2. Educational resources

• 2.1. AFNI Bootcamp Recordings
  • 2.1.1. NIH Bootcamp (Oct, 2017)
  • 2.1.2. MIT Bootcamp (May, 2018)
  • 2.1.3. AFNI Academy (2020)
• 2.2. AFNI Bootcamp handouts
  • 2.2.1. Download all AFNI handouts
  • 2.2.2. Download specific AFNI handout(s)
• 2.3. (Useful) Outside lectures
  • 2.3.1. Overview
  • 2.3.2. FMRIF Summer Course
• 2.4. List of all AFNI GUI tips and keyboard shortcuts
  • 2.4.1. Overview
  • 2.4.2. AFNI For Absolute Beginners
  • 2.4.3. Cursor Shapes and Right-Click Popup Menus
  • 2.4.4. Hidden Clicks to Activate AFNI Features
  • 2.4.5. Keyboard Shortcuts: Image Viewer Window
  • 2.4.6. Keyboard Shortcuts: Graph Viewer Window
  • 2.4.7. Keyboard Shortcuts in the Threshold Slider
• 2.5. List of all AFNI environment variables
  • 2.5.1. Overview
  • 2.5.2. Intro: Unix env vars used by AFNI
  • 2.5.3. Setting env variables in file ~/.afnirc
  • 2.5.4. Env vars: the looong list
  • 2.5.5. Vars for realtime functionality
  • 2.5.6. Vars specific to NIML I/O
  • 2.5.7. Vars for 3dDeconvolve
  • 2.5.8. ATLAS and WHEREAMI env variables
  • 2.5.9. Interacting with other progs and miscellany
• 2.6. List of all startup tips
• 2.7. List of all AFNI colorbars
  • 2.7.1. Colorbars and example images
• 2.8. Classified program list
  • 2.8.1. Interactive viewer GUIs
  • 2.8.2. Voxelwise calcs, esp. stats and tests
  • 2.8.3. Get info/stats within ROIs
  • 2.8.4. Build FMRI pipelines
  • 2.8.5. Align/register/warp/axialize spatially
  • 2.8.6. SUMA surface calculations, formats and viewing
  • 2.8.7. Mask/skull-strip/segment
  • 2.8.8. Make/edit/evaluate stimulus timing files
  • 2.8.9. Edit dset headers
  • 2.8.10. Compute various numbers from datasets
  • 2.8.11. Blur and smooth dsets
  • 2.8.12. Volume editing/image processing
  • 2.8.13. Update AFNI, install software, check setup/info (not demos)
  • 2.8.14. Simple dset calcs (-> make new dsets)
  • 2.8.15. Resting state FMRI parameters
  • 2.8.16. Region-wise group analysis
  • 2.8.17. Make/edit correlation matrices
  • 2.8.18. Make/edit ROIs and clusters, resample
  • 2.8.19. Edit dsets: concatenate, split, add/remove slices
  • 2.8.20. Drive AFNI/SUMA, make images/snapshots/montages
  • 2.8.21. Deal with 1D time series
  • 2.8.22. DWI/DTI/diffusion-related
  • 2.8.23. Convert surfaces from other software
  • 2.8.24. Convert statistics and p-values
  • 2.8.25. Compare dset volumes (masks or valued)
  • 2.8.26. Time series pre-processing
  • 2.8.27. Time series analysis
  • 2.8.28. Quality checks (for 3D+time datasets or results)
  • 2.8.29. Miscellaneous file manipulations
  • 2.8.30. MVM modelling of (correlational or structural) matrices
  • 2.8.31. Interact with multi-echo data
  • 2.8.32. Generate model 1D time series
  • 2.8.33. Fourier related, time series/freq
  • 2.8.34. Dset histograms
  • 2.8.35. Download/install demos
  • 2.8.36. DICOM info and conversion
  • 2.8.37. Copy/convert/manipulate dsets
  • 2.8.38. Changing dset spatial structure
  • 2.8.39. Change dset temporal structure
  • 2.8.40. Supplementary/open programs included in AFNI
  • 2.8.41. Supplemental/underlying programs (no desc needed)
  • 2.8.42. Simulate/generate dsets
  • 2.8.43. Miscellaneous visualization tools
  • 2.8.44. Miscellaneous utilities
  • 2.8.45. Unclassed
  • 2.8.46. Retired (no longer in the build)
  • 2.8.47. R programs (in R; called by others)
• 2.9. Shell script and command line tips
  • 2.9.1. Overview
  • 2.9.2. Know your shell type
  • 2.9.3. Make and run a shell script
  • 2.9.4. Check if a variable exists (tcsh)
  • 2.9.5. Store array in a variable (tcsh)
  • 2.9.6. Extract parts of filenames and/or paths (tcsh)
  • 2.9.7. Finding paths of programs (shell/tcsh)
  • 2.9.8. Make uniformly spaced numbers (shell/tcsh)
  • 2.9.9. String-formatting with printf (shell/tcsh)
  • 2.9.10. Simple math operations (tcsh)
  • 2.9.11. More general math operations, via bc (shell)
  • 2.9.12. Display blocks of text with cat << EOF ... EOF
  • 2.9.13. Replace chars in strings (e.g., rename files)