3. Educational resources¶
- 3.1. AFNI Bootcamp Recordings
- 3.2. AFNI Bootcamp handouts
- 3.3. (Useful) Outside lectures
- 3.4. List of all AFNI GUI tips and keyboard shortcuts
- 3.5. List of all startup tips
- 3.6. List of all AFNI colorbars
- 3.7. Classified program list
- 3.7.1. Interactive viewer GUIs
- 3.7.2. Voxelwise calcs, esp. stats and tests
- 3.7.3. Get info/stats within ROIs
- 3.7.4. Build FMRI pipelines
- 3.7.5. Align/register/warp/axialize spatially
- 3.7.6. SUMA surface calculations, formats and viewing
- 3.7.7. Mask/skull-strip/segment
- 3.7.8. Make/edit/evaluate stimulus timing files
- 3.7.9. Edit dset headers
- 3.7.10. Compute various numbers from datasets
- 3.7.11. Blur and smooth dsets
- 3.7.12. Volume editing/image processing
- 3.7.13. Update AFNI, install software, check setup/info (not demos)
- 3.7.14. Simple dset calcs (-> make new dsets)
- 3.7.15. Resting state FMRI parameters
- 3.7.16. Region-wise group analysis
- 3.7.17. Make/edit correlation matrices
- 3.7.18. Make/edit ROIs and clusters, resample
- 3.7.19. Edit dsets: concatenate, split, add/remove slices
- 3.7.20. Drive AFNI/SUMA, make images/snapshots/montages
- 3.7.21. Deal with 1D time series
- 3.7.22. DWI/DTI/diffusion-related
- 3.7.23. Convert surfaces from other software
- 3.7.24. Convert statistics and p-values
- 3.7.25. Compare dset volumes (masks or valued)
- 3.7.26. Time series pre-processing
- 3.7.27. Time series analysis
- 3.7.28. Quality checks (for 3D+time datasets or results)
- 3.7.29. Miscellaneous file manipulations
- 3.7.30. MVM modelling of (correlational or structural) matrices
- 3.7.31. Interact with multi-echo data
- 3.7.32. Generate model 1D time series
- 3.7.33. Fourier related, time series/freq
- 3.7.34. Dset histograms
- 3.7.35. Download/install demos
- 3.7.36. DICOM info and conversion
- 3.7.37. Copy/convert/manipulate dsets
- 3.7.38. Changing dset spatial structure
- 3.7.39. Change dset temporal structure
- 3.7.40. Supplementary/open programs included in AFNI
- 3.7.41. Supplemental/underlying programs (no desc needed)
- 3.7.42. Simulate/generate dsets
- 3.7.43. Miscellaneous visualization tools
- 3.7.44. Miscellaneous utilities
- 3.7.45. Unclassed
- 3.7.46. Retired (no longer in the build)
- 3.7.47. R programs (written in R; called by other programss)
- 3.8. Shell script and command line tips
- 3.8.1. Overview
- 3.8.2. Know your shell type
- 3.8.3. Make and run a shell script
- 3.8.4. Check if a variable exists (tcsh)
- 3.8.5. Store array in a variable (tcsh)
- 3.8.6. Extract parts of filenames and/or paths (tcsh)
- 3.8.7. Finding paths of programs (shell/tcsh)
- 3.8.8. Make uniformly spaced numbers (shell/tcsh)
- 3.8.9. String-formatting with
printf
(shell/tcsh) - 3.8.10. Simple math operations (tcsh)
- 3.8.11. More general math operations, via
bc
(shell) - 3.8.12. Display blocks of text with
cat << EOF ... EOF
- 3.8.13. Replace chars in strings (e.g., rename files)