Difference between revisions of "AFNI"

Revision as of 20:53, 6 December 2019

Description

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.

Required Modules

Serial

afni

System Variables

HPC_AFNI_DIR

Additional Information

This is a GUI software. Follow the instructions at https://wiki.rc.ufl.edu/doc/GUI_Programs

Basic usage:

module load gui
launch_gui_session --module afni -e afni

Connect with xpra locally using the xpra command

xpra attach ssh:jdoe@i111a-s222.rc.ufl.edu:3713

Citation

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.

@@ Line 33: / Line 33: @@
 -->
 ==System Variables==
-* HPC_{{#uppercase:{{#var:app}}}}_DIR
+* HPC_{{uc:{{#var:app}}}}_DIR
 <!--Configuration-->
 {{#if: {{#var: conf}}|==Configuration==
@@ Line 41: / Line 41: @@
 {{#if: {{#var: exe}}|==Additional Information==
-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:
+This is a GUI software. Follow the instructions at https://wiki.rc.ufl.edu/doc/GUI_Programs
-  module load ufrc afni
+Basic usage:
-  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)
+  module load gui
+  launch_gui_session --module afni -e afni
-If you already use relative paths then the use of 'relative_path' is not required.
+Connect with xpra locally using the xpra command
+ xpra attach ssh:jdoe@i111a-s222.rc.ufl.edu:3713
 |}}