= Configuring FSL with environment variables =
Below is a list of all of the recognised FSL settings which you can change in your FSL [[FslInstallation/ShellSetup|shell setup]] along with their meaning.
||'''Variable name'''||'''Default'''||'''Possible values'''||'''Purpose'''||
||FSLDIR||N/A||-||Points to the folder you installed FSL into, for example `/usr/local/fsl`||
||<rowspan=8>FSLOUTPUTTYPE||<rowspan=8>NIFTI_GZ||NIFTI2_GZ||Output results as a single gzip compressed NIFTI2 format file||
||NIFTI2||Output as a single NIFTI2 format file||
||NIFTI2_PAIR_GZ||Output as gzip compressed NIFTI2 header/image pair||
||NIFTI2_PAIR||Output as NIFTI2 header/image pair||
||NIFTI_GZ||Output results as a single gzip compressed NIFTI format file||
||NIFTI||Output as a single NIFTI format file||
||NIFTI_PAIR_GZ||Output as gzip compressed NIFTI header/image pair||
||NIFTI_PAIR||Output as NIFTI header/image pair||
||<rowspan=2>FSLMULTIFILEQUIT||<rowspan=2>TRUE||TRUE||If a tool encounters multiple files sharing a basename (eg epi.hdr and epi.nii) it will quit with an error||
||FALSE||Try to continue if you find multiple files (undefined results!)||
||FSLTCLSH||`$FSLDIR/bin/fsltclsh`||-||Path to the location of the TCL interpreter you wish to use, defaults to the FSL provided copy||
||FSLWISH||`$FSLDIR/bin/fslwish`||-||Path to the location of the TCL/TK interpreter you wish to use, defaults to the FSL provided copy||
||FSLCONFDIR||`$FSLDIR/config`||-||Path to the location of the configuration files used to compile FSL - only necessary for compiling the source code||
||FSLMACHTYPE||{{{`$FSLDIR/etc/fslconf/fslmachtype.sh`}}}||-||Defines the machine/OS we are running on - the `fslmachtype.sh` script outputs a value suitable for your computer - only necessary for compiling the source code||
||FSLDEVDIR||N/A||-||Defines the location you are building FSL into when compiling the source code. This has to be set if you want to build a single project without running the full compilation script||
||FSL_LOAD_NIFTI_EXTENSIONS||N/A||1||Controls whether FSL tools will load any NIfTI extensions stored in input files, and pass them through to output files. The default behaviour is to '''not''' load NIfTI extensions.||