Biowulf at the NIH
RSS Feed
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/apps/afni/ctf and will be included in your path with the 'module load afni/*' commands.

Running AFNI on Helix

It is possible to run AFNI on Helix, but since most users will be running large numbers of AFNI jobs, it is best to run on Biowulf.

To run a test or interactive job on Helix, simply type

helix% module load afni

helix% ...any AFNI command...

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