fmri pre-processing Juergen Dukart
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1 fmri pre-processing Juergen Dukart
2 Outline Why do we need pre-processing? fmri pre-processing Slice time correction Realignment Unwarping Coregistration Spatial normalisation Smoothing
3 Overview fmri time-series kernel Design matrix Statistical Parametric Map Motion correction Smoothing General Linear Model (Co-registration and) Spatial normalisation Parameter Estimates Standard template
4 Why do we need pre-processing?
5 What do we want?
6 Movement
7 Distortions
8 Inter-subject variability
9 Non-gaussian distribution
10 fmri pre-processing Slice timing correction (optional) Realignment (Motion correction) Unwarping (Distortion correction, optional) Co-registration Link functional scans to anatomical scan Spatial normalisation (unified segmentation) Fitting images to a standard brain Smoothing Increases signal-to-noise ratio and approximates a Gaussian distribution
11 Slice timing (optional) TR: 2 sec Slice1 Slice11 Slice Slice TR:-1 TR:0 TR:1 TR:2 TR:3 TR:4 TR:5 0 TR:-1 TR:0 TR:1 TR:2 TR:3 TR:4 TR:5
12 Slice timing (optional) Slice1 Slice11 Slice TR:-1 TR:0 TR:1 TR:2 TR:3 TR:4 TR:5
13 fmri pre-processing Slice timing correction (optional) Realignment (Motion correction) Unwarping (Distortion correction, optional) Co-registration Link functional scans to anatomical scan Spatial normalisation (unified segmentation) Fitting images to a standard brain Smoothing Increases signal-to-noise ratio and approximates a Gaussian distribution
14 Realignment (motion correction) Translation Z Rotation Yaw Roll X Pitch Y
15 Realignment (motion correction) Xtrans Translations Ytrans Zt rans Rigid body transformations parameterised by: Pitch about X axis cos( ) sin( ) 0 0 sin( ) cos( ) Roll about Y axis cos( ) 0 sin( ) sin( ) 0 cos( ) Yaw about Z axis cos( ) sin( ) 0 0 sin( ) cos( ) Minimizing the squared difference (error) between the images Squared Error
16 Realignment (motion correction
17 fmri pre-processing Slice timing correction (optional) Realignment (Motion correction) Unwarping (Distortion correction, optional) Co-registration Link functional scans to anatomical scan Spatial normalisation (unified segmentation) Fitting images to a standard brain Smoothing Increases signal-to-noise ratio and approximates a Gaussian distribution
18 Distortion correction (unwarp) Fieldmap Raw EPI Undistorted EPI
19 Unwarp can estimate changes in distortion from movement Resulting field map at each time point Measured field map Estimated change in field wrt change in pitch (x-axis) Estimated change in field wrt change in roll (y-axis) 0 = + + distortions in a reference image (FieldMap) subject motion parameters (that we obtain in realignment) change in deformation field with subject movement (estimated via iteration)
20 fmri pre-processing Slice timing correction (optional) Realignment (Motion correction) Unwarping (Distortion correction, optional) Co-registration Link functional scans to anatomical scan Spatial normalisation (unified segmentation) Fitting images to a standard brain Smoothing Increases signal-to-noise ratio and approximates a Gaussian distribution
21 Co-registration Normalized mutual information functional and structural images in the same space
22 Co-registration T2 intensity T1 intensity T2 intensity T1 intensity
23 Spatial normalization Normalizes structural images to a standard brain template (standard space) The obtained transformation (warping) parameters can be applied on co-registered fmri data Improved spatial normalization based on high resolution structural information
24 fmri pre-processing Slice timing correction (optional) Realignment (Motion correction) Unwarping (Distortion correction, optional) Co-registration Link functional scans to anatomical scan Spatial normalisation (unified segmentation) Fitting images to a standard brain Smoothing Increases signal-to-noise ratio and approximates a Gaussian distribution
25 Smoothing
26 Smoothing
27 Thank you for attention
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