Difference between revisions of "FSL"

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==Home Website==
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[[Category:Software]][[Category:Neuroscience]][[Category:Biology]][[Category:Imaging]]
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[http://www.fmrib.ox.ac.uk/fsl/ Website]
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{|<!--CONFIGURATION: REQUIRED-->
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==HPC Installation==
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|{{#vardefine:app|fsl}}
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The FSL software on the cluster is located in the following directory:
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|{{#vardefine:url|http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSL}}
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/apps/fsl/3.2/
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<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
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|{{#vardefine:conf|}}          <!--CONFIGURATION-->
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|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
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|{{#vardefine:pbs|}}            <!--PBS SCRIPTS-->
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|{{#vardefine:policy|}}        <!--POLICY-->
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|{{#vardefine:testing|}}      <!--PROFILING-->
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|{{#vardefine:faq|}}            <!--FAQ-->
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|{{#vardefine:citation|1}}      <!--CITATION-->
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|{{#vardefine:installation|}} <!--INSTALLATION-->
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|}
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<!--BODY-->
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<!--Description-->
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{{#if: {{#var: url}}|
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{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
  
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If you are going to be using the FSL software on the cluster, there are some things you will need to do first.
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FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.
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<!--Modules-->
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==Environment Modules==
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
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==System Variables==
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
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* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
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<!--Configuration-->
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{{#if: {{#var: conf}}|==Configuration==
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See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
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|}}
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<!--Run-->
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{{#if: {{#var: exe}}|==Additional Information==
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|}}
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===Running bedpostx===
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For information on using application, view [[Running Bedpostx]]
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<!--PBS scripts-->
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{{#if: {{#var: pbs}}|==PBS Script Examples==
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See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.
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|}}
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<!--Policy-->
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{{#if: {{#var: policy}}|==Usage Policy==
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WRITE USAGE POLICY HERE (Licensing, usage, access).
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|}}
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<!--Performance-->
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{{#if: {{#var: testing}}|==Performance==
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WRITE_PERFORMANCE_TESTING_RESULTS_HERE
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|}}
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<!--Faq-->
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{{#if: {{#var: faq}}|==FAQ==
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*'''Q:''' **'''A:'''|}}
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<!--Citation-->
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{{#if: {{#var: citation}}|==Citation==
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If you publish research that uses {{#var:app}} you have to cite it as follows:
  
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* For bash shell users:
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#M. Jenkinson, C.F. Beckmann, T.E. Behrens, M.W. Woolrich, S.M. Smith. FSL. NeuroImage, 62:782-90, 2012
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<pre>
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#M.W. Woolrich, S. Jbabdi, B. Patenaude, M. Chappell, S. Makni, T. Behrens, C. Beckmann, M. Jenkinson, S.M. Smith. Bayesian analysis of neuroimaging data in FSL. NeuroImage, 45:S173-86, 2009
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$ export FSLDIR=/apps/fsl/3.2/
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#S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady, and P.M. Matthews. Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage, 23(S1):208-19, 2004
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$ . ${FSLDIR}/etc/fslconf/fsl.sh
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|}}
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$ export PATH=${FSLDIR}/bin:${PATH}
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<!--Installation-->
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</pre>
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{{#if: {{#var: installation}}|==Installation==
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* For tcsh shell users:
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See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
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<pre>
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<!--Turn the Table of Contents and Edit paragraph links ON/OFF-->
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$ setenv FSLDIR /usr/local/fsl
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__NOTOC____NOEDITSECTION__
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$ source ${FSLDIR}/etc/fslconf/fsl.csh
 
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$ setenv PATH ${FSLDIR}/bin:${PATH}  
 
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</pre>
 
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If you are going to be using FSL on an on-going basis, it might be a good idea to place these commands into your start-up scripts. Just put these commands into .bashrc (for bash) or .cshrc (for tcsh) in your home directory.
 
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==Official Documentation==
 
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[http://www.hpc.ufl.edu/doc/fsl/index.html FSL Documentation]
 

Latest revision as of 16:47, 17 January 2023

Description

fsl website  

FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.

Environment Modules

Run module spider fsl to find out what environment modules are available for this application.

System Variables

  • HPC_FSL_DIR - installation directory
  • HPC_FSL_BIN - executable directory

Additional Information

Running bedpostx

For information on using application, view Running Bedpostx



Citation

If you publish research that uses fsl you have to cite it as follows:

  1. M. Jenkinson, C.F. Beckmann, T.E. Behrens, M.W. Woolrich, S.M. Smith. FSL. NeuroImage, 62:782-90, 2012
  2. M.W. Woolrich, S. Jbabdi, B. Patenaude, M. Chappell, S. Makni, T. Behrens, C. Beckmann, M. Jenkinson, S.M. Smith. Bayesian analysis of neuroimaging data in FSL. NeuroImage, 45:S173-86, 2009
  3. S.M. Smith, M. Jenkinson, M.W. Woolrich, C.F. Beckmann, T.E.J. Behrens, H. Johansen-Berg, P.R. Bannister, M. De Luca, I. Drobnjak, D.E. Flitney, R. Niazy, J. Saunders, J. Vickers, Y. Zhang, N. De Stefano, J.M. Brady, and P.M. Matthews. Advances in functional and structural MR image analysis and implementation as FSL. NeuroImage, 23(S1):208-19, 2004


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