AFNI

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AFNI (which might be an acronym for 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. It runs on Unix+X11+Motif systems, including SGI, Solaris, Linux, and Mac OS X. It is available free (in C source code format, and some precompiled binaries) for research purposes.

AFNI installed on the Cheaha is ver AFNI_2011_12_21_1014

Contents

AFNI on Cheaha

AFNI is pre-installed on the Cheaha research computing system. This allows users to run AFNI directly on the cluster without any need to install software.

AFNI Versions

Use the 'module' command to view a list of available AFNI versions. If the version that you require isn't listed, please open a help desk ticket to request the installation.

The following is an example output of the command and doesn't necessarily represent the currently installed versions:

$ module avail afni

---------------------------------------------- /etc/modulefiles -----------------------------------------------
afni/afni_linux

Copying AFNI data to Cheaha

These instructions provide an example of how to create and submit a AFNI job on Cheaha.

First, create the working directory for the job- Replace 'USERNAME' with the account associated username on Cheaha. You can create any directory to run your job. It is recommended that the job directory be on the scratch (i.e. lustre filesystem) instead of the user home directory.

$ mkdir -p $USER_SCRATCH/jobs/afni 
$ cd $USER_SCRATCH/jobs/afni

Next, Copy all the files required for AFNI to the working directory. This has to done from the local machine. Eg. Copy the dat directory "data" from the local host to a remote host's directory "afni"

$ scp -r data cheaha.uabgrid.uab.edu:/data/scratch/USERNAME/jobs/afni 

Run AFNI on Cheaha

1. ssh -X to Cheaha (from local machine)

 $ ssh -X USERNAME@cheaha.uabgrid.uab.edu 

At this point you are on the head node. Please do not run compute intensive jobs on the head node.

2. Qlogin onto a compute node to run computation (on Cheaha terminal)

 $ qlogin -l vf=2G,h_rt=2:00:00

You should be logged in to a compute node with memory requirement of 2G and run time of 2 hours. You can change the above requirements as needed.

3. Load the AFNI module

 $ module load afni/afni_linux 

4. cd to the data directory

 $ cd $USER_SCRATCH/jobs/afni 

5. Run afni

 $ afni 

AFNI should launch as it does on the desktop.

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