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 documentation

• Module Name: AFNI (see the modules page for more information)
• AFNI binaries on Biowulf are updated once a day at 4 am, so loading the 'current-openmp' version will get you the latest binaries. Loading the module will give you the timestamp of the last update, e.g.

  [user@biowulf ~]$ module load afni/current-openmp
  [+] Loading AFNI current-openmp ...
  AFNI/current-openmp last updated  2017-11-01
  

• The default version of AFNI on Biowulf contains some multi-threaded executables. AFNI jobs using multi-threaded executables can be submitted to more than the default 2 CPUs, as described below.
• A copy of AFNI is retained every 3 months, for users who want to complete a run using the same version of the executables. These 3-month snapshots are stored for a year.
• This application produces HTML reports. You can use hpcdrive to view these reports on your local workstation.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load afni
[+] Loading AFNI current-openmp ...
AFNI/current-openmp last updated  2017-05-22

[user@cn3144 ~]$ cd /data/user/afni/AFNI_data2_helix/

[user@cn3144 AFNI_data2_helix]$ time tcsh proc.subj ED
(version 1.24, Jun 4, 2007)
++ 3dcopy: AFNI version=AFNI_2011_12_21_1014 (Jan  8 2015) [64-bit]
++ 3dTcat: AFNI version=AFNI_2011_12_21_1014 (Jan  8 2015) [64-bit]
++ 3dTcat: AFNI version=AFNI_2011_12_21_1014 (Jan  8 2015) [64-bit]
++ 3dTcat: AFNI version=AFNI_2011_12_21_1014 (Jan  8 2015) [64-bit]
++ 3dTcat: AFNI version=AFNI_2011_12_21_1014 (Jan  8 2015) [64-bit]

[....etc...]

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. AFNI.sh). For example:

#!/bin/bash
# this file is called AFNI.sh

module load AFNI
cd /data/$USER/AFNI_data2_helix
tcsh ./proc.subj ED

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] AFNI.sh

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 copied from /usr/local/apps/afni/AFNI_data2_helix.tar.gz, courtesy of Rick Reynolds (NIMH). This tar file includes a script called proc.subj to process data for a single subject.

cd /data/$USER
tar xvzf /usr/local/apps/afni/AFNI_data2_helix.tar.gz

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

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

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

swarm -f swarm.cmd --module afni

If each individual process requires more than 4 GB of RAM, you can specify the required memory with

swarm -g # -f swarm.cmd --module afni