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AFNI on Biowulf

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/apps/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               afni/21Dec2011               afni/7-Feb-2013-openmp       afni/current-openmp(default)
afni/18Oct2012-openmp        afni/7-Feb-2013              afni/current

[user@helix]$ module load afni

[user@helix]$ module list
Currently Loaded Modulefiles:
  1) afni/current

Typing 'module load afni' without a version will load the default (latest) version. AFNI binaries on Biowulf are updated once a day, so loading the 'current' or 'current-openmp' version will get you the latest binaries.

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.

Submitting a swarm of AFNI jobs

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, 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
where # is the number of gigabytes required. See the swarm webpage for more information, or contact the Biowulf staff at