Difference between revisions of "FSL"

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==Home Website==
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[[Category:Software]][[Category:Bioinformatics]][[Category:Neurology]]
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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/4.1
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<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 +
|{{#vardefine:conf|}}          <!--CONFIGURATION-->
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|{{#vardefine:exe|}}            <!--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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This is actually a symbolic link to the most recent minor version of FSL, which as of July 2nd, 2007 was 3.3.11.
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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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==Required Modules==
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===Serial===
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* {{#var:app}}
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<!--
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===Parallel (OpenMP)===
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* intel
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* {{#var:app}}
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===Parallel (MPI)===
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* intel
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* openmpi
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* {{#var:app}}
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-->
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==System Variables==
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* HPC_{{#uppercase:{{#var:app}}}}_DIR
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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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WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
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|}}
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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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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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#M. Jenkinson, C.F. Beckmann, T.E. Behrens, M.W. Woolrich, S.M. Smith. FSL. NeuroImage, 62:782-90, 2012
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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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* For bash shell users:
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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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<pre>
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|}}
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$ export FSLDIR=/apps/fsl/4.1
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<!--Installation-->
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$ . ${FSLDIR}/etc/fslconf/fsl.sh
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{{#if: {{#var: installation}}|==Installation==
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$ export PATH=${FSLDIR}/bin:${PATH}
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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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* For tcsh shell users:
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__NOTOC____NOEDITSECTION__
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<pre>
 
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$ setenv FSLDIR /apps/fsl/4.1
 
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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]
 

Revision as of 22:07, 22 April 2013

Description

fsl website  

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

Required Modules

Serial

  • fsl

System Variables

  • HPC_{{#uppercase:fsl}}_DIR




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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