Difference between revisions of "AFNI"
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Moskalenko (talk | contribs) (Created page with "Category:SoftwareCategory:BioinformaticsCategory:NeurologyCategory:Imaging {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|afni}} |{{#vardefine:url|http://a...") |
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:Neuroscience]][[Category:Imaging]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|afni}} | |{{#vardefine:app|afni}} | ||
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<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
| − | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
|{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | |{{#vardefine:pbs|}} <!--PBS SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
|{{#vardefine:testing|}} <!--PROFILING--> | |{{#vardefine:testing|}} <!--PROFILING--> | ||
|{{#vardefine:faq|}} <!--FAQ--> | |{{#vardefine:faq|}} <!--FAQ--> | ||
| − | |{{#vardefine:citation|}} <!--CITATION--> | + | |{{#vardefine:citation|1}} <!--CITATION--> |
|{{#vardefine:installation|}} <!--INSTALLATION--> | |{{#vardefine:installation|}} <!--INSTALLATION--> | ||
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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. | 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. | ||
<!--Modules--> | <!--Modules--> | ||
| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
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| − | < | ||
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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<!--Run--> | <!--Run--> | ||
{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==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 | ||
| + | |||
|}} | |}} | ||
<!--PBS scripts--> | <!--PBS scripts--> | ||
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{{#if: {{#var: citation}}|==Citation== | {{#if: {{#var: citation}}|==Citation== | ||
If you publish research that uses {{#var:app}} you have to cite it as follows: | If you publish research that uses {{#var:app}} 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. | ||
|}} | |}} | ||
<!--Installation--> | <!--Installation--> | ||
Latest revision as of 20:52, 11 August 2022
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.
Environment Modules
Run module spider afni to find out what environment modules are available for this application.
System Variables
- HPC_AFNI_DIR - installation directory
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.