Haskins fMRI Workshop Part I: Data Acquisition & Preprocessing

fMRI Setup

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

Magnet... Source: flying_objects.html

3D space definitions 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

slice orientations axial sagittal coronal

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....

Slice Locations

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

kki0032 trial timecourse

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”

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/ seconds post-stimulus. 1 2 acquisition order

motion parameters

motion artefacts

motion parameters

motion processing

smoothing versus 6.25

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

skull stripping...

kki0032

end of part 1.