Haskins fMRI Workshop Part I: Data Acquisition & Preprocessing
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Transcript of Haskins fMRI Workshop Part I: Data Acquisition & Preprocessing
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Haskins fMRI WorkshopPart I:
Data Acquisition & Preprocessing
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fMRI Setup
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Collaborations
Yale UniversityYale MR Imaging Center
Dartmouth CollegeDepartment of Psychological
and Brain Sciences
Kennedy Krieger InstituteF.M. Kirby Research Center for Functional Brain Imaging
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Magnet...
Source: www.howstuffworks.com Source: http://www.simplyphysics.com/flying_objects.html
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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 hemisphereTal 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
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slice orientations
axial
sagittal coronal
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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....
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Slice Locations
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Simulated Hemodynamic Response
Noise SD = 0
Noise SD = 10
Noise SD = 100
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kki0032 trial timecourse
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Preprocessing steps
functional data:• adjust for slice acquisition time
sinc interpolation; “temporal realignment”• adjust for motion
“motion correction”; “(spatial) realignment”
• apply spatial smoothinggaussian filter
anatomic data:• strip skull from image• align with a common template
“normalization”
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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.
12
acquisitionorder
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motion parameters
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motion artefacts
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motion artefacts
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motion parameters
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motion processing
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smoothing -- 3.125 versus 6.25
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normalizationBasic 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
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skull stripping...
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kki0032
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kki0032
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kki0032
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end of part 1.