional "brain mapping" is achieved by detecting the increased blood flow to the activated areas of the brain during a sequence of MRI scans.

9. National Alliance for Medical Image Computing http://na-mic.org Slicer workshop: prototype tools for fMRI and multi-volume applications How is it being used? Mapping of the brain Informing neurosurgery Understanding of disease/disease processes … Neuromarketing...

10. National Alliance for Medical Image Computing http://na-mic.org Slicer workshop: prototype tools for fMRI and multi-volume applications Functional Magnetic Resonance Imaging MRI: single volumetric dataset to study brain structure fMRI: volumetric time-series, e.g. acquire one volume every 2 sec for 5 min, to study brain function over time. (Same slices from three volumes.) Low res: ~3mm 3 voxels (One slice in a single volume.) High res: 1mm 3 voxels

11. National Alliance for Medical Image Computing http://na-mic.org fMRI Setup

12. National Alliance for Medical Image Computing http://na-mic.org Slicer workshop: prototype tools for fMRI and multi-volume applications fMRI: data Takes temporal volumetric sampling of blood oxygen level in blood flow (BOLD signal) in brain of subject performing a motor or cognitive task, or attending to a sensory stimulus. Experimental protocol: blocked or event-related design Data collected: a time-series of brain volumes (e.g. 150 x 64 x 64 x 32 voxels) Blood Oxygenation Level Dependent (BOLD) signal indirect measure of neural activity  neural activity   blood oxygen   fMRI signal

13. National Alliance for Medical Image Computing http://na-mic.org Slicer workshop: prototype tools for fMRI and multi-volume applications time extract voxel or ROI timecourse… t fMRI Signal (% change) voxel or ROI time course protocol... ~ 11+ min … and compare to protocol t fMRI: simple signal detection overview Rest (c1) Auditory (c2) … … … … c1 c2

14. National Alliance for Medical Image Computing http://na-mic.org Slicer workshop: prototype tools for fMRI and multi-volume applications Form statistical inferences: test hypothesis that protocol-related signal is present in the data e.g. using t-test Convert into a p-value Threshold to form a parametric map of activation

15. National Alliance for Medical Image Computing http://na-mic.org Slicer workshop: prototype tools for fMRI and multi-volume applications 1.Statistical parametric map of activation (superimposed on high resolution anatomical MRI image) fMRI: what to visualize? 2. Interactive plot of voxel time-course, compared to protocol (visual check)

16. National Alliance for Medical Image Computing http://na-mic.org Slicer workshop: prototype tools for fMRI and multi-volume applications Other new techniques (future work fMRIEngine): Techniques based on the mutual information between the protocol and the voxel timecourse: Junmo Kim, John W. Fisher III, Andy Tsai, Cindy Wible, Alan S. Willsky, William M. Wells III. “Incorporating Spatial Priors into an Information Theoretic Approach for fMRI Data Analysis.” MICCAI 2000: 62-71. Andy Tsai, John W. Fisher III, Cindy Wible, William M. Wells III, Junmo Kim, Alan S. Willsky. “Analysis of Functional MRI Data Using Mutual Information.” MICCAI 1999; 473-480. Techniques that incorporate spatial priors: Eric Cosman, John Fisher, Wanmei Ou, and William Wells“Exact MAP Activity Detection in fMRI Using A GLM with an Ising Spatial Prior”. MICCAI 2004. Wanmei Ou : MS thesis