AFNI documentation and links

AFNI is totally awesome fMRI software! AFNI (Analysis of Functional Neuro Images) is fast, both for computation and display, and capable of nice intersubject averaging. AFNI has been ourr main fMRI analysis tool in the past.

Start AFNI on akasha by typing afni at the Unix command prompt. This will start the latest version of AFNI. The pnm format files that AFNI saves may be converted to your favorite image format with the program xv.

Official AFNI stuff (from AFNI author Bob Cox):

  1. The AFNI home page.
  2. Educational material for AFNI.
  3. A directory of the official AFNI documentation. (postscript and pdf format files)
Unofficial AFNI stuff (written by Saskatoonians);
  1. The Complete Idiot's Guide to Making a Map in AFNI. A local guide written by Ben Norris.
  2. Making AFNI Masks. A local guide written by Ben Norris.
  3. Counting active voxels. A local guide written by Ben Norris.
  4. Some notes on how to use the Talairachto and Where Am I functions for Talairach space navigation.
  5. How to make a Average Brain.
  6. Some notes on ANOVA analysis.
  7. How to write looping scripts for AFNI.
  8. Steps for 3D rendering Very important: you will need the astrip+tlrc.HEAD and astrip+tlrc.BRIK files to form the anatomical basis of your 3D brain maps in Talairach coordinates. (Hold down the shift key when you click your mouse on the file links to save the file to your disk.)