1. Haskins fMRI Workshop Part I: Data Acquisition & Preprocessing

2. fMRI Setup

3. Collaborations Yale University Yale MR Imaging Center Dartmouth College Department of Psychological and Brain Sciences Kennedy Krieger Institute F.M. Kirby Research Center for Functional Brain Imaging

4. Magnet... Source: www.howstuffworks.comwww.howstuffworks.comSource: http://www.simplyphysics.com/http://www.simplyphysics.com/ flying_objects.html

5. 3D space definitions http://www.sph.sc.edu/comd/rorden/anatomy/home.html Standard coordinates are listed as mm distances from the origin (the anterior commisure) along the x/y/z dimensions. some examples: Broca’s area, left hemisphere Tal x=-54 y=27 z=9 right cerebellum: Tal x=33 y=-45 z=-39 left occipitotemporal region: Tal x=-39 y=-45 z=-19

6. slice orientations axial sagittal coronal

7. Typical Acquisition Sequence 1)three-plane “localizer” 2)sagittal “scout” 3)axial T1 anatomic 4)several functional runs... 5)high-resolution anatomic (MP-RAGE) 6)Diffusion Tensor Imaging....

8. Slice Locations

9. Simulated Hemodynamic Response Noise SD = 0 Noise SD = 10 Noise SD = 100

10. kki0032 trial timecourse

11. Preprocessing steps functional data: adjust for slice acquisition time sinc interpolation; “temporal realignment” adjust for motion “motion correction”; “(spatial) realignment” apply spatial smoothing gaussian filter anatomic data: strip skull from image align with a common template “normalization”

12. slice acquisition time... We typically acquire 20 (functional) slices in each 2-second interval. Each one takes 100 msec. Must account for this in analysis... functional data: adjust for slice acquisition time stimulus onset at time 0 slice #1 (circles) is acquired at times 0/2/4/6/8... seconds exactly. slice #2 (diamonds) is acquired 100msec later, at times 0.1/2.1/4.1/6.1/8.1... seconds post-stimulus. 1 2 acquisition order

13. motion parameters

14. motion artefacts

16. motion parameters

17. motion processing

18. smoothing -- 3.125 versus 6.25

19. normalization Basic idea: find a transformation that will spatially shift this subject’s brain to align with a template, so that subjects can be averaged together. This also allows us to use a pre-labelled atlas to identify structures. important concepts: spatial transformations: linear: translation, rotation, scaling; nonlinear: warps degrees of freedom (DOF) 6: Rigid Body; 7: adds global rescale; 12: affine (adds shear) similarity functions; search & optimization; resolutions skull stripping

20. skull stripping...

21. kki0032

24. end of part 1.