AFNI (Analysis of Functional NeuroImages) is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity. AFNI is developed by the Scientific and Statistical Computing Core, NIMH. [AFNI website]

AFNI on Biowulf is installed in /usr/local/afni. Users should set up their environment for AFNI using the 'module' commands as below: (More about Modules)

[user@helix]$ module avail afni

--------------------------- /usr/local/Modules/3.2.9/modulefiles --------------------------
afni/18Oct2012(default) afni/18Oct2012-openmp   afni/21Dec2011

[user@helix]$ module load afni/18Oct2012-openmp

[user@helix]$ module list
Currently Loaded Modulefiles:
  1) afni/18Oct2012-openmp

Typing 'module load afni' without a version will load the default (latest) version. The CTF MEG software is also installed on Biowulf in /usr/local/ctf and will be included in your path with the 'module load afni/*' commands.

If you expect to be running swarms of AFNI jobs, you should put the 'module load' command into your .bashrc or .cshrc file.

Typically, AFNI on Biowulf is used to simultaneously process a large number of independent datasets via the swarm utility.

A small sample set of data for 3 subjects can be downloaded from http://afni.nimh.nih.gov/pub/dist/edu/data/AFNI_data2_helix.tgz, courtesy of Rick Reynolds (NIMH). This tar file includes a script called proc.subj to process data for a single subject.

A swarm command file to process these 3 datasets would look like

#-------- this file is called swarm.cmd -----------------
cd /data/username/AFNI_data2_helix; tcsh ./proc.subj ED
cd /data/username/AFNI_data2_helix; tcsh ./proc.subj EE
cd /data/username/AFNI_data2_helix; tcsh ./proc.subj EF
#--------------------------------------------------------

If each AFNI process requires less than 1 GB of RAM, This swarm command file would be submitted to the batch system with:

swarm -f swarm.cmd

If each individual process requires more than 1 GB of RAM, you can specify the required memory with

swarm -g # -f swarm.cmd