<AFNI>Task based process

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3dClustSim

• Estimate the probability of false positive (noise-only) clusters.
• 3dClustSim computes a cluster-size threshold for a given voxel-wise p-value threshold such that the probability of anything surviving the dual thresholds is at some given level (specified by the ‘-athr’ option).
• real FMRI data does not actually have a Gaussian-shaped ACF(AutoCorrelation Function), so the estimated ACF is then fit (in 3dFWHMx) to a mixed model (Gaussian plus mono-exponential) of the form

Reference: https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dClustSim.html

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• Suggested Choices for Basis Functions:
  
  • deconvolution (variable-shape regression): TENT(b,c,n)
  • regression (fixed-shape regression): GAM, BLOCK(d,p) or BLOCK(d)

https://afni.nimh.nih.gov/pub/dist/doc/misc/Decon/2007_0504_basis_funcs.html

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• Basic about AFNI: https://ngp.usc.edu/files/2013/06/Gimbel_AFNI.pdf
• https://afni.nimh.nih.gov/pub/dist/edu/latest/afni_handouts/afni03_interactive.pdf

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• Regression

  • The full model statistic is an F­statistic that shows how well all the regressors of interest explain the variability in the voxel time series data
  • The individual stimulus classes also will get individual F­ (if –fout added) and/or t­statistics indicating the significance of their individual incremental contributions to the data time series fit
  • 6 rigid parameters generated from: 3dvolreg with the -1Dfile option
  • -stim_times： local&global times
    https://afni.nimh.nih.gov/pub/dist/edu/latest/afni_handouts/afni05_regression.pdf
    https://afni.nimh.nih.gov/pub/dist/edu/latest/afni_handouts/afni06_decon.pdf
    https://afni.nimh.nih.gov/pub/dist/HOWTO/howto/ht05_group/html/afni_howto5_subj.html

• AFNI Start to Finish Tutorial, Part 18: View Fitted Timeseries: https://www.youtube.com/watch?v=bvXxcZYRwlk

• AFNI Start to Finish Tutorial, Part 19: Cluster Correction: https://www.youtube.com/watch?v=5awY_A4wRYg