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  • 12. Tutorials, Examples »
  • 12.15. Using FreeSurfer

12.15. Using FreeSurfer¶

  • 12.15.1. How to use FS recon-all with AFNI
    • Introduction
    • Start-to-finish FS example
    • Run recon-all faster: -parallel
    • A note of filenames/paths with FS
    • A general tcsh script for FS+SUMA
    • A note on @SUMA_Make_Spec_FS outputs
    • Minor note on FS setup
  • 12.15.2. Run FS on a cluster (NIH’s Biowulf) with AFNI
    • Introduction
    • Overview
    • Module loading FS (and other things) in a script
    • Using scratch disks as temporary directories
    • A general biowulf script
    • Looping over a group of subjects
  • 12.15.3. More useful outputs from @SUMA_Make_Spec_FS
    • Introduction
    • The renumbered (REN) atlas dsets
    • The fs*.nii.gz mask dsets
    • QC images
    • ROI, tissue and mask quantities (stats*.1D files)

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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
  • 11. Non-human processing
  • 12. Tutorials, Examples
    • 12.1. Self Guided Demo Scripts
    • 12.2. AFNI GUI features
    • 12.3. AFNI general behavior
    • 12.4. APQC: afni_proc.py quality control
    • 12.5. FATCAT: DWI {Pre-pre-, Pre-, Post-pre}processing
    • 12.6. FATCAT Visualization
    • 12.7. Walnut Brain
    • 12.8. Drawing ROIs
    • 12.9. Cluster Explorer
    • 12.10. FATCAT Matrix Plot
    • 12.11. 3dMVM Validator
    • 12.12. Automatic Images
    • 12.13. Sound features in AFNI
    • 12.14. Working with ROIs
    • 12.15. Using FreeSurfer
      • 12.15.1. How to use FS recon-all with AFNI
      • 12.15.2. Run FS on a cluster (NIH’s Biowulf) with AFNI
      • 12.15.3. More useful outputs from @SUMA_Make_Spec_FS
    • 12.16. Reface and Deface datasets
    • 12.17. SurfLayers Demo
    • 12.18. Meta analysis 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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