Configuring FSL with environment variables

Variable name

Default

Possible values

Purpose

FSLDIR

N/A

-

Points to the folder you installed FSL into, for example /usr/local/fsl

FSLOUTPUTTYPE

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

FSLMULTIFILEQUIT

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.