Configuring FSL with environment variables
Below is a list of all of the recognised FSL settings which you can change in your fsl.sh (or fsl.csh) file, 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 |
NIFTY_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 |
||
NIFTY_PAIR |
Output as NIFTI header/image pair |
||
ANALYZE_GZ |
Output as gzip compressed ANALYZE header/image pair |
||
ANALYZE |
Output as ANALYZE 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 |