AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity. It should be used for research purposes only.
Starting with version 2016_2_09 - the first AFNI version on HiPerGator2 - use the 'launch_afni' command to access afni executables. In addition, if you use absolute paths (starting with /ufrc/) in your arguments you have to convert them to relative paths. We have a relative_path script in the ufrc module for it. For example, the following commands in a job script will run the 3dcalc analysis:
module load ufrc afni launch_afni 3dcalc -a $(relative_path /ufrc/group/user/Map_repository/S01_19_DA/fnirted_FA.nii.gz) -expr 'step(a)' -prefix $(relative_path /ufrc/group/user/test_afni.nii.gz)
If you already use relative paths then the use of 'relative_path' is not required.
If you publish research that uses afni you have to cite it as follows:
RW Cox. AFNI: Software for analysis and visualization of functional magnetic resonance neuroimages. Computers and Biomedical Research, 29:162-173, 1996.
RW Cox and JS Hyde. Software tools for analysis and visualization of FMRI Data. NMR in Biomedicine, 10:171-178, 1997.
S Gold, B Christian, S Arndt, G Zeien, T Cizadlo, DL Johnson, M Flaum, and NC Andreasen. Functional MRI statistical software packages: a comparative analysis. Human Brain Mapping, 6:73-84, 1998.