Configuring FSL with environment variables

Below is a list of all of the recognised FSL settings which you can change in your FSL 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

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.

 

FslEnvironmentVariables (last edited 13:46:56 25-11-2022 by PaulMcCarthy)