AFNI on Biowulf

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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]

Setting up an AFNI job

AFNI on Biowulf is installed in /usr/local/afni. Users will probably want to add the AFNI bin directory to their path.
csh or tcsh users should add the following to their .cshrc file:

setenv PATH /usr/local/afni/linux_glibc22/:$PATH

Bash users should add the following to their .bash_profile file:

export PATH=/usr/local/afni/linux_glibc22/:$PATH

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
#--------------------------------------------------------

This swarm command file would be submitted to the batch system with:

swarm -f swarm.cmd

Swarm will send two command lines to each node by default. Biowulf nodes have at least 2 GB of RAM, so each individual process should not require more than 1GB of RAM for 2 such processes to run successfully on a node. If the individual processes require more than 1GB of RAM, you can force swarm to send only one command line to each node, or to specifically request nodes with larger memory. See the swarm webpage for more information, or contact the Biowulf staff at staff@biowulf.nih.gov

This document is available as http://biowulf.nih.gov/apps/afni.html
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