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 |
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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!) |
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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. |