4. All program helps

• 4.1. Alphabetical list of program helps
  • 4.1.1. Links to program help files
  • 4.1.2. Links to program manuals
• 4.2. Classified program list
  • 4.2.1. Interactive viewer GUIs
  • 4.2.2. Voxelwise calcs, esp. stats and tests
  • 4.2.3. Get info/stats within ROIs
  • 4.2.4. Build FMRI pipelines
  • 4.2.5. Align/register/warp/axialize spatially
  • 4.2.6. Spline fitting
  • 4.2.7. SUMA surface calculations, formats and viewing
  • 4.2.8. Mask/skull-strip/segment
  • 4.2.9. Make/edit/evaluate stimulus timing files
  • 4.2.10. Edit dset headers
  • 4.2.11. Compute various numbers from datasets
  • 4.2.12. Check/compare dsets and their headers
  • 4.2.13. Blur and smooth dsets
  • 4.2.14. Volume editing/image processing
  • 4.2.15. Update AFNI, install software, check setup/info (not demos)
  • 4.2.16. Simple dset calcs (-> make new dsets)
  • 4.2.17. Resting state FMRI parameters
  • 4.2.18. Region-wise group analysis
  • 4.2.19. Make/edit correlation matrices
  • 4.2.20. Make/edit ROIs and clusters, resample
  • 4.2.21. Edit dsets: concatenate, split, add/remove slices
  • 4.2.22. Drive AFNI/SUMA, make images/snapshots/montages
  • 4.2.23. Deal with 1D time series
  • 4.2.24. DWI/DTI/diffusion-related
  • 4.2.25. Convert surfaces from other software
  • 4.2.26. Convert statistics and p-values
  • 4.2.27. Compare dset volumes (masks or valued)
  • 4.2.28. Work with JSON files (e.g., sidecars)
  • 4.2.29. Time series pre-processing
  • 4.2.30. Time series analysis
  • 4.2.31. Quality checks (for 3D+time datasets or results)
  • 4.2.32. Miscellaneous file manipulations
  • 4.2.33. MVM modelling of (correlational or structural) matrices
  • 4.2.34. Interact with multi-echo data
  • 4.2.35. Generate model 1D time series
  • 4.2.36. Fourier related, time series/freq
  • 4.2.37. Dset histograms
  • 4.2.38. Download/install demos
  • 4.2.39. DICOM info and conversion
  • 4.2.40. Copy/convert/manipulate dsets
  • 4.2.41. Changing dset spatial structure
  • 4.2.42. Change dset temporal structure
  • 4.2.43. Supplementary/open programs included in AFNI
  • 4.2.44. Supplemental/underlying programs (no desc needed)
  • 4.2.45. Simulate/generate dsets
  • 4.2.46. Miscellaneous visualization tools
  • 4.2.47. Miscellaneous utilities
  • 4.2.48. Unclassed
  • 4.2.49. Retired (no longer in the build)
  • 4.2.50. R programs (written in R; called by other programs)