11. Tutorials, Examples

• 11.1. Self Guided Demo Scripts
  • 11.1.1. @DriveSuma
  • 11.1.2. @DriveAfni
  • 11.1.3. @DO.examples
• 11.2. AFNI GUI features
  • 11.2.1. The Plus/Minus (PMplot) Curves in Graphs
• 11.3. AFNI general behavior
  • 11.3.1. Using volumetric (and other) files in AFNI
  • 11.3.2. Using 1D files in AFNI
  • 11.3.3. General options for AFNI programs
• 11.4. APQC: afni_proc.py quality control
  • 11.4.1. Overview for APQC
  • 11.4.2. APQC-HTML navigation: example
  • 11.4.3. Browsing APQC outputs
• 11.5. FATCAT: DWI {Pre-pre-, Pre-, Post-pre}processing
  • 11.5.1. Background and additional software
  • 11.5.2. General fat_proc script properties
  • 11.5.3. Pre-preproc, I: convert and niceify
  • 11.5.4. Pre-preproc, II: examine and filter
  • 11.5.5. Preproc: FreeSurfer (+ @SUMA_Make_Spec_FS)
  • 11.5.6. Preproc: TORTOISE
  • 11.5.7. Post-preproc, I: tensor estimation and checking
  • 11.5.8. Post-preproc, II: mapping ROIs to DTI space
  • 11.5.9. Post-preproc, III: ROI map preparation
  • 11.5.10. Post-preproc, IV: Tracking
• 11.6. FATCAT Visualization
  • 11.6.1. Do_06_VISdti_SUMA_visual_ex1.tcsh
  • 11.6.2. Do_09_VISdti_SUMA_visual_ex2.tcsh
  • 11.6.3. Do_09_VISdti_SUMA_visual_ex3.tcsh
  • 11.6.4. Connectoming
• 11.7. Walnut Brain
  • 11.7.1. Prying Brains Apart
• 11.8. Drawing ROIs
  • 11.8.1. Demo:
• 11.9. Cluster Explorer
  • 11.9.1. Introducing Cluster Explorer
  • 11.9.2. Scripts
• 11.10. FATCAT Matrix Plot
  • 11.10.1. FATCAT_matplot
• 11.11. 3dMVM Validator
  • 11.11.1. Overview.
  • 11.11.2. Walking in your footsteps.
  • 11.11.3. Positive Role Model.
  • 11.11.4. Tab’s on me if you think I’m lyin’.
  • 11.11.5. General Linear Tests.
  • 11.11.6. More coming soon
• 11.12. Automatic Images
  • 11.12.1. Overview
  • 11.12.2. Using @chauffeur_afni
  • 11.12.3. Using @snapshot_volreg
  • 11.12.4. Using @djunct_4d_imager
  • 11.12.5. Using 2dcat
• 11.13. Sound features in AFNI
  • 11.13.1. Overview
  • 11.13.2. Keypresses, formats and functionality
  • 11.13.3. Example
• 11.14. Working with ROIs
  • 11.14.1. Combine ROI masks, visualize and make corr matrices
  • 11.14.2. Manifold ways to make+view spheres in SUMA
  • 11.14.3. Examples of things with ROIs: resampling and clusterizing
• 11.15. Using FreeSurfer
  • 11.15.1. How to use FS recon-all with AFNI
  • 11.15.2. Run FS on a cluster (NIH’s Biowulf) with AFNI
  • 11.15.3. More useful outputs from @SUMA_Make_Spec_FS
• 11.16. Reface and Deface datasets
  • 11.16.1. Using @afni_refacer_run
• 11.17. SurfLayers Demo
  • 11.17.1. SurfLayers Demo 1
  • 11.17.2. Clipping Planes in SUMA
• 11.18. Meta analysis examples
  • 11.18.1. Basic meta analysis with BML