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1. Preprocessing of FMRI Data

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  1. 1. Preprocessing of FMRI Data fMRI Graduate Course October 22, 2003

  2. What is preprocessing? • Correcting for non-task-related variability in experimental data • Usually done without consideration of experimental design; thus, pre-analysis • Occasionally called post-processing, in reference to being after acquisition • Attempts to remove, rather than model, data variability

  3. Signal, noise, and the General Linear Model Amplitude (solve for) Measured Data Noise Design Model Cf. Boynton et al., 1996

  4. Signal-Noise-Ratio (SNR) Task-Related Variability Non-task-related Variability

  5. Preprocessing Steps • Slice Timing Correction • Motion Correction • Coregistration • Normalization • Spatial Smoothing • Segmentation • Region of Interest Identification • Bias field correction

  6. Tools for Preprocessing • SPM • Brain Voyager • VoxBo • AFNI • Custom BIAC scripts

  7. Slice Timing Correction

  8. Why do we correct for slice timing? • Corrects for differences in acquisition time within a TR • Especially important for long TRs (where expected HDR amplitude may vary significantly) • Accuracy of interpolation also decreases with increasing TR • When should it be done? • Before motion correction: interpolates data from (potentially) different voxels • Better for interleaved acquisition • After motion correction: changes in slice of voxels results in changes in time within TR • Better for sequential acquisition

  9. Effects of uncorrected slice timing • Base Hemodynamic Response • Base HDR + Noise • Base HDR + Slice Timing Errors • Base HDR + Noise + Slice Timing Errors

  10. Base HDR: 2s TR

  11. Base HDR + Noise r = 0.77 r = 0.81 r = 0.80

  12. Base HDR + Slice Timing Errors r = 0.92 r = 0.85 r = 0.62

  13. HDR + Noise + Slice Timing r = 0.65 r = 0.67 r = 0.19

  14. Interpolation Strategies • Linear interpolation • Spline interpolation • Sinc interpolation

  15. Motion Correction

  16. Head Motion: Good, Bad,…

  17. … and catastrophically bad

  18. Why does head motion introduce problems? A B C

  19. Simulated Head Motion

  20. Severe Head Motion: Simulation Two 4s movements of 8mm in -Y direction (during task epochs) Motion

  21. Severe Head Motion: Real Data Two 4s movements of 8mm in –Y direction (during task epochs) Motion

  22. Correcting Head Motion • Rigid body transformation • 6 parameters: 3 translation, 3 rotation • Minimization of some cost function • E.g., sum of squared differences

  23. Effects of Head Motion Correction

  24. Limitations of Motion Correction • Artifact-related limitations • Loss of data at edges of imaging volume • Ghosts in image do not change in same manner as real data • Distortions in fMRI images • Distortions may be dependent on position in field, not position in head • Intrinsic problems with correction of both slice timing and head motion

  25. A B D Prevention is the best medicine C

  26. Coregistration

  27. Should you Coregister? • Advantages • Aids in normalization • Allows display of activation on anatomical images • Allows comparison across modalities • Necessary if no coplanar anatomical images • Disadvantages • May severely distort functional data • May reduce correspondence between functional and anatomical images

  28. Normalization

  29. Standardized Spaces • Talairach space (proportional grid system) • From atlas of Talairach and Tournoux (1988) • Based on single subject (60y, Female, Cadaver) • Single hemisphere • Related to Brodmann coordinates • Montreal Neurological Institute (MNI) space • Combination of many MRI scans on normal controls • All right-handed subjects • Approximated to Talaraich space • Slightly larger • Taller from AC to top by 5mm; deeper from AC to bottom by 10mm • Used by SPM, National fMRI Database, International Consortium for Brain Mapping

  30. Normalization to Template Normalization Template Normalized Data

  31. Posterior Commissure Anterior Commissure Anterior and Posterior Commissures

  32. Should you normalize? • Advantages • Allows generalization of results to larger population • Improves comparison with other studies • Provides coordinate space for reporting results • Enables averaging across subjects • Disadvantages • Reduces spatial resolution • May reduce activation strength by subject averaging • Time consuming, potentially problematic • Doing bad normalization is much worse than not normalizing

  33. Slice-Based Normalization Before Adjustment (15 Subjects) After Adjustment to Reference Image Registration courtesy Dr. Martin McKeown (BIAC)

  34. Spatial Smoothing

  35. Techniques for Smoothing • Application of Gaussian kernel • Usually expressed in #mm FWHM • “Full Width – Half Maximum” • Typically ~2 times voxel size

  36. Effects of Smoothing on Activity Unsmoothed Data Smoothed Data (kernel width 5 voxels)

  37. Should you spatially smooth? • Advantages • Increases Signal to Noise Ratio (SNR) • Matched Filter Theorem: Maximum increase in SNR by filter with same shape/size as signal • Reduces number of comparisons • Allows application of Gaussian Field Theory • May improve comparisons across subjects • Signal may be spread widely across cortex, due to intersubject variability • Disadvantages • Reduces spatial resolution • Challenging to smooth accurately if size/shape of signal is not known

  38. Segmentation • Classifies voxels within an image into different anatomical divisions • Gray Matter • White Matter • Cerebro-spinal Fluid (CSF) Image courtesy J. Bizzell & A. Belger

  39. Histogram of Voxel Intensities

  40. Region of Interest Drawing

  41. Why use an ROI-based approach? • Allows direct, unbiased measurement of activity in an anatomical region • Assumes functional divisions tend to follow anatomical divisions • Improves ability to identify topographic changes • Motor mapping (central sulcus) • Social perception mapping (superior temporal sulcus) • Complements voxel-based analyses

  42. Drawing ROIs • Drawing Tools • BIAC software (e.g., Overlay2) • Analyze • IRIS/SNAP (G. Gerig) • Reference Works • Print atlases • Online atlases • Analysis Tools • roi_analysis_script.m

  43. ROI Examples

  44. BIAC is studying biological motion and social perception – here by determining how context modulates brain activity in elicited when a subject watches a character shift gaze toward or away from a target.

  45. Additional Resources • SPM website • http://www.fil.ion.ucl.ac.uk/spm/course/notes01.html • SPM Manual • Brain viewers • http://www.bic.mni.mcgill.ca/cgi/icbm_view/

  46. 2. Issues in Experimental Design fMRI Graduate Course October 23, 2003

  47. What is Experimental Design? • Controlling the timing and quality of presented stimuli to influence resulting brain processes • What can we control? • Experimental comparisons (what is to be measured?) • Stimulus properties (what is presented?) • Stimulus timing (when is it presented?) • Subject instructions (what do subjects do with it?)

  48. Goals of Experimental Design • To maximize the ability to test hypotheses • To facilitate generation of new hypotheses