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  • 10. Templates & Atlases

10. Templates & Atlases¶

  • 10.1. AFNI Atlases
    • 10.1.1. Atlases and AFNI
    • 10.1.2. Re. Spaces
    • 10.1.3. Re. Transformations
    • 10.1.4. Re. Templates
    • 10.1.5. Re. Atlases
    • 10.1.6. Re. Environment Variables
    • 10.1.7. Distributed Atlases
  • 10.2. How to make an atlas for yourself
    • 10.2.1. Overview
    • 10.2.2. Identifying and making regions
    • 10.2.3. Add the atlas-y-ness information to the dataset header
    • 10.2.4. Add the atlas to a NIML text file
    • 10.2.5. Update AFNI environment list (for GUI functionality)
    • 10.2.6. Add a template space to AFNI’s master list
    • 10.2.7. Add the template space to the environment variable
  • 10.3. @SSwarper base volumes
    • 10.3.1. @SSwarper
    • 10.3.2. Reference templates for @SSwarper
    • 10.3.3. Example for making a reference dset: TT_N27_SSW.nii.gz
    • 10.3.4. Example for making a reference dset: HaskinsPeds_NL_template1.0_SSW.nii.gz
  • 10.4. India Brain Template (IBT)
    • 10.4.1. Overview
  • 10.5. Other templates and atlases
    • 10.5.1. Overview
    • 10.5.2. Links to additional datasets
  • 10.6. List of atlases (and more) in afni_atlases_dist
    • 10.6.1. Atlases and masks in current afni_atlases_dist
    • 10.6.2. “Other” datasets in current afni_atlases_dist
    • 10.6.3. Older datasets, no longer distributed by default

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Table of Contents

  • 1. Installation and Background
  • 2. Starting with AFNI
  • 3. Educational resources
  • 4. All program helps
  • 5. AFNI GUI (afni)
  • 6. SUMA GUI (suma)
  • 7. FATCAT
  • 8. NIFTI
  • 9. Statistics
  • 10. Templates & Atlases
    • 10.1. AFNI Atlases
    • 10.2. How to make an atlas for yourself
    • 10.3. @SSwarper base volumes
    • 10.4. India Brain Template (IBT)
    • 10.5. Other templates and atlases
    • 10.6. List of atlases (and more) in afni_atlases_dist
  • 11. Non-human processing
  • 12. Tutorials, Examples
  • 13. Demo Material
  • 14. Codex: AFNI Code Examples from publications
  • 15. Citations and Reference Works
  • 16. Developer Documentation
  • 17. Contributors
  • 18. Glossary
  • 19. Main AFNI pages

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