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AFNI, SUMA and FATCAT: v23.2.11
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11.
Tutorials, Examples
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11.15.
Using FreeSurfer
11.15.
Using FreeSurfer
¶
11.15.1. 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
11.15.2. 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
11.15.3. 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)
Table of Contents
1. Installation and Background
2. Starting with AFNI
3. Educational resources
4. All program helps
5. AFNI (and afni)
6. SUMA
7. FATCAT
8. Statistics
9. Templates & Atlases
10. Non-human processing
11. Tutorials, Examples
11.1.
Self Guided Demo Scripts
11.2.
AFNI GUI features
11.3.
AFNI general behavior
11.4.
APQC: afni_proc.py quality control
11.5.
FATCAT: DWI {Pre-pre-, Pre-, Post-pre}processing
11.6.
FATCAT Visualization
11.7.
Walnut Brain
11.8.
Drawing ROIs
11.9.
Cluster Explorer
11.10.
FATCAT Matrix Plot
11.11.
3dMVM Validator
11.12.
Automatic Images
11.13.
Sound features in AFNI
11.14.
Working with ROIs
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
11.17.
SurfLayers Demo
11.18.
Meta analysis examples
12. Demo Material
13. Codex: AFNI Code Examples from publications
14. Citing
15. Developer Documentation
16. Contributors
17. Glossary
18. Main AFNI pages
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