=====FSL=====
FSL is the fMRI Software Library analysis package developed by the FMRIB laboratory at Oxford University. Useful FMRIB links are:

  * [[http://www.fmrib.ox.ac.uk/fsl|FSL]] - The FMRIB software homepage.
  * [[http://www.fmrib.ox.ac.uk/fslcourse|FSL Tutorial]] - The FMRIB course tutorial.

To change your FSL version:

<code>
export FSLDIR=/usr/local/packages/fsl-5.0.1
. ${FSLDIR}/etc/fslconf/fsl.sh

Then call the tools with the fullpath:
${FSLDIR}/bin/fsl
</code>
====FSL Workshop Material (12/9/2008)====
FSL Overview: Rich Yaxley & O'Dhaniel Mullette-Gillman
  * {{:biac:fsl_preprocessing.pdf|fsl_preprocessing.pdf}}

Experimental Design: McKell Carter & Amy Winecoff
  * {{:biac:notes_for_fsl_workshop.doc|notes_for_fsl_workshop.doc}}

Advanced Experimental Design: David Smith & John Clithero
  * {{:biac:fsl_workshop_advanced_design.pdf|fsl_workshop_advanced_design.pdf}}
  * [[http://www.fmrib.ox.ac.uk/fsl/feat5/output.html]]

Scripting: Chris Petty & Justin Meyer
  * [[:biac:fsl:guide#iii_writing_a_batch_script_for_fsl|Writing a Batch Script]]

====BIAC FSL Guide====
Step-by-step instructions for using FSL at BIAC can be found at:
  * [[biac:fsl:guide|FSL Guide]]

A sample FSL analysis; requres access to the Class.01 directory.
  * [[biac:fsl:Class_Example|FSL Class Example: First Level]]
  * [[biac:fsl:Class_SecondLevel|FSL Class Example: Second Level]]



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==== BIAC 2012/2013 Course Guide ====
by Zoe Englander

{{:biac:fslcourse.pdf| FSL 2013 }}
{{:biac:command_line_demo.pdf| Command Line demo}}
{{:biac:roianalysis.ppt| ROI Analysis Tutorial}}